From aumanga at biggjapan.com  Fri Jun 12 01:53:36 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 12 Jun 2009 14:53:36 +0900
Subject: [Biojava-l] Drawing chromatogram with fixed width for all Callboxes
 (With of CallBoxBound )
Message-ID: <4A31ED60.8090600@biggjapan.com>

Hi all,

I want to draw the chromatogram of AB1 file with fixed width for all 
'CallBoxes'.I want to do this because I am going to read .ace file and 
draw the Chromatograms of all AB1 with correct alignment with each 
other. (Just like in ChromasPro).
Is there any option to do this? Or Do I have to modify the code ?

Best Regrags,
Umanga

From aumanga at biggjapan.com  Fri Jun 12 04:20:36 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 12 Jun 2009 17:20:36 +0900
Subject: [Biojava-l] Cannot update or checkout BioJava SVN  source
Message-ID: <4A320FD4.2090405@biggjapan.com>

Greetings ,

I wanted to update my copy of SVN but it gives
"svn: Can't find a temporary directory: Internal error" .
Then I tried to checkout a new copy but still it give this error.
I read somewhere this error is given because of not enough free space on 
the server.

Any tips,

Umanga

From andreas at sdsc.edu  Fri Jun 12 09:35:57 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 12 Jun 2009 06:35:57 -0700
Subject: [Biojava-l] Cannot update or checkout BioJava SVN source
In-Reply-To: <4A320FD4.2090405@biggjapan.com>
References: <4A320FD4.2090405@biggjapan.com>
Message-ID: <59a41c430906120635k2d0ef3eag46ff44061566fa1c@mail.gmail.com>

Hi Umanga,

I just checked the anonymous access with
svn list svn://code.open-bio.org/biojava

and the developer access with
svn list svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/trunk

both works for me and I assume the svn server works ok...
Andreas


On Fri, Jun 12, 2009 at 1:20 AM, Ashika Umanga
Umagiliya<aumanga at biggjapan.com> wrote:
> Greetings ,
>
> I wanted to update my copy of SVN but it gives
> "svn: Can't find a temporary directory: Internal error" .
> Then I tried to checkout a new copy but still it give this error.
> I read somewhere this error is given because of not enough free space on the
> server.
>
> Any tips,
>
> Umanga
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From koen.bruynseels at cropdesign.com  Mon Jun 15 14:08:04 2009
From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com)
Date: Mon, 15 Jun 2009 20:08:04 +0200
Subject: [Biojava-l] Koen Bruynseels is out of the office.
Message-ID: <OF6E459872.D58F7328-ONC12575D6.00639DA1-C12575D6.00639DA1@basf-c-s.be>


I will be out of the office starting  06/14/2009 and will not return until
06/23/2009.

I will respond to your message when I return.


From aumanga at biggjapan.com  Tue Jun 16 03:24:19 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 16:24:19 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
Message-ID: <4A3748A3.8050807@biggjapan.com>

Greetings all,

Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png


As shown in image (1) , I draw the basecall sequences of AB1 file,by 
parsing the ACE file generated by Phrap.That is ,for upper part I do not 
read AB1 file.Only read values from ACE file.(values under 'RD' tag in 
ACE file.)In the example, two files are 'sampleA-S-R.AB1' and 
'sampleA-S-F.AB1'.

For the bottom part- that is to draw Chromatogram, I use Biojavas 
'ChromatogramGraphic' class.

I wanted to align these two parts- that is align 'sampleA-S-R.AB1' 
basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like 
in ChromasPro).

But I noticed that basecall sequence of 'ChromatogramGraphic' is totally 
different than that of from ACE file.
Refer to image (2) ; you can see the two sequences generated by same AB1 
file is different in lenght also.

What could be the problem here? Any suggestions please

thanks in advance.
umanga

From aumanga at biggjapan.com  Tue Jun 16 03:24:19 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 16:24:19 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
Message-ID: <4A3748A3.8050807@biggjapan.com>

Greetings all,

Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png


As shown in image (1) , I draw the basecall sequences of AB1 file,by 
parsing the ACE file generated by Phrap.That is ,for upper part I do not 
read AB1 file.Only read values from ACE file.(values under 'RD' tag in 
ACE file.)In the example, two files are 'sampleA-S-R.AB1' and 
'sampleA-S-F.AB1'.

For the bottom part- that is to draw Chromatogram, I use Biojavas 
'ChromatogramGraphic' class.

I wanted to align these two parts- that is align 'sampleA-S-R.AB1' 
basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like 
in ChromasPro).

But I noticed that basecall sequence of 'ChromatogramGraphic' is totally 
different than that of from ACE file.
Refer to image (2) ; you can see the two sequences generated by same AB1 
file is different in lenght also.

What could be the problem here? Any suggestions please

thanks in advance.
umanga

From aumanga at biggjapan.com  Tue Jun 16 05:06:01 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 18:06:01 +0900
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
Message-ID: <4A376079.8020902@biggjapan.com>

Greetings all,

When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls 
read is lower than the basecalls in a Phrap ACE file.

For example I parse the AB1 file using biojava ABIChromatogram , it gave 
the following basecalls:

ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
ttacttacacatatgttcttccctaataacagagttttacgatccgaag
accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
tatccggtattagctccggtttcccgaagttatcccagtcttataggta
ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
ttcatcctgagccaggatcaaactctccaa

Total number is 520 ,


But in Phrap ACE file the corrosponding entry is :
(should get compliment sequence to compare)

RD 2008-10-24_A02_S_R.ab1 1404 0 0
gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
ttaa

My question is why biojava parser only give 520 bases? Is there a way to 
parse all 1404 bases as seen in Phrap ACE file?

Thanks in advance,
umanga


From aumanga at biggjapan.com  Tue Jun 16 05:06:01 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 18:06:01 +0900
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
Message-ID: <4A376079.8020902@biggjapan.com>

Greetings all,

When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls 
read is lower than the basecalls in a Phrap ACE file.

For example I parse the AB1 file using biojava ABIChromatogram , it gave 
the following basecalls:

ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
ttacttacacatatgttcttccctaataacagagttttacgatccgaag
accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
tatccggtattagctccggtttcccgaagttatcccagtcttataggta
ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
ttcatcctgagccaggatcaaactctccaa

Total number is 520 ,


But in Phrap ACE file the corrosponding entry is :
(should get compliment sequence to compare)

RD 2008-10-24_A02_S_R.ab1 1404 0 0
gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
ttaa

My question is why biojava parser only give 520 bases? Is there a way to 
parse all 1404 bases as seen in Phrap ACE file?

Thanks in advance,
umanga


From ayates at ebi.ac.uk  Tue Jun 16 05:10:54 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 16 Jun 2009 10:10:54 +0100
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A3748A3.8050807@biggjapan.com>
References: <4A3748A3.8050807@biggjapan.com>
Message-ID: <4A37619E.4090807@ebi.ac.uk>

Hi Ashika,

AB1 files will contain a different basecall to one generated by phrap
since (as far as my memory serves me) ABI's platform has a basecaller
built in. This is the one which is coded into the AB1 file & therefore
chromatogram graphic will pick up on that one. However it's very odd
that the Phrap calls are so distant from the trace itself.

I would have hoped that the ACE file would have contained some kind of
called base -> peak position in the chromatogram. There is always the
option of getting phred to output a SCF file which should contain this
information & see what it thinks its doing. SCFs can be parsed by
BioJava so you should be able to push it straight into your program &
let it handle it.

Andy

Ashika Umanga Umagiliya wrote:
> Greetings all,
> 
> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
> 
> 
> As shown in image (1) , I draw the basecall sequences of AB1 file,by
> parsing the ACE file generated by Phrap.That is ,for upper part I do not
> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
> 'sampleA-S-F.AB1'.
> 
> For the bottom part- that is to draw Chromatogram, I use Biojavas
> 'ChromatogramGraphic' class.
> 
> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like
> in ChromasPro).
> 
> But I noticed that basecall sequence of 'ChromatogramGraphic' is totally
> different than that of from ACE file.
> Refer to image (2) ; you can see the two sequences generated by same AB1
> file is different in lenght also.
> 
> What could be the problem here? Any suggestions please
> 
> thanks in advance.
> umanga
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From ayates at ebi.ac.uk  Tue Jun 16 05:21:12 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 16 Jun 2009 10:21:12 +0100
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
In-Reply-To: <4A376079.8020902@biggjapan.com>
References: <4A376079.8020902@biggjapan.com>
Message-ID: <4A376408.1090602@ebi.ac.uk>

Hi,

Are you sure that the AB1 file actually contains more than 520bp? Have a
check there first (using something like trev should display the AB1
processed data) and then we can see if its a problem in the data or the
program.

Andy

Ashika Umanga Umagiliya wrote:
> Greetings all,
> 
> When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls
> read is lower than the basecalls in a Phrap ACE file.
> 
> For example I parse the AB1 file using biojava ABIChromatogram , it gave
> the following basecalls:
> 
> ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
> ttacttacacatatgttcttccctaataacagagttttacgatccgaag
> accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
> gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
> tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
> gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
> agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
> tatccggtattagctccggtttcccgaagttatcccagtcttataggta
> ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
> gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
> ttcatcctgagccaggatcaaactctccaa
> 
> Total number is 520 ,
> 
> 
> But in Phrap ACE file the corrosponding entry is :
> (should get compliment sequence to compare)
> 
> RD 2008-10-24_A02_S_R.ab1 1404 0 0
> gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
> aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
> cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
> gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
> aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
> agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
> atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
> caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
> acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
> gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
> ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
> tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
> ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
> atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
> tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
> ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
> tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
> gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
> CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
> AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
> CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
> TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
> TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
> AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
> CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
> GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
> TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
> AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
> ttaa
> 
> My question is why biojava parser only give 520 bases? Is there a way to
> parse all 1404 bases as seen in Phrap ACE file?
> 
> Thanks in advance,
> umanga
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From aumanga at biggjapan.com  Tue Jun 16 05:39:27 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 18:39:27 +0900
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
In-Reply-To: <4A376408.1090602@ebi.ac.uk>
References: <4A376079.8020902@biggjapan.com> <4A376408.1090602@ebi.ac.uk>
Message-ID: <4A37684F.5080206@biggjapan.com>

HI Andy,

Thank you for the tip. I checked the AB1 with 'trev' and it gave the 
number of bases as 520.
But I wonder in Phrap ACE file how it show 1404 bases.

Best Regards,
Umanga

Andy Yates wrote:
> Hi,
>
> Are you sure that the AB1 file actually contains more than 520bp? Have a
> check there first (using something like trev should display the AB1
> processed data) and then we can see if its a problem in the data or the
> program.
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Greetings all,
>>
>> When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls
>> read is lower than the basecalls in a Phrap ACE file.
>>
>> For example I parse the AB1 file using biojava ABIChromatogram , it gave
>> the following basecalls:
>>
>> ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
>> ttacttacacatatgttcttccctaataacagagttttacgatccgaag
>> accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
>> gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
>> tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
>> gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
>> agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
>> tatccggtattagctccggtttcccgaagttatcccagtcttataggta
>> ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
>> gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
>> ttcatcctgagccaggatcaaactctccaa
>>
>> Total number is 520 ,
>>
>>
>> But in Phrap ACE file the corrosponding entry is :
>> (should get compliment sequence to compare)
>>
>> RD 2008-10-24_A02_S_R.ab1 1404 0 0
>> gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
>> aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
>> cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
>> gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
>> aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
>> agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
>> atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
>> caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
>> acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
>> gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
>> ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
>> tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
>> ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
>> atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
>> tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
>> ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
>> tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
>> gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
>> CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
>> AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
>> CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
>> TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
>> TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
>> AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
>> CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
>> GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
>> TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
>> AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
>> ttaa
>>
>> My question is why biojava parser only give 520 bases? Is there a way to
>> parse all 1404 bases as seen in Phrap ACE file?
>>
>> Thanks in advance,
>> umanga
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>     


From aumanga at biggjapan.com  Tue Jun 16 05:41:54 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 18:41:54 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A37619E.4090807@ebi.ac.uk>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
Message-ID: <4A3768E2.7090003@biggjapan.com>

Hi Andy,

Thank you for the reply.
Earlier problem was I had not applied the compliment in the ChromatoGraph.
Now I could inspect the alignment with the Phrap calls

Please refer :  http://i43.tinypic.com/e5iu12.png

I have drawn orange underlines from where the two sequences matches.
But I had to hardcode x1 and x2 offset values to make the graphs align 
with the Phrap basecalls.
 So as for my question 
http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if 
somehow get all (or fill) all the callbases same as in ACE , I can align 
easily.


Best Regards,
Umanga





Andy Yates wrote:
> Hi Ashika,
>
> AB1 files will contain a different basecall to one generated by phrap
> since (as far as my memory serves me) ABI's platform has a basecaller
> built in. This is the one which is coded into the AB1 file & therefore
> chromatogram graphic will pick up on that one. However it's very odd
> that the Phrap calls are so distant from the trace itself.
>
> I would have hoped that the ACE file would have contained some kind of
> called base -> peak position in the chromatogram. There is always the
> option of getting phred to output a SCF file which should contain this
> information & see what it thinks its doing. SCFs can be parsed by
> BioJava so you should be able to push it straight into your program &
> let it handle it.
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Greetings all,
>>
>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
>>
>>
>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>> parsing the ACE file generated by Phrap.That is ,for upper part I do not
>> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>> 'sampleA-S-F.AB1'.
>>
>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>> 'ChromatogramGraphic' class.
>>
>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like
>> in ChromasPro).
>>
>> But I noticed that basecall sequence of 'ChromatogramGraphic' is totally
>> different than that of from ACE file.
>> Refer to image (2) ; you can see the two sequences generated by same AB1
>> file is different in lenght also.
>>
>> What could be the problem here? Any suggestions please
>>
>> thanks in advance.
>> umanga
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>     


From ayates at ebi.ac.uk  Tue Jun 16 05:56:10 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 16 Jun 2009 10:56:10 +0100
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
In-Reply-To: <4A37684F.5080206@biggjapan.com>
References: <4A376079.8020902@biggjapan.com> <4A376408.1090602@ebi.ac.uk>
	<4A37684F.5080206@biggjapan.com>
Message-ID: <4A376C3A.9020500@ebi.ac.uk>

Well the most likely explanation is that since Phred is doing its own
basecalling it will be using the unprocessed data which is in the AB1
file. This is always longer than the processed data you see in the AB1
file normally and has not been massaged WRT trace trimming, noise
reduction and base lining. So my guess WRT such a huge number of bases
is that phred has gone into the "soup" regions of a trace from the
beginning and the end.

Andy

Ashika Umanga Umagiliya wrote:
> HI Andy,
> 
> Thank you for the tip. I checked the AB1 with 'trev' and it gave the
> number of bases as 520.
> But I wonder in Phrap ACE file how it show 1404 bases.
> 
> Best Regards,
> Umanga
> 
> Andy Yates wrote:
>> Hi,
>>
>> Are you sure that the AB1 file actually contains more than 520bp? Have a
>> check there first (using something like trev should display the AB1
>> processed data) and then we can see if its a problem in the data or the
>> program.
>>
>> Andy
>>
>> Ashika Umanga Umagiliya wrote:
>>  
>>> Greetings all,
>>>
>>> When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls
>>> read is lower than the basecalls in a Phrap ACE file.
>>>
>>> For example I parse the AB1 file using biojava ABIChromatogram , it gave
>>> the following basecalls:
>>>
>>> ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
>>> ttacttacacatatgttcttccctaataacagagttttacgatccgaag
>>> accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
>>> gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
>>> tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
>>> gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
>>> agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
>>> tatccggtattagctccggtttcccgaagttatcccagtcttataggta
>>> ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
>>> gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
>>> ttcatcctgagccaggatcaaactctccaa
>>>
>>> Total number is 520 ,
>>>
>>>
>>> But in Phrap ACE file the corrosponding entry is :
>>> (should get compliment sequence to compare)
>>>
>>> RD 2008-10-24_A02_S_R.ab1 1404 0 0
>>> gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
>>> aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
>>> cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
>>> gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
>>> aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
>>> agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
>>> atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
>>> caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
>>> acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
>>> gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
>>> ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
>>> tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
>>> ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
>>> atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
>>> tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
>>> ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
>>> tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
>>> gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
>>> CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
>>> AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
>>> CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
>>> TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
>>> TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
>>> AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
>>> CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
>>> GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
>>> TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
>>> AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
>>> ttaa
>>>
>>> My question is why biojava parser only give 520 bases? Is there a way to
>>> parse all 1404 bases as seen in Phrap ACE file?
>>>
>>> Thanks in advance,
>>> umanga
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>     

From abdul.qaddos at gmail.com  Tue Jun 16 20:48:55 2009
From: abdul.qaddos at gmail.com (Abdul Qaddus)
Date: Wed, 17 Jun 2009 05:48:55 +0500
Subject: [Biojava-l] Fwd: Need help for resolving the args[0] issues.
In-Reply-To: <a6b292990906160005r6a1ddcd4k6deb2dc2ab5ebcd9@mail.gmail.com>
References: <a6b292990906160005r6a1ddcd4k6deb2dc2ab5ebcd9@mail.gmail.com>
Message-ID: <a6b292990906161748u136c0ef2hec608facd638a845@mail.gmail.com>

Hello Support,
I am a new developer of biojava, I have a good knowledge about java and bio,
but this is new tool for me, I have some problem while working in this
tools, below I have write down the code for reading the Gen Bank file and
then convert into "DNA", "RNA" or "Protein". I have already add the biojava
library into my source code. When I have read this code I have come to know
from your arguments portion for the execution of this code, I have need
three argument, one for the filename, second for the file type and third is
the alphabet.
Now the problem is that how I will pass these three parameter values into
source code for args[0], args[1] and args[2]. When I have passed these
values by using the string pattern then this code generte a errors, "illegel
statement". Please help me out how I can fixed this problem, I will be very
thankful to you if you will reply me soon


package biojava;
import java.io.*;

import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;

public class ReadFasta2 {

  /**
   * This program will read any file supported by SeqIOTools it takes three
   * arguments, the first is the file name the second is the name of
   * a file format supported by SeqIOTools. eg fasta, genbank etc.
   * The third argument is the alphabet (eg dna, rna, protein).
   *
   * Both the format and alphabet names are case insensitive.
   *
   */
  public static void main(String[] args) {
    try {
      //prepare a BufferedReader for file io
      BufferedReader br = new BufferedReader(new FileReader(args[0]));

      String format = args[1];
      String alphabet = args[2];

      /*
       * get a Sequence Iterator over all the sequences in the file.
       * SeqIOTools.fileToBiojava() returns an Object. If the file read
       * is an alignment format like MSF and Alignment object is returned
       * otherwise a SequenceIterator is returned.
       */
      SequenceIterator iter =
          (SequenceIterator)SeqIOTools.fileToBiojava(format,alphabet, br);
    }
    catch (FileNotFoundException ex) {
      //can't find file specified by args[0]
      ex.printStackTrace();
    }catch (BioException ex) {
      //error parsing requested format
      ex.printStackTrace();
    }
  }
}
-- 
Abdul Qaddus
www.futurelinkers.com
Cell No:- +92-3336540863



-- 
Abdul Qaddus
www.futurelinkers.com
Cell No:- +92-3336540863

From aumanga at biggjapan.com  Tue Jun 16 22:49:46 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Wed, 17 Jun 2009 11:49:46 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A377471.9090509@ebi.ac.uk>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
	<4A3768E2.7090003@biggjapan.com> <4A377471.9090509@ebi.ac.uk>
Message-ID: <4A3859CA.5020803@biggjapan.com>

Hi Andy ,

Thanks for the help.I was doing all wrong !
Instead of using AB1 raw data , I used SCF  generated by Phrep and used 
the offset values from ACE file.
Now all are aligned , here a snapshot : http://i39.tinypic.com/xbymf.png

But still one problem .As can be seen in the picture, at the end of the 
graph, some part of the trace-plot is missing for last bases.
Any idea whats going on here ?

Thanks in advance,
Umanga

Andy Yates wrote:
> Hi Umanga,
>
> In terms of getting the offset I'm not sure. That information should be
> provided via the ACE file or from some other output from phrap; its not
> the responsibility of the AB1 file to contain this information. The
> phred output (which phrap uses under the scenes I think) which does
> contain this information is the SCF output but in this situation you are
> not rendering the processed output from the ABI sequencer. You are
> actually displaying:
>
> ABI Raw output -> phred basecalled/processed
>
> So if there is a reason why you want to show the ABI processed data then
> I'm not sure how to marry it to the phrap output. Otherwise just use the
> traces phrap outputs and see what happens.
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Hi Andy,
>>
>> Thank you for the reply.
>> Earlier problem was I had not applied the compliment in the ChromatoGraph.
>> Now I could inspect the alignment with the Phrap calls
>>
>> Please refer :  http://i43.tinypic.com/e5iu12.png
>>
>> I have drawn orange underlines from where the two sequences matches.
>> But I had to hardcode x1 and x2 offset values to make the graphs align
>> with the Phrap basecalls.
>> So as for my question
>> http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if
>> somehow get all (or fill) all the callbases same as in ACE , I can align
>> easily.
>>
>>
>> Best Regards,
>> Umanga
>>
>>
>>
>>
>>
>> Andy Yates wrote:
>>     
>>> Hi Ashika,
>>>
>>> AB1 files will contain a different basecall to one generated by phrap
>>> since (as far as my memory serves me) ABI's platform has a basecaller
>>> built in. This is the one which is coded into the AB1 file & therefore
>>> chromatogram graphic will pick up on that one. However it's very odd
>>> that the Phrap calls are so distant from the trace itself.
>>>
>>> I would have hoped that the ACE file would have contained some kind of
>>> called base -> peak position in the chromatogram. There is always the
>>> option of getting phred to output a SCF file which should contain this
>>> information & see what it thinks its doing. SCFs can be parsed by
>>> BioJava so you should be able to push it straight into your program &
>>> let it handle it.
>>>
>>> Andy
>>>
>>> Ashika Umanga Umagiliya wrote:
>>>  
>>>       
>>>> Greetings all,
>>>>
>>>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>>>> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
>>>>
>>>>
>>>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>>>> parsing the ACE file generated by Phrap.That is ,for upper part I do not
>>>> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
>>>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>>>> 'sampleA-S-F.AB1'.
>>>>
>>>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>>>> 'ChromatogramGraphic' class.
>>>>
>>>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>>>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like
>>>> in ChromasPro).
>>>>
>>>> But I noticed that basecall sequence of 'ChromatogramGraphic' is totally
>>>> different than that of from ACE file.
>>>> Refer to image (2) ; you can see the two sequences generated by same AB1
>>>> file is different in lenght also.
>>>>
>>>> What could be the problem here? Any suggestions please
>>>>
>>>> thanks in advance.
>>>> umanga
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>     
>>>>         


From ayates at ebi.ac.uk  Wed Jun 17 04:16:58 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 17 Jun 2009 09:16:58 +0100
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A3859CA.5020803@biggjapan.com>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
	<4A3768E2.7090003@biggjapan.com> <4A377471.9090509@ebi.ac.uk>
	<4A3859CA.5020803@biggjapan.com>
Message-ID: <4A38A67A.1000509@ebi.ac.uk>

Hi Umanga,

Glad you've got it rendering though now :)

My best guess is that the trace have been truncated by the generating
program or the file writing is incomplete which I doubt due to the way
SCF files are constructed. So my money is on Phrap/Phred doing a bit of
quality control with the end of the trace. Why it hasn't truncated the
base calls as well I do not know and is probably a question better
suited to the people who write/maintain Phred & Phrap.

Sorry I can't be of that much more help :(

Andy

Ashika Umanga Umagiliya wrote:
> Hi Andy ,
> 
> Thanks for the help.I was doing all wrong !
> Instead of using AB1 raw data , I used SCF  generated by Phrep and used
> the offset values from ACE file.
> Now all are aligned , here a snapshot : http://i39.tinypic.com/xbymf.png
> 
> But still one problem .As can be seen in the picture, at the end of the
> graph, some part of the trace-plot is missing for last bases.
> Any idea whats going on here ?
> 
> Thanks in advance,
> Umanga
> 
> Andy Yates wrote:
>> Hi Umanga,
>>
>> In terms of getting the offset I'm not sure. That information should be
>> provided via the ACE file or from some other output from phrap; its not
>> the responsibility of the AB1 file to contain this information. The
>> phred output (which phrap uses under the scenes I think) which does
>> contain this information is the SCF output but in this situation you are
>> not rendering the processed output from the ABI sequencer. You are
>> actually displaying:
>>
>> ABI Raw output -> phred basecalled/processed
>>
>> So if there is a reason why you want to show the ABI processed data then
>> I'm not sure how to marry it to the phrap output. Otherwise just use the
>> traces phrap outputs and see what happens.
>>
>> Andy
>>
>> Ashika Umanga Umagiliya wrote:
>>  
>>> Hi Andy,
>>>
>>> Thank you for the reply.
>>> Earlier problem was I had not applied the compliment in the
>>> ChromatoGraph.
>>> Now I could inspect the alignment with the Phrap calls
>>>
>>> Please refer :  http://i43.tinypic.com/e5iu12.png
>>>
>>> I have drawn orange underlines from where the two sequences matches.
>>> But I had to hardcode x1 and x2 offset values to make the graphs align
>>> with the Phrap basecalls.
>>> So as for my question
>>> http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if
>>> somehow get all (or fill) all the callbases same as in ACE , I can align
>>> easily.
>>>
>>>
>>> Best Regards,
>>> Umanga
>>>
>>>
>>>
>>>
>>>
>>> Andy Yates wrote:
>>>    
>>>> Hi Ashika,
>>>>
>>>> AB1 files will contain a different basecall to one generated by phrap
>>>> since (as far as my memory serves me) ABI's platform has a basecaller
>>>> built in. This is the one which is coded into the AB1 file & therefore
>>>> chromatogram graphic will pick up on that one. However it's very odd
>>>> that the Phrap calls are so distant from the trace itself.
>>>>
>>>> I would have hoped that the ACE file would have contained some kind of
>>>> called base -> peak position in the chromatogram. There is always the
>>>> option of getting phred to output a SCF file which should contain this
>>>> information & see what it thinks its doing. SCFs can be parsed by
>>>> BioJava so you should be able to push it straight into your program &
>>>> let it handle it.
>>>>
>>>> Andy
>>>>
>>>> Ashika Umanga Umagiliya wrote:
>>>>  
>>>>      
>>>>> Greetings all,
>>>>>
>>>>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>>>>> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
>>>>>
>>>>>
>>>>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>>>>> parsing the ACE file generated by Phrap.That is ,for upper part I
>>>>> do not
>>>>> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
>>>>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>>>>> 'sampleA-S-F.AB1'.
>>>>>
>>>>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>>>>> 'ChromatogramGraphic' class.
>>>>>
>>>>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>>>>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so
>>>>> on...(like
>>>>> in ChromasPro).
>>>>>
>>>>> But I noticed that basecall sequence of 'ChromatogramGraphic' is
>>>>> totally
>>>>> different than that of from ACE file.
>>>>> Refer to image (2) ; you can see the two sequences generated by
>>>>> same AB1
>>>>> file is different in lenght also.
>>>>>
>>>>> What could be the problem here? Any suggestions please
>>>>>
>>>>> thanks in advance.
>>>>> umanga
>>>>> _______________________________________________
>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>             

From aumanga at biggjapan.com  Wed Jun 17 05:00:50 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Wed, 17 Jun 2009 18:00:50 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A38A67A.1000509@ebi.ac.uk>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
	<4A3768E2.7090003@biggjapan.com> <4A377471.9090509@ebi.ac.uk>
	<4A3859CA.5020803@biggjapan.com> <4A38A67A.1000509@ebi.ac.uk>
Message-ID: <4A38B0C2.4030806@biggjapan.com>

Hi again Andy ,

Thank you for all your help , it was a matter of setting an option in  
ChromatogramGraphic


ChromatogramGraphic chromaGfx;
.
.
chromaGfx.setOption(Option.SUBPATH_LENGTH, new Integer(
                    Integer.MAX_VALUE));


Now I can see the entire trace-plot ..  Everything is just fine :)


Best Regards,
Umanga

Andy Yates wrote:
> Hi Umanga,
>
> Glad you've got it rendering though now :)
>
> My best guess is that the trace have been truncated by the generating
> program or the file writing is incomplete which I doubt due to the way
> SCF files are constructed. So my money is on Phrap/Phred doing a bit of
> quality control with the end of the trace. Why it hasn't truncated the
> base calls as well I do not know and is probably a question better
> suited to the people who write/maintain Phred & Phrap.
>
> Sorry I can't be of that much more help :(
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Hi Andy ,
>>
>> Thanks for the help.I was doing all wrong !
>> Instead of using AB1 raw data , I used SCF  generated by Phrep and used
>> the offset values from ACE file.
>> Now all are aligned , here a snapshot : http://i39.tinypic.com/xbymf.png
>>
>> But still one problem .As can be seen in the picture, at the end of the
>> graph, some part of the trace-plot is missing for last bases.
>> Any idea whats going on here ?
>>
>> Thanks in advance,
>> Umanga
>>
>> Andy Yates wrote:
>>     
>>> Hi Umanga,
>>>
>>> In terms of getting the offset I'm not sure. That information should be
>>> provided via the ACE file or from some other output from phrap; its not
>>> the responsibility of the AB1 file to contain this information. The
>>> phred output (which phrap uses under the scenes I think) which does
>>> contain this information is the SCF output but in this situation you are
>>> not rendering the processed output from the ABI sequencer. You are
>>> actually displaying:
>>>
>>> ABI Raw output -> phred basecalled/processed
>>>
>>> So if there is a reason why you want to show the ABI processed data then
>>> I'm not sure how to marry it to the phrap output. Otherwise just use the
>>> traces phrap outputs and see what happens.
>>>
>>> Andy
>>>
>>> Ashika Umanga Umagiliya wrote:
>>>  
>>>       
>>>> Hi Andy,
>>>>
>>>> Thank you for the reply.
>>>> Earlier problem was I had not applied the compliment in the
>>>> ChromatoGraph.
>>>> Now I could inspect the alignment with the Phrap calls
>>>>
>>>> Please refer :  http://i43.tinypic.com/e5iu12.png
>>>>
>>>> I have drawn orange underlines from where the two sequences matches.
>>>> But I had to hardcode x1 and x2 offset values to make the graphs align
>>>> with the Phrap basecalls.
>>>> So as for my question
>>>> http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if
>>>> somehow get all (or fill) all the callbases same as in ACE , I can align
>>>> easily.
>>>>
>>>>
>>>> Best Regards,
>>>> Umanga
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Andy Yates wrote:
>>>>    
>>>>         
>>>>> Hi Ashika,
>>>>>
>>>>> AB1 files will contain a different basecall to one generated by phrap
>>>>> since (as far as my memory serves me) ABI's platform has a basecaller
>>>>> built in. This is the one which is coded into the AB1 file & therefore
>>>>> chromatogram graphic will pick up on that one. However it's very odd
>>>>> that the Phrap calls are so distant from the trace itself.
>>>>>
>>>>> I would have hoped that the ACE file would have contained some kind of
>>>>> called base -> peak position in the chromatogram. There is always the
>>>>> option of getting phred to output a SCF file which should contain this
>>>>> information & see what it thinks its doing. SCFs can be parsed by
>>>>> BioJava so you should be able to push it straight into your program &
>>>>> let it handle it.
>>>>>
>>>>> Andy
>>>>>
>>>>> Ashika Umanga Umagiliya wrote:
>>>>>  
>>>>>      
>>>>>           
>>>>>> Greetings all,
>>>>>>
>>>>>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>>>>>> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
>>>>>>
>>>>>>
>>>>>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>>>>>> parsing the ACE file generated by Phrap.That is ,for upper part I
>>>>>> do not
>>>>>> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
>>>>>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>>>>>> 'sampleA-S-F.AB1'.
>>>>>>
>>>>>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>>>>>> 'ChromatogramGraphic' class.
>>>>>>
>>>>>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>>>>>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so
>>>>>> on...(like
>>>>>> in ChromasPro).
>>>>>>
>>>>>> But I noticed that basecall sequence of 'ChromatogramGraphic' is
>>>>>> totally
>>>>>> different than that of from ACE file.
>>>>>> Refer to image (2) ; you can see the two sequences generated by
>>>>>> same AB1
>>>>>> file is different in lenght also.
>>>>>>
>>>>>> What could be the problem here? Any suggestions please
>>>>>>
>>>>>> thanks in advance.
>>>>>> umanga
>>>>>> _______________________________________________
>>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>>             
>>>>>>             


From andreas at sdsc.edu  Wed Jun 17 14:11:17 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 17 Jun 2009 11:11:17 -0700
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A38B0C2.4030806@biggjapan.com>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
	<4A3768E2.7090003@biggjapan.com> <4A377471.9090509@ebi.ac.uk>
	<4A3859CA.5020803@biggjapan.com> <4A38A67A.1000509@ebi.ac.uk>
	<4A38B0C2.4030806@biggjapan.com>
Message-ID: <59a41c430906171111y53f8080u956e909a185e9a48@mail.gmail.com>

Great that it works now!

Do you want to post some more documentation on the wiki page? We seem
to get queries regarding this every now and then so having more docu
might be helpful...

Cheers,
Andreas


On Wed, Jun 17, 2009 at 2:00 AM, Ashika Umanga
Umagiliya<aumanga at biggjapan.com> wrote:
> Hi again Andy ,
>
> Thank you for all your help , it was a matter of setting an option in
> ?ChromatogramGraphic
>
>
> ChromatogramGraphic chromaGfx;
> .
> .
> chromaGfx.setOption(Option.SUBPATH_LENGTH, new Integer(
> ? ? ? ? ? ? ? ? ? Integer.MAX_VALUE));
>
>
> Now I can see the entire trace-plot .. ?Everything is just fine :)
>
>
> Best Regards,
> Umanga
>
> Andy Yates wrote:
>>
>> Hi Umanga,
>>
>> Glad you've got it rendering though now :)
>>
>> My best guess is that the trace have been truncated by the generating
>> program or the file writing is incomplete which I doubt due to the way
>> SCF files are constructed. So my money is on Phrap/Phred doing a bit of
>> quality control with the end of the trace. Why it hasn't truncated the
>> base calls as well I do not know and is probably a question better
>> suited to the people who write/maintain Phred & Phrap.
>>
>> Sorry I can't be of that much more help :(
>>
>> Andy
>>
>> Ashika Umanga Umagiliya wrote:
>>
>>>
>>> Hi Andy ,
>>>
>>> Thanks for the help.I was doing all wrong !
>>> Instead of using AB1 raw data , I used SCF ?generated by Phrep and used
>>> the offset values from ACE file.
>>> Now all are aligned , here a snapshot : http://i39.tinypic.com/xbymf.png
>>>
>>> But still one problem .As can be seen in the picture, at the end of the
>>> graph, some part of the trace-plot is missing for last bases.
>>> Any idea whats going on here ?
>>>
>>> Thanks in advance,
>>> Umanga
>>>
>>> Andy Yates wrote:
>>>
>>>>
>>>> Hi Umanga,
>>>>
>>>> In terms of getting the offset I'm not sure. That information should be
>>>> provided via the ACE file or from some other output from phrap; its not
>>>> the responsibility of the AB1 file to contain this information. The
>>>> phred output (which phrap uses under the scenes I think) which does
>>>> contain this information is the SCF output but in this situation you are
>>>> not rendering the processed output from the ABI sequencer. You are
>>>> actually displaying:
>>>>
>>>> ABI Raw output -> phred basecalled/processed
>>>>
>>>> So if there is a reason why you want to show the ABI processed data then
>>>> I'm not sure how to marry it to the phrap output. Otherwise just use the
>>>> traces phrap outputs and see what happens.
>>>>
>>>> Andy
>>>>
>>>> Ashika Umanga Umagiliya wrote:
>>>>
>>>>>
>>>>> Hi Andy,
>>>>>
>>>>> Thank you for the reply.
>>>>> Earlier problem was I had not applied the compliment in the
>>>>> ChromatoGraph.
>>>>> Now I could inspect the alignment with the Phrap calls
>>>>>
>>>>> Please refer : ?http://i43.tinypic.com/e5iu12.png
>>>>>
>>>>> I have drawn orange underlines from where the two sequences matches.
>>>>> But I had to hardcode x1 and x2 offset values to make the graphs align
>>>>> with the Phrap basecalls.
>>>>> So as for my question
>>>>> http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html ,
>>>>> if
>>>>> somehow get all (or fill) all the callbases same as in ACE , I can
>>>>> align
>>>>> easily.
>>>>>
>>>>>
>>>>> Best Regards,
>>>>> Umanga
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Andy Yates wrote:
>>>>>
>>>>>>
>>>>>> Hi Ashika,
>>>>>>
>>>>>> AB1 files will contain a different basecall to one generated by phrap
>>>>>> since (as far as my memory serves me) ABI's platform has a basecaller
>>>>>> built in. This is the one which is coded into the AB1 file & therefore
>>>>>> chromatogram graphic will pick up on that one. However it's very odd
>>>>>> that the Phrap calls are so distant from the trace itself.
>>>>>>
>>>>>> I would have hoped that the ACE file would have contained some kind of
>>>>>> called base -> peak position in the chromatogram. There is always the
>>>>>> option of getting phred to output a SCF file which should contain this
>>>>>> information & see what it thinks its doing. SCFs can be parsed by
>>>>>> BioJava so you should be able to push it straight into your program &
>>>>>> let it handle it.
>>>>>>
>>>>>> Andy
>>>>>>
>>>>>> Ashika Umanga Umagiliya wrote:
>>>>>>
>>>>>>>
>>>>>>> Greetings all,
>>>>>>>
>>>>>>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>>>>>>> image 2 (end of graph): ?http://i44.tinypic.com/2vt4iu8.png
>>>>>>>
>>>>>>>
>>>>>>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>>>>>>> parsing the ACE file generated by Phrap.That is ,for upper part I
>>>>>>> do not
>>>>>>> read AB1 file.Only read values from ACE file.(values under 'RD' tag
>>>>>>> in
>>>>>>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>>>>>>> 'sampleA-S-F.AB1'.
>>>>>>>
>>>>>>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>>>>>>> 'ChromatogramGraphic' class.
>>>>>>>
>>>>>>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>>>>>>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so
>>>>>>> on...(like
>>>>>>> in ChromasPro).
>>>>>>>
>>>>>>> But I noticed that basecall sequence of 'ChromatogramGraphic' is
>>>>>>> totally
>>>>>>> different than that of from ACE file.
>>>>>>> Refer to image (2) ; you can see the two sequences generated by
>>>>>>> same AB1
>>>>>>> file is different in lenght also.
>>>>>>>
>>>>>>> What could be the problem here? Any suggestions please
>>>>>>>
>>>>>>> thanks in advance.
>>>>>>> umanga
>>>>>>> _______________________________________________
>>>>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From aumanga at biggjapan.com  Wed Jun 17 22:51:44 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Thu, 18 Jun 2009 11:51:44 +0900
Subject: [Biojava-l] SCF Parser issues with gaps and unread peak values ?
Message-ID: <4A39ABC0.8090503@biggjapan.com>

Greetings all,

Please refer to image at:  http://i43.tinypic.com/sfdjs6.png

As shown in Figure1 , I am drawing bases using Phrap ACE file and 
drawing chromatographs using
Biojava 'ChromatoGraphics' . I use .SCF file generated by phrep.

As can be seen in Figure 1 , the alignment breaks from the 'Magenta 
callbase-box'.The reason is may be the 'SCF parser' has ignored one of 
the peaks which should be a 'T'.


Figure 2 : Shows what need to be happen.If somehow if I can fill it with 
a T (or may be sometimes a Gap) I can save the alignment between sequences.

Figure 3 : Shows the same Chromatograph using ChromasPro , It has 
identified the peak as a T.

I went throught the biojavas SCF  parser , I noticed that it finally 
creates a 'SimpleAlignment'.Can I utilize 'GappedSymbolList' and fix this?
Is there a way to read the gaps (or incases like this , the correct base 
T) and make these two align.

Thanks in advance,
Umanga

From aumanga at biggjapan.com  Thu Jun 18 21:28:56 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 19 Jun 2009 10:28:56 +0900
Subject: [Biojava-l] SCF Parser issues with gaps and unread peak values ?
In-Reply-To: <4A3A163A.6080304@ebi.ac.uk>
References: <4A39ABC0.8090503@biggjapan.com> <4A3A163A.6080304@ebi.ac.uk>
Message-ID: <4A3AE9D8.108@biggjapan.com>

Hi Andy,

Thank you for the help.
Yes,looking at the trace the bases has to be TGTTGTTAGG as you said.

I get Chromatogram using SCF parse like :

Chromatogram chroma = SCF.create(scfFile);

then when I print the bases using

chroma.getBaseCalls()

It shows the bases sequence "TGTTGTAGG" (T is missing).
So I put a System.out.println() to the decode method in SCF parser class 
, that ie at :


 static class DefaultUncertaintyDecoder implements  
BaseCallUncertaintyDecoder {
        public DefaultUncertaintyDecoder() { }

        public Symbol decode(byte call) throws IllegalSymbolException {
            char c = (char) call;
            System.out.print(""+c);
..
..


But here also it showed "TGTTGTAGG" (with missubg T).

So I thought this is not an issue with rendering logic, but in the parser.


Thanks again,
Umanga




Andy Yates wrote:
> Hi Umanga,
>
> Looking at your graphic the SCF parser hasn't missed out the T. Looking
> at the trace I can read the bases to be TGTTGTTAGGG. What I think has
> happened is the callboxes are assuming a more uniformed trace since the
> G has bled a bit too much into the previous T.
>
> My knowledge of the callbox code is non-existent as my previous work on
> these types of graphics did not call for this kind of rendering (we
> didn't use any base calls as we were looking for variation in samples
> with varying copy numbers so they were quite subtle). Have a look in the
> options for the call box rendering & see if there is anything which can
> limit the size of a callbox & the bounds it is rendered to. Also looking
> at the basecalled positions might be a good idea as that would give a
> clue about what the graphics are attempting to do WRT this data
>
> Hope that helps.
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Greetings all,
>>
>> Please refer to image at:  http://i43.tinypic.com/sfdjs6.png
>>
>> As shown in Figure1 , I am drawing bases using Phrap ACE file and
>> drawing chromatographs using
>> Biojava 'ChromatoGraphics' . I use .SCF file generated by phrep.
>>
>> As can be seen in Figure 1 , the alignment breaks from the 'Magenta
>> callbase-box'.The reason is may be the 'SCF parser' has ignored one of
>> the peaks which should be a 'T'.
>>
>>
>> Figure 2 : Shows what need to be happen.If somehow if I can fill it with
>> a T (or may be sometimes a Gap) I can save the alignment between sequences.
>>
>> Figure 3 : Shows the same Chromatograph using ChromasPro , It has
>> identified the peak as a T.
>>
>> I went throught the biojavas SCF  parser , I noticed that it finally
>> creates a 'SimpleAlignment'.Can I utilize 'GappedSymbolList' and fix this?
>> Is there a way to read the gaps (or incases like this , the correct base
>> T) and make these two align.
>>
>> Thanks in advance,
>> Umanga
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>     


From abdul.qaddos at gmail.com  Fri Jun 19 02:52:38 2009
From: abdul.qaddos at gmail.com (Abdul Qaddus)
Date: Fri, 19 Jun 2009 11:52:38 +0500
Subject: [Biojava-l] Need help for resolving the issue args[0]
In-Reply-To: <a6b292990906182350q4c0a6fc4u8783bd8b021c8321@mail.gmail.com>
References: <a6b292990906182350q4c0a6fc4u8783bd8b021c8321@mail.gmail.com>
Message-ID: <a6b292990906182352k1168b1e2l611c3cb7b941b7b8@mail.gmail.com>

 Hello Support,
I am a new developer of biojava, I have a good knowledge about java and bio,
but this is new tool for me, I have some problem while working in this
tools, below I have write down the code for reading the Gen Bank file and
then convert into "DNA", "RNA" or "Protein". I have already add the biojava
library into my source code. When I have read this code I have come to know
from your arguments portion for the execution of this code, I have need
three argument, one for the filename, second for the file type and third is
the alphabet.
Now the problem is that how I will pass these three parameter values into
source code for args[0], args[1] and args[2]. When I have passed these
values by using the string pattern then this code generte a errors, "illegel
statement". Please help me out how I can fixed this problem, I will be very
thankful to you if you will reply me soon


package biojava;
import java.io.*;

import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;

public class ReadFasta2 {

 /**
  * This program will read any file supported by SeqIOTools it takes three
  * arguments, the first is the file name the second is the name of
  * a file format supported by SeqIOTools. eg fasta, genbank etc.
  * The third argument is the alphabet (eg dna, rna, protein).
  *
  * Both the format and alphabet names are case insensitive.
  *
  */
 public static void main(String[] args) {
   try {
     //prepare a BufferedReader for file io
     BufferedReader br = new BufferedReader(new FileReader(args[0]));

     String format = args[1];
     String alphabet = args[2];

     /*
      * get a Sequence Iterator over all the sequences in the file.
      * SeqIOTools.fileToBiojava() returns an Object. If the file read
      * is an alignment format like MSF and Alignment object is returned
      * otherwise a SequenceIterator is returned.
      */
     SequenceIterator iter =
         (SequenceIterator)SeqIOTools.fileToBiojava(format,alphabet, br);
   }
   catch (FileNotFoundException ex) {
     //can't find file specified by args[0]
     ex.printStackTrace();
   }catch (BioException ex) {
     //error parsing requested format
     ex.printStackTrace();
   }
 }
}
--




-- 
Abdul Qaddus
www.futurelinkers.com
Cell No:- +92-3336540863

From mark.schreiber at novartis.com  Fri Jun 19 02:57:09 2009
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 19 Jun 2009 14:57:09 +0800
Subject: [Biojava-l] Need help for resolving the issue args[0]
In-Reply-To: <a6b292990906182352k1168b1e2l611c3cb7b941b7b8@mail.gmail.com>
Message-ID: <OF3E1E7BF7.498CFB66-ON482575DA.00262486-482575DA.002631AC@ah.novartis.com>

Can you post the stack trace?



biojava-l-bounces at lists.open-bio.org wrote on 06/19/2009 02:52:38 PM:

>  Hello Support,
> I am a new developer of biojava, I have a good knowledge about java and 
bio,
> but this is new tool for me, I have some problem while working in this
> tools, below I have write down the code for reading the Gen Bank file 
and
> then convert into "DNA", "RNA" or "Protein". I have already add the 
biojava
> library into my source code. When I have read this code I have come to 
know
> from your arguments portion for the execution of this code, I have need
> three argument, one for the filename, second for the file type and third 
is
> the alphabet.
> Now the problem is that how I will pass these three parameter values 
into
> source code for args[0], args[1] and args[2]. When I have passed these
> values by using the string pattern then this code generte a errors, 
"illegel
> statement". Please help me out how I can fixed this problem, I will be 
very
> thankful to you if you will reply me soon
> 
> 
> package biojava;
> import java.io.*;
> 
> import org.biojava.bio.*;
> import org.biojava.bio.seq.*;
> import org.biojava.bio.seq.io.*;
> 
> public class ReadFasta2 {
> 
>  /**
>   * This program will read any file supported by SeqIOTools it takes 
three
>   * arguments, the first is the file name the second is the name of
>   * a file format supported by SeqIOTools. eg fasta, genbank etc.
>   * The third argument is the alphabet (eg dna, rna, protein).
>   *
>   * Both the format and alphabet names are case insensitive.
>   *
>   */
>  public static void main(String[] args) {
>    try {
>      //prepare a BufferedReader for file io
>      BufferedReader br = new BufferedReader(new FileReader(args[0]));
> 
>      String format = args[1];
>      String alphabet = args[2];
> 
>      /*
>       * get a Sequence Iterator over all the sequences in the file.
>       * SeqIOTools.fileToBiojava() returns an Object. If the file read
>       * is an alignment format like MSF and Alignment object is returned
>       * otherwise a SequenceIterator is returned.
>       */
>      SequenceIterator iter =
>          (SequenceIterator)SeqIOTools.fileToBiojava(format,alphabet, 
br);
>    }
>    catch (FileNotFoundException ex) {
>      //can't find file specified by args[0]
>      ex.printStackTrace();
>    }catch (BioException ex) {
>      //error parsing requested format
>      ex.printStackTrace();
>    }
>  }
> }
> --
> 
> 
> 
> 
> -- 
> Abdul Qaddus
> www.futurelinkers.com
> Cell No:- +92-3336540863
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

_________________________

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The information contained in this e-mail message is intended only for the 
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under applicable law. If the reader of this message is not the intended 
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prohibited. If you have received this communication in error, please 
notify the sender immediately by e-mail and delete the material from any 
computer.  Thank you.

From ayates at ebi.ac.uk  Fri Jun 19 11:37:10 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 19 Jun 2009 16:37:10 +0100
Subject: [Biojava-l] SCF Parser issues with gaps and unread peak values ?
In-Reply-To: <4A3AE9D8.108@biggjapan.com>
References: <4A39ABC0.8090503@biggjapan.com> <4A3A163A.6080304@ebi.ac.uk>
	<4A3AE9D8.108@biggjapan.com>
Message-ID: <4A3BB0A6.2070202@ebi.ac.uk>

Hi Umanga,

That does sound like a problem with the decoder. It's been quite a bit
of time since I last looked at the SCF code. Maybe Franklin who posted
to this list recently (whom I'm guessing is a bit more used to SCF file
formats at the moment) could help if he would be so willing :)

Andy

Ashika Umanga Umagiliya wrote:
> Hi Andy,
> 
> Thank you for the help.
> Yes,looking at the trace the bases has to be TGTTGTTAGG as you said.
> 
> I get Chromatogram using SCF parse like :
> 
> Chromatogram chroma = SCF.create(scfFile);
> 
> then when I print the bases using
> 
> chroma.getBaseCalls()
> 
> It shows the bases sequence "TGTTGTAGG" (T is missing).
> So I put a System.out.println() to the decode method in SCF parser class
> , that ie at :
> 
> 
> static class DefaultUncertaintyDecoder implements 
> BaseCallUncertaintyDecoder {
>        public DefaultUncertaintyDecoder() { }
> 
>        public Symbol decode(byte call) throws IllegalSymbolException {
>            char c = (char) call;
>            System.out.print(""+c);
> ..
> ..
> 
> 
> But here also it showed "TGTTGTAGG" (with missubg T).
> 
> So I thought this is not an issue with rendering logic, but in the parser.
> 
> 
> Thanks again,
> Umanga
> 
> 
> 
> 
> Andy Yates wrote:
>> Hi Umanga,
>>
>> Looking at your graphic the SCF parser hasn't missed out the T. Looking
>> at the trace I can read the bases to be TGTTGTTAGGG. What I think has
>> happened is the callboxes are assuming a more uniformed trace since the
>> G has bled a bit too much into the previous T.
>>
>> My knowledge of the callbox code is non-existent as my previous work on
>> these types of graphics did not call for this kind of rendering (we
>> didn't use any base calls as we were looking for variation in samples
>> with varying copy numbers so they were quite subtle). Have a look in the
>> options for the call box rendering & see if there is anything which can
>> limit the size of a callbox & the bounds it is rendered to. Also looking
>> at the basecalled positions might be a good idea as that would give a
>> clue about what the graphics are attempting to do WRT this data
>>
>> Hope that helps.
>>
>> Andy
>>
>> Ashika Umanga Umagiliya wrote:
>>  
>>> Greetings all,
>>>
>>> Please refer to image at:  http://i43.tinypic.com/sfdjs6.png
>>>
>>> As shown in Figure1 , I am drawing bases using Phrap ACE file and
>>> drawing chromatographs using
>>> Biojava 'ChromatoGraphics' . I use .SCF file generated by phrep.
>>>
>>> As can be seen in Figure 1 , the alignment breaks from the 'Magenta
>>> callbase-box'.The reason is may be the 'SCF parser' has ignored one of
>>> the peaks which should be a 'T'.
>>>
>>>
>>> Figure 2 : Shows what need to be happen.If somehow if I can fill it with
>>> a T (or may be sometimes a Gap) I can save the alignment between
>>> sequences.
>>>
>>> Figure 3 : Shows the same Chromatograph using ChromasPro , It has
>>> identified the peak as a T.
>>>
>>> I went throught the biojavas SCF  parser , I noticed that it finally
>>> creates a 'SimpleAlignment'.Can I utilize 'GappedSymbolList' and fix
>>> this?
>>> Is there a way to read the gaps (or incases like this , the correct base
>>> T) and make these two align.
>>>
>>> Thanks in advance,
>>> Umanga
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>     
> 
> 

From jp at javaclass.co.uk  Fri Jun 19 13:37:38 2009
From: jp at javaclass.co.uk (JP)
Date: Fri, 19 Jun 2009 18:37:38 +0100
Subject: [Biojava-l] Simple Question - Creating a Java object (some form of
	Tree) from a Newick format file
Message-ID: <4adc29060906191037u53cb1622p2e982543f5c22cba@mail.gmail.com>

Does anyone know of a tool to create a tree by parsing a Newick Tree format
file in Java ?
Is there anything in biojava to read this ?

Many Thanks
JP

From holland at eaglegenomics.com  Fri Jun 19 13:56:15 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Fri, 19 Jun 2009 18:56:15 +0100
Subject: [Biojava-l] Simple Question - Creating a Java object (some form
 of Tree) from a Newick format file
In-Reply-To: <4adc29060906191037u53cb1622p2e982543f5c22cba@mail.gmail.com>
References: <4adc29060906191037u53cb1622p2e982543f5c22cba@mail.gmail.com>
Message-ID: <1245434175.8158.6.camel@buzzybee>

Biojava has a parser which understands Nexus files, including the
embedded Newick tree data. You could probably extract and modify the
Newick bits to run standalone. The Nexus code is written up here:

http://biojava.org/wiki/BioJava:PhyloSOC07_doc
http://www.biojava.org/docs/api/org/biojavax/bio/phylo/io/nexus/package-summary.html
http://www.mail-archive.com/biojava-l at lists.open-bio.org/msg00892.html

cheers,
Richard


On Fri, 2009-06-19 at 18:37 +0100, JP wrote:
> Does anyone know of a tool to create a tree by parsing a Newick Tree format
> file in Java ?
> Is there anything in biojava to read this ?
> 
> Many Thanks
> JP
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From andreas at sdsc.edu  Sat Jun 20 12:45:51 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 20 Jun 2009 09:45:51 -0700
Subject: [Biojava-l] BioJava user meeting at ISMB/BOSC
Message-ID: <59a41c430906200945q598503ccj52717cf708b67083@mail.gmail.com>

Hi,

Next week the ISMB and BOSC conferences will take place in Stockholm,
Sweden. As has become kind of a tradition, we will have a BioJava user
meeting around BOSC.

If you are in Stockholm at the time please join us on Sunday, late
afternoon. We will meet during the "Birds of a Feather" session.
http://open-bio.org/wiki/BOSC_2009/Birds-of-a-Feather

Looking forward to meeting you there,
Andreas

From mcolosimo at mitre.org  Mon Jun 22 09:19:01 2009
From: mcolosimo at mitre.org (Colosimo, Marc E.)
Date: Mon, 22 Jun 2009 09:19:01 -0400
Subject: [Biojava-l] Simple Question - Creating a Java object
In-Reply-To: <mailman.11.1245513607.22652.biojava-l@lists.open-bio.org>
References: <mailman.11.1245513607.22652.biojava-l@lists.open-bio.org>
Message-ID: <2A8C361000E22F4895ACA58412E8F06CF4DB53CF@IMCMBX3.MITRE.ORG>

If you just want to view a tree, try TreeViewJ <http://sourceforge.net/projects/treeviewj/>. The GUI can read in newick and phyloXML trees and import trees from Nexus files. It can export back out to newick and phyloXML or as SVG or JPEG images. I have more code that I'll be checking in soon. 

Best,
Marc


From: Richard Holland <holland at eaglegenomics.com>
Subject: Re: [Biojava-l] Simple Question - Creating a Java object
	(some form of Tree) from a Newick format file
To: JP <jp at javaclass.co.uk>
Cc: biojava-l at biojava.org
Message-ID: <1245434175.8158.6.camel at buzzybee>
Content-Type: text/plain

Biojava has a parser which understands Nexus files, including the
embedded Newick tree data. You could probably extract and modify the
Newick bits to run standalone. The Nexus code is written up here:

http://biojava.org/wiki/BioJava:PhyloSOC07_doc
http://www.biojava.org/docs/api/org/biojavax/bio/phylo/io/nexus/package-summary.html
http://www.mail-archive.com/biojava-l at lists.open-bio.org/msg00892.html

cheers,
Richard


On Fri, 2009-06-19 at 18:37 +0100, JP wrote:
> Does anyone know of a tool to create a tree by parsing a Newick Tree format
> file in Java ?
> Is there anything in biojava to read this ?
> 
> Many Thanks
> JP
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From jp at javaclass.co.uk  Mon Jun 22 11:32:58 2009
From: jp at javaclass.co.uk (JP)
Date: Mon, 22 Jun 2009 16:32:58 +0100
Subject: [Biojava-l] Reading a newick format tree file
	(getTreeAsWeightedJGraphT) generates an
	ArrayIndexOutOfBoundsException in TreeBlock
Message-ID: <4adc29060906220832i3e64b699u3b842122df400cb0@mail.gmail.com>

I have tried to use the getTreeAsWeightedJGraphT functionality in TreesBlock
as highlighted in the wikipedia page:

My code for completeness sake (a direct and lazy copy and paste)

String newickFileContents = FileUtils.readTextFile(treeFile, false);  //
> reads the text file without newlines
> WeightedGraph<String, DefaultWeightedEdge> jg = new
> SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
> TreesBlock sample_tree = new TreesBlock();
> TreesBlock.NewickTreeString s = new TreesBlock.NewickTreeString();
> s.setTreeString(newickFileContents);
> sample_tree.addTree("test", s);
> jg = sample_tree.getTreeAsWeightedJGraphT("test");
> System.out.println(newickFileContents);
> System.out.println(jg.toString());
>

The data file is attached (newwick format), and this is the returned error
message...

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 79169
>     at
> org.biojavax.bio.phylo.io.nexus.TreesBlock.getTreeAsWeightedJGraphT(TreesBlock.java:562)
>     at
> edu.imperial.msc.multiglass.tree.TreeBuilder.<init>(TreeBuilder.java:50)
>     at
> edu.imperial.msc.multiglass.launcher.MultiGlassLauncher.main(MultiGlassLauncher.java:59)


Any idea why this is so ?


The data file:

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EDUCTZ-CPLX:0.0,FORMATEDEHYDROGN-CPLX:0.0,DIMESULFREDUCT-CPLX:0.0):0.07446,((TMAOREDUCTI-CPLX:0.06642,(NUOI-MONOMER+:0.05547,(TORA-MONOMER+:0.0,NUOF-MONOMER+:0.0,NUOH-MONOMER+:0.0):0.05553):0.00308):0.00631,(DMSA-MONOMER+:0.0,NUOE-MONOMER+:0.0,NUOJ-MONOMER+:0.0,NUOA-MONOMER+:0.0,FDNG-MONOMER+:0.0):0.06519):0.00154):0.00494,(NIRB-MONOMER+:0.0,NIRD-MONOMER+:0.0):0.05981):0.00246,((((G6898-MONOMER:0.0555,CYT-O-UBIOX-CPLX:0.0555):4.0E-5,(DMSC-MONOMER+:0.0499,G6848-MONOMER:0.0501):0.00546):0.00422,(CYOC-MONOMER+:0.03134,(((NUOL-MONOMER+:0.0,NUOK-MONOMER+:0.0):0.03366,(NUON-MONOMER+:0.0,NUOG-MONOMER+:0.0):0.03334):0.00181,(MONOMER0-153+:0.0,HYCC-MONOMER+:0.0,MONOMER0-141+:0.0,MONOMER0-142+:0.0,MONOMER0-143+:0.0):0.03569):0.00316):0.01559):0.00765,((NARZ-MONOMER+:0.0,NARV-MONOMER+:0.0,NARY-MONOMER+:0.0):0.03933,(NUOC-MONOMER+:0.0493,(FDOH-MONOMER+:0.04558,((FDOI-MONOMER+:0.0,G7062-MONOMER:0.0,CYTOCHROME-B561-MONOMER:0.0,G6554-MONOMER:0.0,HYAC-MONOMER+:0.0):0.04529,((FDNH-MONOMER+:0.0,DMSB-MONOMER+:0.0):0.04442,(CYOD-MONOMER+:0.04169,(EG11815-MONOMER:0.04104,((NADH-DHII-MONOMER:0.0385,CYOA-MONOMER+:0.0385):0.00206,(CYOB-MONOMER+:0.02924,(NADH-DHI-CPLX:0.01758,(NUOM-MONOMER+:0.01618,(NUOB-MONOMER+:0.01068,(CYT-D-UBIOX-CPLX:0.0,(AMPG-MONOMER+:0.12371,(YCGO-MONOMER+:0.0,(EG10921-MONOMER:0.0,((((((B2170-MONOMER:0.09906,(ARAE-MONOMER+:0.0,XYLE-MONOMER+:0.0,GALP-MONOMER+:0.0):0.10094):0.03897,G7146-MONOMER:0.11103):0.01702,(YEEO-MONOMER+:0.0,ACRD-MONOMER+:0.0,DINF-MONOMER+:0.0):0.09548):0.04436,(G6322-MONOMER:0.0,(YIDC:0.13752,(EG10266-MONOMER:0.02635,(G7686-MONOMER:0.0328,((EG12240-MONOMER:0.0,MACA:0.0):0.02955,(EG11703-MONOMER:0.02568,((EG11354-MONOMER:0.0,EG11954-MONOMER:0.0):0.01877,(G7233-MONOMER:0.01221,(((G7710-MONOMER:0.0,G6884-MONOMER:0.0,G7028-MONOMER:0.0,MDTA:0.0,EG11975-MONOMER:0.0,G6412-MONOMER:0.0,EG12224-MONOMER:0.0,EG11764-MONOMER:0.0,EG12290-MONOMER:0.0,EG11976-MONOMER:0.0,G370-MONOMER+:0.0,G6113-MONOMER:0.0):0.0385,(G7537-MONOMER:0.0,G7709-MONOMER:0.0,G7705-MONOMER:0.0,G7708-MONOMER:0.0,G7702-MONOMER:0.0,G7704-MONOMER:0.0,G7707-MONOMER:0.0,EG11798-MONOMER:0.0,G7703-MONOMER:0.0,G7706-MONOMER:0.0):0.0385):0.01248,((EG10346-MONOMER:0.02149,EG10300-MONOMER:0.03451):0.00529,(EG11977-MONOMER:0.03761,((SECA:0.03256,(SECE:0.02799,((SECD:0.0,SECF:0.0):0.028,(TATA:0.0,EG11305-MONOMER:0.0,G7808-MONOMER:0.0,SECG:0.0):0.028):1.0E-5):0.00444):9.8E-4,(EG11479-MONOMER:0.0,SECY:0.0):0.03352):0.00364):0.00221):0.01109):0.02529):0.00773):0.00658):0.00345):0.0022):0.00621):0.02887):0.03379):0.0338):0.06123,((KEFC-MONOMER+:0.0,YBAL-MONOMER+:0.0,KEFB-MONOMER+:0.0):0.04687,((((YJDE-MONOMER+:2.8E-4,(XASA-MONOMER+:0.03318,(G7024-MONOMER:0.04346,(((G7033-MONOMER:0.0,EG10113-MONOMER:0.0):0.0,(YIIP-MONOMER+:0.0,(CHAA-MONOMER+:0.0,(NHAA-MONOMER+:0.0,(YJCE-MONOMER+:0.07944,(G7572-MONOMER:0.143,G6859-MONOMER:0.0):0.09906):0.0315):0.0195):0.0325):0.021):0.0231,G7013-MONOMER:0.01559):0.0044):0.01091):0.01622):0.01259,(G6255-MONOMER:0.03498,(EG11160-MONOMER:0.0,EG11180-MONOMER:0.0):0.03602):0.0268):0.00198,NHAB-MONOMER+:0.01328):0.02343,AQPZ-MONOMER+:0.03251):0.0221):0.0385):0.01305,(EG10456-MONOMER:0.07723,(BTUE-MONOMER+:0.05425,(G7701-MONOMER:0.14596,((EG10724-MONOMER:0.11438,(NIRC-MONOMER+:0.0455,(NARU-MONOMER+:0.0,NARK-MONOMER+:0.0):0.0455):0.00712):0.02444,(PNTA-MONOMER+:0.06542,((EG11735-MONOMER:0.0455,FMNREDUCT-MONOMER:0.0455):0.01048,(G7558-MONOMER:0.04307,((YDHE-MONOMER+:0.04205,(G6320-MONOMER:0.02323,(ZNUA-MONOMER+:0.05917,((EG12334-MONOMER:0.03549,(FEPB-MONOMER+:0.0,FHUD-MONOMER+:0.0,FECB-MONOMER+:0.0):0.03551):0.00602,EG11167-MONOMER:0.04148):0.01733):0.02802):0.01982):0.01359,(G7186-MONOMER:0.0553,(G6445-MONOMER:0.0,TRKA-MONOMER+:0.0,KCH-MONOMER:0.0,EG11536-MONOMER:0.0):0.0557):0.02291):0.01468):0.01343):0.01018):0.0234):0.00508):0.02662):0.01009):0.03488):0.01556):0.04564):0.07748):0.06963):0.0207):0.01032):0.00142):0.00676):0.01061):5.9E-4):5.0E-4):0.00263):7.4E-4):2.6E-4):0.00371):0.00176):0.00853):0.00667):0.00227):0.00413):0.00575):0.00297):0.00285):0.02912):0.00302):0.01183):5.9E-4):7.5E-4):0.00127):0.02648):0.18336,EG11158-MONOMER:0.0):0.0715,EG11202-MONOMER:0.0):0.25,EG10443-MONOMER:0.99848):1.00152;


From ranjithkurungadam at gmail.com  Wed Jun 24 05:29:39 2009
From: ranjithkurungadam at gmail.com (ranjith kurungadam)
Date: Wed, 24 Jun 2009 14:59:39 +0530
Subject: [Biojava-l] : prob in reading sequence
Message-ID: <f31c43780906240229i5a2f4f32v8f5989c2a48ad69b@mail.gmail.com>

hello
//rof :  m new to this community..
going on wit my final semester M.Sc project work. m trying to do some
nucleotide sequence manipulation using biojava.

//rof : while trying to read different bio formats i found that the method
SeqIOTools.readEmbl( ) method instantiates the SequenceIterator object with
some unknown values wen a genbank format is read, but its ok wen a fasta is
read as stream.hasnext( ) gives Exception.
i got confused as this is not the case wit other methods readFastaDNA( ) and
readGenbank( )..

//Expecting ur support

From holland at eaglegenomics.com  Wed Jun 24 05:36:34 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 24 Jun 2009 10:36:34 +0100
Subject: [Biojava-l] : prob in reading sequence
In-Reply-To: <f31c43780906240229i5a2f4f32v8f5989c2a48ad69b@mail.gmail.com>
References: <f31c43780906240229i5a2f4f32v8f5989c2a48ad69b@mail.gmail.com>
Message-ID: <1245836195.4184.18.camel@buzzybee>

readEmbl() is for reading EMBL format files. It's not suprising it
causes problems if you use it to try to read Genbank or FASTA!

Also, SeqIOTools is deprecated and not really supported any more. You
should take a look at RichSequence.IOTools instead:

http://www.biojava.org/docs/api15b/org/biojavax/bio/seq/RichSequence.IOTools.html

cheers,
Richard

On Wed, 2009-06-24 at 14:59 +0530, ranjith kurungadam wrote:
> hello
> //rof :  m new to this community..
> going on wit my final semester M.Sc project work. m trying to do some
> nucleotide sequence manipulation using biojava.
> 
> //rof : while trying to read different bio formats i found that the method
> SeqIOTools.readEmbl( ) method instantiates the SequenceIterator object with
> some unknown values wen a genbank format is read, but its ok wen a fasta is
> read as stream.hasnext( ) gives Exception.
> i got confused as this is not the case wit other methods readFastaDNA( ) and
> readGenbank( )..
> 
> //Expecting ur support
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From andreas at sdsc.edu  Thu Jun 25 01:37:25 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 24 Jun 2009 22:37:25 -0700
Subject: [Biojava-l] BOSC presentation
Message-ID: <59a41c430906242237o45f0c6c6o2de4f3f0ad7f28a1@mail.gmail.com>

Hi,

Here the slides I prepared for the BioJava talk at BOSC on Sunday.

http://biojava.org/wiki/BOSC2009_Presentation

Andreas

From noreply at netlogmail.com  Thu Jun 25 14:47:30 2009
From: noreply at netlogmail.com (Saulo)
Date: Thu, 25 Jun 2009 14:47:30 -0400
Subject: [Biojava-l] Visit my Netlog profile
Message-ID: <200906251847.n5PIlU26006722@portal.open-bio.org>

Hey,

I have created a Netlog profile with my pictures, videos, blogs and events and I want to add you as a friend so you can see it. You first need to register on Netlog! When you log in, you can create your own profile.

Take a look:
http://en.netlog.com/go/mailurl/type=invite_1&mailid=342282513&id=1&url=-L2dvL3JlZ2lzdGVyL2lkPTExMjQ2MTU3OTMmaT10OTE_

Greetings,
Saulo

----------------------------------------------------------------
Don't want to receive invitations from your friends anymore?
http://en.netlog.com/go/mailurl/type=invite_1&mailid=342282513&id=2&url=-L2dvL25vbWFpbHMvaW52aXRlL2VtYWlsPS1ZbWx2YW1GMllTMXNRR3hwYzNSekxtOXdaVzR0WW1sdkxtOXlad19fJmNvZGU9MDE1MzI3MDYmaWQ9MTEyNDYxNTc5MyZpPXQ5Mg__

From jp at javaclass.co.uk  Mon Jun 22 11:05:31 2009
From: jp at javaclass.co.uk (JP)
Date: Mon, 22 Jun 2009 15:05:31 -0000
Subject: [Biojava-l] Reading a newick format tree file generates an
	ArrayIndexOutOfBoundsException (TreeBlock, getTreeAsWeightedJGraphT)
Message-ID: <4adc29060906220805t16e3f7c3k84f1f306c3861c39@mail.gmail.com>

I have tried to use the getTreeAsWeightedJGraphT functionality in TreesBlock
as highlighted in the wikipedia page:

My code for completeness sake (a direct and lazy copy and paste)

String newickFileContents = FileUtils.readTextFile(treeFile, false);  //
> reads the text file without newlines
> WeightedGraph<String, DefaultWeightedEdge> jg = new
> SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
> TreesBlock sample_tree = new TreesBlock();
> TreesBlock.NewickTreeString s = new TreesBlock.NewickTreeString();
> s.setTreeString(newickFileContents);
> sample_tree.addTree("test", s);
> jg = sample_tree.getTreeAsWeightedJGraphT("test");
> System.out.println(newickFileContents);
> System.out.println(jg.toString());
>

The data file is attached (newwick format), and this is the returned error
message...

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 79169
>     at
> org.biojavax.bio.phylo.io.nexus.TreesBlock.getTreeAsWeightedJGraphT(TreesBlock.java:562)
>     at
> edu.imperial.msc.multiglass.tree.TreeBuilder.<init>(TreeBuilder.java:50)
>     at
> edu.imperial.msc.multiglass.launcher.MultiGlassLauncher.main(MultiGlassLauncher.java:59)


Any idea why this is so ?
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From aumanga at biggjapan.com  Fri Jun 12 05:53:36 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 12 Jun 2009 14:53:36 +0900
Subject: [Biojava-l] Drawing chromatogram with fixed width for all Callboxes
 (With of CallBoxBound )
Message-ID: <4A31ED60.8090600@biggjapan.com>

Hi all,

I want to draw the chromatogram of AB1 file with fixed width for all 
'CallBoxes'.I want to do this because I am going to read .ace file and 
draw the Chromatograms of all AB1 with correct alignment with each 
other. (Just like in ChromasPro).
Is there any option to do this? Or Do I have to modify the code ?

Best Regrags,
Umanga


From aumanga at biggjapan.com  Fri Jun 12 08:20:36 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 12 Jun 2009 17:20:36 +0900
Subject: [Biojava-l] Cannot update or checkout BioJava SVN  source
Message-ID: <4A320FD4.2090405@biggjapan.com>

Greetings ,

I wanted to update my copy of SVN but it gives
"svn: Can't find a temporary directory: Internal error" .
Then I tried to checkout a new copy but still it give this error.
I read somewhere this error is given because of not enough free space on 
the server.

Any tips,

Umanga


From andreas at sdsc.edu  Fri Jun 12 13:35:57 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 12 Jun 2009 06:35:57 -0700
Subject: [Biojava-l] Cannot update or checkout BioJava SVN source
In-Reply-To: <4A320FD4.2090405@biggjapan.com>
References: <4A320FD4.2090405@biggjapan.com>
Message-ID: <59a41c430906120635k2d0ef3eag46ff44061566fa1c@mail.gmail.com>

Hi Umanga,

I just checked the anonymous access with
svn list svn://code.open-bio.org/biojava

and the developer access with
svn list svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/trunk

both works for me and I assume the svn server works ok...
Andreas


On Fri, Jun 12, 2009 at 1:20 AM, Ashika Umanga
Umagiliya<aumanga at biggjapan.com> wrote:
> Greetings ,
>
> I wanted to update my copy of SVN but it gives
> "svn: Can't find a temporary directory: Internal error" .
> Then I tried to checkout a new copy but still it give this error.
> I read somewhere this error is given because of not enough free space on the
> server.
>
> Any tips,
>
> Umanga
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From koen.bruynseels at cropdesign.com  Mon Jun 15 18:08:04 2009
From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com)
Date: Mon, 15 Jun 2009 20:08:04 +0200
Subject: [Biojava-l] Koen Bruynseels is out of the office.
Message-ID: <OF6E459872.D58F7328-ONC12575D6.00639DA1-C12575D6.00639DA1@basf-c-s.be>


I will be out of the office starting  06/14/2009 and will not return until
06/23/2009.

I will respond to your message when I return.



From aumanga at biggjapan.com  Tue Jun 16 07:24:19 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 16:24:19 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
Message-ID: <4A3748A3.8050807@biggjapan.com>

Greetings all,

Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png


As shown in image (1) , I draw the basecall sequences of AB1 file,by 
parsing the ACE file generated by Phrap.That is ,for upper part I do not 
read AB1 file.Only read values from ACE file.(values under 'RD' tag in 
ACE file.)In the example, two files are 'sampleA-S-R.AB1' and 
'sampleA-S-F.AB1'.

For the bottom part- that is to draw Chromatogram, I use Biojavas 
'ChromatogramGraphic' class.

I wanted to align these two parts- that is align 'sampleA-S-R.AB1' 
basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like 
in ChromasPro).

But I noticed that basecall sequence of 'ChromatogramGraphic' is totally 
different than that of from ACE file.
Refer to image (2) ; you can see the two sequences generated by same AB1 
file is different in lenght also.

What could be the problem here? Any suggestions please

thanks in advance.
umanga


From aumanga at biggjapan.com  Tue Jun 16 07:24:19 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 16:24:19 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
Message-ID: <4A3748A3.8050807@biggjapan.com>

Greetings all,

Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png


As shown in image (1) , I draw the basecall sequences of AB1 file,by 
parsing the ACE file generated by Phrap.That is ,for upper part I do not 
read AB1 file.Only read values from ACE file.(values under 'RD' tag in 
ACE file.)In the example, two files are 'sampleA-S-R.AB1' and 
'sampleA-S-F.AB1'.

For the bottom part- that is to draw Chromatogram, I use Biojavas 
'ChromatogramGraphic' class.

I wanted to align these two parts- that is align 'sampleA-S-R.AB1' 
basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like 
in ChromasPro).

But I noticed that basecall sequence of 'ChromatogramGraphic' is totally 
different than that of from ACE file.
Refer to image (2) ; you can see the two sequences generated by same AB1 
file is different in lenght also.

What could be the problem here? Any suggestions please

thanks in advance.
umanga


From aumanga at biggjapan.com  Tue Jun 16 09:06:01 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 18:06:01 +0900
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
Message-ID: <4A376079.8020902@biggjapan.com>

Greetings all,

When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls 
read is lower than the basecalls in a Phrap ACE file.

For example I parse the AB1 file using biojava ABIChromatogram , it gave 
the following basecalls:

ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
ttacttacacatatgttcttccctaataacagagttttacgatccgaag
accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
tatccggtattagctccggtttcccgaagttatcccagtcttataggta
ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
ttcatcctgagccaggatcaaactctccaa

Total number is 520 ,


But in Phrap ACE file the corrosponding entry is :
(should get compliment sequence to compare)

RD 2008-10-24_A02_S_R.ab1 1404 0 0
gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
ttaa

My question is why biojava parser only give 520 bases? Is there a way to 
parse all 1404 bases as seen in Phrap ACE file?

Thanks in advance,
umanga



From aumanga at biggjapan.com  Tue Jun 16 09:06:01 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 18:06:01 +0900
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
Message-ID: <4A376079.8020902@biggjapan.com>

Greetings all,

When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls 
read is lower than the basecalls in a Phrap ACE file.

For example I parse the AB1 file using biojava ABIChromatogram , it gave 
the following basecalls:

ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
ttacttacacatatgttcttccctaataacagagttttacgatccgaag
accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
tatccggtattagctccggtttcccgaagttatcccagtcttataggta
ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
ttcatcctgagccaggatcaaactctccaa

Total number is 520 ,


But in Phrap ACE file the corrosponding entry is :
(should get compliment sequence to compare)

RD 2008-10-24_A02_S_R.ab1 1404 0 0
gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
ttaa

My question is why biojava parser only give 520 bases? Is there a way to 
parse all 1404 bases as seen in Phrap ACE file?

Thanks in advance,
umanga



From ayates at ebi.ac.uk  Tue Jun 16 09:10:54 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 16 Jun 2009 10:10:54 +0100
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A3748A3.8050807@biggjapan.com>
References: <4A3748A3.8050807@biggjapan.com>
Message-ID: <4A37619E.4090807@ebi.ac.uk>

Hi Ashika,

AB1 files will contain a different basecall to one generated by phrap
since (as far as my memory serves me) ABI's platform has a basecaller
built in. This is the one which is coded into the AB1 file & therefore
chromatogram graphic will pick up on that one. However it's very odd
that the Phrap calls are so distant from the trace itself.

I would have hoped that the ACE file would have contained some kind of
called base -> peak position in the chromatogram. There is always the
option of getting phred to output a SCF file which should contain this
information & see what it thinks its doing. SCFs can be parsed by
BioJava so you should be able to push it straight into your program &
let it handle it.

Andy

Ashika Umanga Umagiliya wrote:
> Greetings all,
> 
> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
> 
> 
> As shown in image (1) , I draw the basecall sequences of AB1 file,by
> parsing the ACE file generated by Phrap.That is ,for upper part I do not
> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
> 'sampleA-S-F.AB1'.
> 
> For the bottom part- that is to draw Chromatogram, I use Biojavas
> 'ChromatogramGraphic' class.
> 
> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like
> in ChromasPro).
> 
> But I noticed that basecall sequence of 'ChromatogramGraphic' is totally
> different than that of from ACE file.
> Refer to image (2) ; you can see the two sequences generated by same AB1
> file is different in lenght also.
> 
> What could be the problem here? Any suggestions please
> 
> thanks in advance.
> umanga
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From ayates at ebi.ac.uk  Tue Jun 16 09:21:12 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 16 Jun 2009 10:21:12 +0100
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
In-Reply-To: <4A376079.8020902@biggjapan.com>
References: <4A376079.8020902@biggjapan.com>
Message-ID: <4A376408.1090602@ebi.ac.uk>

Hi,

Are you sure that the AB1 file actually contains more than 520bp? Have a
check there first (using something like trev should display the AB1
processed data) and then we can see if its a problem in the data or the
program.

Andy

Ashika Umanga Umagiliya wrote:
> Greetings all,
> 
> When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls
> read is lower than the basecalls in a Phrap ACE file.
> 
> For example I parse the AB1 file using biojava ABIChromatogram , it gave
> the following basecalls:
> 
> ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
> ttacttacacatatgttcttccctaataacagagttttacgatccgaag
> accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
> gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
> tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
> gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
> agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
> tatccggtattagctccggtttcccgaagttatcccagtcttataggta
> ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
> gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
> ttcatcctgagccaggatcaaactctccaa
> 
> Total number is 520 ,
> 
> 
> But in Phrap ACE file the corrosponding entry is :
> (should get compliment sequence to compare)
> 
> RD 2008-10-24_A02_S_R.ab1 1404 0 0
> gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
> aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
> cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
> gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
> aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
> agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
> atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
> caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
> acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
> gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
> ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
> tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
> ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
> atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
> tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
> ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
> tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
> gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
> CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
> AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
> CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
> TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
> TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
> AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
> CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
> GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
> TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
> AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
> ttaa
> 
> My question is why biojava parser only give 520 bases? Is there a way to
> parse all 1404 bases as seen in Phrap ACE file?
> 
> Thanks in advance,
> umanga
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From aumanga at biggjapan.com  Tue Jun 16 09:39:27 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 18:39:27 +0900
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
In-Reply-To: <4A376408.1090602@ebi.ac.uk>
References: <4A376079.8020902@biggjapan.com> <4A376408.1090602@ebi.ac.uk>
Message-ID: <4A37684F.5080206@biggjapan.com>

HI Andy,

Thank you for the tip. I checked the AB1 with 'trev' and it gave the 
number of bases as 520.
But I wonder in Phrap ACE file how it show 1404 bases.

Best Regards,
Umanga

Andy Yates wrote:
> Hi,
>
> Are you sure that the AB1 file actually contains more than 520bp? Have a
> check there first (using something like trev should display the AB1
> processed data) and then we can see if its a problem in the data or the
> program.
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Greetings all,
>>
>> When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls
>> read is lower than the basecalls in a Phrap ACE file.
>>
>> For example I parse the AB1 file using biojava ABIChromatogram , it gave
>> the following basecalls:
>>
>> ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
>> ttacttacacatatgttcttccctaataacagagttttacgatccgaag
>> accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
>> gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
>> tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
>> gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
>> agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
>> tatccggtattagctccggtttcccgaagttatcccagtcttataggta
>> ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
>> gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
>> ttcatcctgagccaggatcaaactctccaa
>>
>> Total number is 520 ,
>>
>>
>> But in Phrap ACE file the corrosponding entry is :
>> (should get compliment sequence to compare)
>>
>> RD 2008-10-24_A02_S_R.ab1 1404 0 0
>> gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
>> aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
>> cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
>> gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
>> aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
>> agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
>> atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
>> caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
>> acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
>> gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
>> ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
>> tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
>> ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
>> atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
>> tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
>> ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
>> tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
>> gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
>> CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
>> AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
>> CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
>> TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
>> TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
>> AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
>> CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
>> GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
>> TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
>> AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
>> ttaa
>>
>> My question is why biojava parser only give 520 bases? Is there a way to
>> parse all 1404 bases as seen in Phrap ACE file?
>>
>> Thanks in advance,
>> umanga
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>     



From aumanga at biggjapan.com  Tue Jun 16 09:41:54 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Tue, 16 Jun 2009 18:41:54 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A37619E.4090807@ebi.ac.uk>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
Message-ID: <4A3768E2.7090003@biggjapan.com>

Hi Andy,

Thank you for the reply.
Earlier problem was I had not applied the compliment in the ChromatoGraph.
Now I could inspect the alignment with the Phrap calls

Please refer :  http://i43.tinypic.com/e5iu12.png

I have drawn orange underlines from where the two sequences matches.
But I had to hardcode x1 and x2 offset values to make the graphs align 
with the Phrap basecalls.
 So as for my question 
http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if 
somehow get all (or fill) all the callbases same as in ACE , I can align 
easily.


Best Regards,
Umanga





Andy Yates wrote:
> Hi Ashika,
>
> AB1 files will contain a different basecall to one generated by phrap
> since (as far as my memory serves me) ABI's platform has a basecaller
> built in. This is the one which is coded into the AB1 file & therefore
> chromatogram graphic will pick up on that one. However it's very odd
> that the Phrap calls are so distant from the trace itself.
>
> I would have hoped that the ACE file would have contained some kind of
> called base -> peak position in the chromatogram. There is always the
> option of getting phred to output a SCF file which should contain this
> information & see what it thinks its doing. SCFs can be parsed by
> BioJava so you should be able to push it straight into your program &
> let it handle it.
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Greetings all,
>>
>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
>>
>>
>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>> parsing the ACE file generated by Phrap.That is ,for upper part I do not
>> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>> 'sampleA-S-F.AB1'.
>>
>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>> 'ChromatogramGraphic' class.
>>
>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like
>> in ChromasPro).
>>
>> But I noticed that basecall sequence of 'ChromatogramGraphic' is totally
>> different than that of from ACE file.
>> Refer to image (2) ; you can see the two sequences generated by same AB1
>> file is different in lenght also.
>>
>> What could be the problem here? Any suggestions please
>>
>> thanks in advance.
>> umanga
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>     



From ayates at ebi.ac.uk  Tue Jun 16 09:56:10 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 16 Jun 2009 10:56:10 +0100
Subject: [Biojava-l] Question about AB1 parser (ABIFChromatogram)
In-Reply-To: <4A37684F.5080206@biggjapan.com>
References: <4A376079.8020902@biggjapan.com> <4A376408.1090602@ebi.ac.uk>
	<4A37684F.5080206@biggjapan.com>
Message-ID: <4A376C3A.9020500@ebi.ac.uk>

Well the most likely explanation is that since Phred is doing its own
basecalling it will be using the unprocessed data which is in the AB1
file. This is always longer than the processed data you see in the AB1
file normally and has not been massaged WRT trace trimming, noise
reduction and base lining. So my guess WRT such a huge number of bases
is that phred has gone into the "soup" regions of a trace from the
beginning and the end.

Andy

Ashika Umanga Umagiliya wrote:
> HI Andy,
> 
> Thank you for the tip. I checked the AB1 with 'trev' and it gave the
> number of bases as 520.
> But I wonder in Phrap ACE file how it show 1404 bases.
> 
> Best Regards,
> Umanga
> 
> Andy Yates wrote:
>> Hi,
>>
>> Are you sure that the AB1 file actually contains more than 520bp? Have a
>> check there first (using something like trev should display the AB1
>> processed data) and then we can see if its a problem in the data or the
>> program.
>>
>> Andy
>>
>> Ashika Umanga Umagiliya wrote:
>>  
>>> Greetings all,
>>>
>>> When I parse a AB1 file using 'ABIFChromatogram' the number of basecalls
>>> read is lower than the basecalls in a Phrap ACE file.
>>>
>>> For example I parse the AB1 file using biojava ABIChromatogram , it gave
>>> the following basecalls:
>>>
>>> ttaagcaggttaagcgtcctccctgttggtaccgtcaagagtgcacaaa
>>> ttacttacacatatgttcttccctaataacagagttttacgatccgaag
>>> accttcatcactcacgcggcgttgctccgtcaggctttcgcccattgcg
>>> gaagattccctactgctgcctcccgtaggagtctggaccgtgtctcagt
>>> tccagtgtggccgatcaccctctcaggtcggctatgcatcgttgccttg
>>> gtaagccgttaccttaccaactagctaatgcagcgcggatccatctata
>>> agtgacagcaagaccgtctttcacttttgaaccatgcggttcaaaatat
>>> tatccggtattagctccggtttcccgaagttatcccagtcttataggta
>>> ggttatccacgtgttactcacccgtccgccgctaacatcagagaagcaa
>>> gcttctcgtccgttcgctcgatttgcatgtattaggcacgccgccagcg
>>> ttcatcctgagccaggatcaaactctccaa
>>>
>>> Total number is 520 ,
>>>
>>>
>>> But in Phrap ACE file the corrosponding entry is :
>>> (should get compliment sequence to compare)
>>>
>>> RD 2008-10-24_A02_S_R.ab1 1404 0 0
>>> gaatggttgtagagagattggtatgttgtagtggtgtgttgtgtgtgaat
>>> aggtagtaatggtaggagatgttcatgttttcgttgtgtaagaagattat
>>> cgagagagaagatatgttggtattaaatgggaggggataagaacaaaaga
>>> gaacaaatatgtgtgatatatagatttggggaaagggaggtggtagatat
>>> aattgggttgggtgggtaggactggtgattggattggtgtgatggggagg
>>> agttggtagtaatgtgttgtggttttttgattttgcgtttagttagacat
>>> atatgtaacgagaggattgattgagatagtaaatatgagacgggattagc
>>> caaggatcagaagaggaggggggaaaggtggggagaggaagggaggattg
>>> acgataggagaggtgtctagtgtgggtgagaggtgggtgaatatttggtg
>>> gagatgtgtgggtatttagatgttgtgagattggattgtggacgtagggt
>>> ggatgtggtttgggagttggagaatgggtgtgtagttgtggatatagtta
>>> tcaggttgtgagaagtggagaagaggggagagaagagagggggggaaaga
>>> ggaaagaagagagaaatagaaggagattatgggagggtggaagggacgta
>>> atgagtgttgatttatgatgtatagtttagatgggtggtatggatatttt
>>> tgggcgagggaaggagtgaggggatagatggacagagggttntggagcta
>>> ttgttttgtttcttgatgtgggtgttggggtgttgattttgtagttctac
>>> tttagtttgggtgtagaacagggggattcaaggtcagagtgagtgtgggg
>>> gtaaggaagttgatagttgtcagttccttntgaagtTGGAGAGTTTGATC
>>> CTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCG
>>> AACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGGGTGAGTAA
>>> CACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGC
>>> TAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTC
>>> TTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGT
>>> AACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGC
>>> CACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGG
>>> GAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGA
>>> TGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGT
>>> AAGTAACTGTGCACATCTTGACGGTACCtaacatggaggcctgttcctcg
>>> ttaa
>>>
>>> My question is why biojava parser only give 520 bases? Is there a way to
>>> parse all 1404 bases as seen in Phrap ACE file?
>>>
>>> Thanks in advance,
>>> umanga
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>     


From abdul.qaddos at gmail.com  Wed Jun 17 00:48:55 2009
From: abdul.qaddos at gmail.com (Abdul Qaddus)
Date: Wed, 17 Jun 2009 05:48:55 +0500
Subject: [Biojava-l] Fwd: Need help for resolving the args[0] issues.
In-Reply-To: <a6b292990906160005r6a1ddcd4k6deb2dc2ab5ebcd9@mail.gmail.com>
References: <a6b292990906160005r6a1ddcd4k6deb2dc2ab5ebcd9@mail.gmail.com>
Message-ID: <a6b292990906161748u136c0ef2hec608facd638a845@mail.gmail.com>

Hello Support,
I am a new developer of biojava, I have a good knowledge about java and bio,
but this is new tool for me, I have some problem while working in this
tools, below I have write down the code for reading the Gen Bank file and
then convert into "DNA", "RNA" or "Protein". I have already add the biojava
library into my source code. When I have read this code I have come to know
from your arguments portion for the execution of this code, I have need
three argument, one for the filename, second for the file type and third is
the alphabet.
Now the problem is that how I will pass these three parameter values into
source code for args[0], args[1] and args[2]. When I have passed these
values by using the string pattern then this code generte a errors, "illegel
statement". Please help me out how I can fixed this problem, I will be very
thankful to you if you will reply me soon


package biojava;
import java.io.*;

import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;

public class ReadFasta2 {

  /**
   * This program will read any file supported by SeqIOTools it takes three
   * arguments, the first is the file name the second is the name of
   * a file format supported by SeqIOTools. eg fasta, genbank etc.
   * The third argument is the alphabet (eg dna, rna, protein).
   *
   * Both the format and alphabet names are case insensitive.
   *
   */
  public static void main(String[] args) {
    try {
      //prepare a BufferedReader for file io
      BufferedReader br = new BufferedReader(new FileReader(args[0]));

      String format = args[1];
      String alphabet = args[2];

      /*
       * get a Sequence Iterator over all the sequences in the file.
       * SeqIOTools.fileToBiojava() returns an Object. If the file read
       * is an alignment format like MSF and Alignment object is returned
       * otherwise a SequenceIterator is returned.
       */
      SequenceIterator iter =
          (SequenceIterator)SeqIOTools.fileToBiojava(format,alphabet, br);
    }
    catch (FileNotFoundException ex) {
      //can't find file specified by args[0]
      ex.printStackTrace();
    }catch (BioException ex) {
      //error parsing requested format
      ex.printStackTrace();
    }
  }
}
-- 
Abdul Qaddus
www.futurelinkers.com
Cell No:- +92-3336540863



-- 
Abdul Qaddus
www.futurelinkers.com
Cell No:- +92-3336540863


From aumanga at biggjapan.com  Wed Jun 17 02:49:46 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Wed, 17 Jun 2009 11:49:46 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A377471.9090509@ebi.ac.uk>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
	<4A3768E2.7090003@biggjapan.com> <4A377471.9090509@ebi.ac.uk>
Message-ID: <4A3859CA.5020803@biggjapan.com>

Hi Andy ,

Thanks for the help.I was doing all wrong !
Instead of using AB1 raw data , I used SCF  generated by Phrep and used 
the offset values from ACE file.
Now all are aligned , here a snapshot : http://i39.tinypic.com/xbymf.png

But still one problem .As can be seen in the picture, at the end of the 
graph, some part of the trace-plot is missing for last bases.
Any idea whats going on here ?

Thanks in advance,
Umanga

Andy Yates wrote:
> Hi Umanga,
>
> In terms of getting the offset I'm not sure. That information should be
> provided via the ACE file or from some other output from phrap; its not
> the responsibility of the AB1 file to contain this information. The
> phred output (which phrap uses under the scenes I think) which does
> contain this information is the SCF output but in this situation you are
> not rendering the processed output from the ABI sequencer. You are
> actually displaying:
>
> ABI Raw output -> phred basecalled/processed
>
> So if there is a reason why you want to show the ABI processed data then
> I'm not sure how to marry it to the phrap output. Otherwise just use the
> traces phrap outputs and see what happens.
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Hi Andy,
>>
>> Thank you for the reply.
>> Earlier problem was I had not applied the compliment in the ChromatoGraph.
>> Now I could inspect the alignment with the Phrap calls
>>
>> Please refer :  http://i43.tinypic.com/e5iu12.png
>>
>> I have drawn orange underlines from where the two sequences matches.
>> But I had to hardcode x1 and x2 offset values to make the graphs align
>> with the Phrap basecalls.
>> So as for my question
>> http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if
>> somehow get all (or fill) all the callbases same as in ACE , I can align
>> easily.
>>
>>
>> Best Regards,
>> Umanga
>>
>>
>>
>>
>>
>> Andy Yates wrote:
>>     
>>> Hi Ashika,
>>>
>>> AB1 files will contain a different basecall to one generated by phrap
>>> since (as far as my memory serves me) ABI's platform has a basecaller
>>> built in. This is the one which is coded into the AB1 file & therefore
>>> chromatogram graphic will pick up on that one. However it's very odd
>>> that the Phrap calls are so distant from the trace itself.
>>>
>>> I would have hoped that the ACE file would have contained some kind of
>>> called base -> peak position in the chromatogram. There is always the
>>> option of getting phred to output a SCF file which should contain this
>>> information & see what it thinks its doing. SCFs can be parsed by
>>> BioJava so you should be able to push it straight into your program &
>>> let it handle it.
>>>
>>> Andy
>>>
>>> Ashika Umanga Umagiliya wrote:
>>>  
>>>       
>>>> Greetings all,
>>>>
>>>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>>>> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
>>>>
>>>>
>>>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>>>> parsing the ACE file generated by Phrap.That is ,for upper part I do not
>>>> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
>>>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>>>> 'sampleA-S-F.AB1'.
>>>>
>>>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>>>> 'ChromatogramGraphic' class.
>>>>
>>>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>>>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like
>>>> in ChromasPro).
>>>>
>>>> But I noticed that basecall sequence of 'ChromatogramGraphic' is totally
>>>> different than that of from ACE file.
>>>> Refer to image (2) ; you can see the two sequences generated by same AB1
>>>> file is different in lenght also.
>>>>
>>>> What could be the problem here? Any suggestions please
>>>>
>>>> thanks in advance.
>>>> umanga
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>     
>>>>         



From ayates at ebi.ac.uk  Wed Jun 17 08:16:58 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 17 Jun 2009 09:16:58 +0100
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A3859CA.5020803@biggjapan.com>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
	<4A3768E2.7090003@biggjapan.com> <4A377471.9090509@ebi.ac.uk>
	<4A3859CA.5020803@biggjapan.com>
Message-ID: <4A38A67A.1000509@ebi.ac.uk>

Hi Umanga,

Glad you've got it rendering though now :)

My best guess is that the trace have been truncated by the generating
program or the file writing is incomplete which I doubt due to the way
SCF files are constructed. So my money is on Phrap/Phred doing a bit of
quality control with the end of the trace. Why it hasn't truncated the
base calls as well I do not know and is probably a question better
suited to the people who write/maintain Phred & Phrap.

Sorry I can't be of that much more help :(

Andy

Ashika Umanga Umagiliya wrote:
> Hi Andy ,
> 
> Thanks for the help.I was doing all wrong !
> Instead of using AB1 raw data , I used SCF  generated by Phrep and used
> the offset values from ACE file.
> Now all are aligned , here a snapshot : http://i39.tinypic.com/xbymf.png
> 
> But still one problem .As can be seen in the picture, at the end of the
> graph, some part of the trace-plot is missing for last bases.
> Any idea whats going on here ?
> 
> Thanks in advance,
> Umanga
> 
> Andy Yates wrote:
>> Hi Umanga,
>>
>> In terms of getting the offset I'm not sure. That information should be
>> provided via the ACE file or from some other output from phrap; its not
>> the responsibility of the AB1 file to contain this information. The
>> phred output (which phrap uses under the scenes I think) which does
>> contain this information is the SCF output but in this situation you are
>> not rendering the processed output from the ABI sequencer. You are
>> actually displaying:
>>
>> ABI Raw output -> phred basecalled/processed
>>
>> So if there is a reason why you want to show the ABI processed data then
>> I'm not sure how to marry it to the phrap output. Otherwise just use the
>> traces phrap outputs and see what happens.
>>
>> Andy
>>
>> Ashika Umanga Umagiliya wrote:
>>  
>>> Hi Andy,
>>>
>>> Thank you for the reply.
>>> Earlier problem was I had not applied the compliment in the
>>> ChromatoGraph.
>>> Now I could inspect the alignment with the Phrap calls
>>>
>>> Please refer :  http://i43.tinypic.com/e5iu12.png
>>>
>>> I have drawn orange underlines from where the two sequences matches.
>>> But I had to hardcode x1 and x2 offset values to make the graphs align
>>> with the Phrap basecalls.
>>> So as for my question
>>> http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if
>>> somehow get all (or fill) all the callbases same as in ACE , I can align
>>> easily.
>>>
>>>
>>> Best Regards,
>>> Umanga
>>>
>>>
>>>
>>>
>>>
>>> Andy Yates wrote:
>>>    
>>>> Hi Ashika,
>>>>
>>>> AB1 files will contain a different basecall to one generated by phrap
>>>> since (as far as my memory serves me) ABI's platform has a basecaller
>>>> built in. This is the one which is coded into the AB1 file & therefore
>>>> chromatogram graphic will pick up on that one. However it's very odd
>>>> that the Phrap calls are so distant from the trace itself.
>>>>
>>>> I would have hoped that the ACE file would have contained some kind of
>>>> called base -> peak position in the chromatogram. There is always the
>>>> option of getting phred to output a SCF file which should contain this
>>>> information & see what it thinks its doing. SCFs can be parsed by
>>>> BioJava so you should be able to push it straight into your program &
>>>> let it handle it.
>>>>
>>>> Andy
>>>>
>>>> Ashika Umanga Umagiliya wrote:
>>>>  
>>>>      
>>>>> Greetings all,
>>>>>
>>>>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>>>>> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
>>>>>
>>>>>
>>>>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>>>>> parsing the ACE file generated by Phrap.That is ,for upper part I
>>>>> do not
>>>>> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
>>>>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>>>>> 'sampleA-S-F.AB1'.
>>>>>
>>>>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>>>>> 'ChromatogramGraphic' class.
>>>>>
>>>>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>>>>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so
>>>>> on...(like
>>>>> in ChromasPro).
>>>>>
>>>>> But I noticed that basecall sequence of 'ChromatogramGraphic' is
>>>>> totally
>>>>> different than that of from ACE file.
>>>>> Refer to image (2) ; you can see the two sequences generated by
>>>>> same AB1
>>>>> file is different in lenght also.
>>>>>
>>>>> What could be the problem here? Any suggestions please
>>>>>
>>>>> thanks in advance.
>>>>> umanga
>>>>> _______________________________________________
>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>             


From aumanga at biggjapan.com  Wed Jun 17 09:00:50 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Wed, 17 Jun 2009 18:00:50 +0900
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A38A67A.1000509@ebi.ac.uk>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
	<4A3768E2.7090003@biggjapan.com> <4A377471.9090509@ebi.ac.uk>
	<4A3859CA.5020803@biggjapan.com> <4A38A67A.1000509@ebi.ac.uk>
Message-ID: <4A38B0C2.4030806@biggjapan.com>

Hi again Andy ,

Thank you for all your help , it was a matter of setting an option in  
ChromatogramGraphic


ChromatogramGraphic chromaGfx;
.
.
chromaGfx.setOption(Option.SUBPATH_LENGTH, new Integer(
                    Integer.MAX_VALUE));


Now I can see the entire trace-plot ..  Everything is just fine :)


Best Regards,
Umanga

Andy Yates wrote:
> Hi Umanga,
>
> Glad you've got it rendering though now :)
>
> My best guess is that the trace have been truncated by the generating
> program or the file writing is incomplete which I doubt due to the way
> SCF files are constructed. So my money is on Phrap/Phred doing a bit of
> quality control with the end of the trace. Why it hasn't truncated the
> base calls as well I do not know and is probably a question better
> suited to the people who write/maintain Phred & Phrap.
>
> Sorry I can't be of that much more help :(
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Hi Andy ,
>>
>> Thanks for the help.I was doing all wrong !
>> Instead of using AB1 raw data , I used SCF  generated by Phrep and used
>> the offset values from ACE file.
>> Now all are aligned , here a snapshot : http://i39.tinypic.com/xbymf.png
>>
>> But still one problem .As can be seen in the picture, at the end of the
>> graph, some part of the trace-plot is missing for last bases.
>> Any idea whats going on here ?
>>
>> Thanks in advance,
>> Umanga
>>
>> Andy Yates wrote:
>>     
>>> Hi Umanga,
>>>
>>> In terms of getting the offset I'm not sure. That information should be
>>> provided via the ACE file or from some other output from phrap; its not
>>> the responsibility of the AB1 file to contain this information. The
>>> phred output (which phrap uses under the scenes I think) which does
>>> contain this information is the SCF output but in this situation you are
>>> not rendering the processed output from the ABI sequencer. You are
>>> actually displaying:
>>>
>>> ABI Raw output -> phred basecalled/processed
>>>
>>> So if there is a reason why you want to show the ABI processed data then
>>> I'm not sure how to marry it to the phrap output. Otherwise just use the
>>> traces phrap outputs and see what happens.
>>>
>>> Andy
>>>
>>> Ashika Umanga Umagiliya wrote:
>>>  
>>>       
>>>> Hi Andy,
>>>>
>>>> Thank you for the reply.
>>>> Earlier problem was I had not applied the compliment in the
>>>> ChromatoGraph.
>>>> Now I could inspect the alignment with the Phrap calls
>>>>
>>>> Please refer :  http://i43.tinypic.com/e5iu12.png
>>>>
>>>> I have drawn orange underlines from where the two sequences matches.
>>>> But I had to hardcode x1 and x2 offset values to make the graphs align
>>>> with the Phrap basecalls.
>>>> So as for my question
>>>> http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if
>>>> somehow get all (or fill) all the callbases same as in ACE , I can align
>>>> easily.
>>>>
>>>>
>>>> Best Regards,
>>>> Umanga
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Andy Yates wrote:
>>>>    
>>>>         
>>>>> Hi Ashika,
>>>>>
>>>>> AB1 files will contain a different basecall to one generated by phrap
>>>>> since (as far as my memory serves me) ABI's platform has a basecaller
>>>>> built in. This is the one which is coded into the AB1 file & therefore
>>>>> chromatogram graphic will pick up on that one. However it's very odd
>>>>> that the Phrap calls are so distant from the trace itself.
>>>>>
>>>>> I would have hoped that the ACE file would have contained some kind of
>>>>> called base -> peak position in the chromatogram. There is always the
>>>>> option of getting phred to output a SCF file which should contain this
>>>>> information & see what it thinks its doing. SCFs can be parsed by
>>>>> BioJava so you should be able to push it straight into your program &
>>>>> let it handle it.
>>>>>
>>>>> Andy
>>>>>
>>>>> Ashika Umanga Umagiliya wrote:
>>>>>  
>>>>>      
>>>>>           
>>>>>> Greetings all,
>>>>>>
>>>>>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>>>>>> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
>>>>>>
>>>>>>
>>>>>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>>>>>> parsing the ACE file generated by Phrap.That is ,for upper part I
>>>>>> do not
>>>>>> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
>>>>>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>>>>>> 'sampleA-S-F.AB1'.
>>>>>>
>>>>>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>>>>>> 'ChromatogramGraphic' class.
>>>>>>
>>>>>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>>>>>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so
>>>>>> on...(like
>>>>>> in ChromasPro).
>>>>>>
>>>>>> But I noticed that basecall sequence of 'ChromatogramGraphic' is
>>>>>> totally
>>>>>> different than that of from ACE file.
>>>>>> Refer to image (2) ; you can see the two sequences generated by
>>>>>> same AB1
>>>>>> file is different in lenght also.
>>>>>>
>>>>>> What could be the problem here? Any suggestions please
>>>>>>
>>>>>> thanks in advance.
>>>>>> umanga
>>>>>> _______________________________________________
>>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>>             
>>>>>>             



From andreas at sdsc.edu  Wed Jun 17 18:11:17 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 17 Jun 2009 11:11:17 -0700
Subject: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?
In-Reply-To: <4A38B0C2.4030806@biggjapan.com>
References: <4A3748A3.8050807@biggjapan.com> <4A37619E.4090807@ebi.ac.uk>
	<4A3768E2.7090003@biggjapan.com> <4A377471.9090509@ebi.ac.uk>
	<4A3859CA.5020803@biggjapan.com> <4A38A67A.1000509@ebi.ac.uk>
	<4A38B0C2.4030806@biggjapan.com>
Message-ID: <59a41c430906171111y53f8080u956e909a185e9a48@mail.gmail.com>

Great that it works now!

Do you want to post some more documentation on the wiki page? We seem
to get queries regarding this every now and then so having more docu
might be helpful...

Cheers,
Andreas


On Wed, Jun 17, 2009 at 2:00 AM, Ashika Umanga
Umagiliya<aumanga at biggjapan.com> wrote:
> Hi again Andy ,
>
> Thank you for all your help , it was a matter of setting an option in
> ?ChromatogramGraphic
>
>
> ChromatogramGraphic chromaGfx;
> .
> .
> chromaGfx.setOption(Option.SUBPATH_LENGTH, new Integer(
> ? ? ? ? ? ? ? ? ? Integer.MAX_VALUE));
>
>
> Now I can see the entire trace-plot .. ?Everything is just fine :)
>
>
> Best Regards,
> Umanga
>
> Andy Yates wrote:
>>
>> Hi Umanga,
>>
>> Glad you've got it rendering though now :)
>>
>> My best guess is that the trace have been truncated by the generating
>> program or the file writing is incomplete which I doubt due to the way
>> SCF files are constructed. So my money is on Phrap/Phred doing a bit of
>> quality control with the end of the trace. Why it hasn't truncated the
>> base calls as well I do not know and is probably a question better
>> suited to the people who write/maintain Phred & Phrap.
>>
>> Sorry I can't be of that much more help :(
>>
>> Andy
>>
>> Ashika Umanga Umagiliya wrote:
>>
>>>
>>> Hi Andy ,
>>>
>>> Thanks for the help.I was doing all wrong !
>>> Instead of using AB1 raw data , I used SCF ?generated by Phrep and used
>>> the offset values from ACE file.
>>> Now all are aligned , here a snapshot : http://i39.tinypic.com/xbymf.png
>>>
>>> But still one problem .As can be seen in the picture, at the end of the
>>> graph, some part of the trace-plot is missing for last bases.
>>> Any idea whats going on here ?
>>>
>>> Thanks in advance,
>>> Umanga
>>>
>>> Andy Yates wrote:
>>>
>>>>
>>>> Hi Umanga,
>>>>
>>>> In terms of getting the offset I'm not sure. That information should be
>>>> provided via the ACE file or from some other output from phrap; its not
>>>> the responsibility of the AB1 file to contain this information. The
>>>> phred output (which phrap uses under the scenes I think) which does
>>>> contain this information is the SCF output but in this situation you are
>>>> not rendering the processed output from the ABI sequencer. You are
>>>> actually displaying:
>>>>
>>>> ABI Raw output -> phred basecalled/processed
>>>>
>>>> So if there is a reason why you want to show the ABI processed data then
>>>> I'm not sure how to marry it to the phrap output. Otherwise just use the
>>>> traces phrap outputs and see what happens.
>>>>
>>>> Andy
>>>>
>>>> Ashika Umanga Umagiliya wrote:
>>>>
>>>>>
>>>>> Hi Andy,
>>>>>
>>>>> Thank you for the reply.
>>>>> Earlier problem was I had not applied the compliment in the
>>>>> ChromatoGraph.
>>>>> Now I could inspect the alignment with the Phrap calls
>>>>>
>>>>> Please refer : ?http://i43.tinypic.com/e5iu12.png
>>>>>
>>>>> I have drawn orange underlines from where the two sequences matches.
>>>>> But I had to hardcode x1 and x2 offset values to make the graphs align
>>>>> with the Phrap basecalls.
>>>>> So as for my question
>>>>> http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html ,
>>>>> if
>>>>> somehow get all (or fill) all the callbases same as in ACE , I can
>>>>> align
>>>>> easily.
>>>>>
>>>>>
>>>>> Best Regards,
>>>>> Umanga
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Andy Yates wrote:
>>>>>
>>>>>>
>>>>>> Hi Ashika,
>>>>>>
>>>>>> AB1 files will contain a different basecall to one generated by phrap
>>>>>> since (as far as my memory serves me) ABI's platform has a basecaller
>>>>>> built in. This is the one which is coded into the AB1 file & therefore
>>>>>> chromatogram graphic will pick up on that one. However it's very odd
>>>>>> that the Phrap calls are so distant from the trace itself.
>>>>>>
>>>>>> I would have hoped that the ACE file would have contained some kind of
>>>>>> called base -> peak position in the chromatogram. There is always the
>>>>>> option of getting phred to output a SCF file which should contain this
>>>>>> information & see what it thinks its doing. SCFs can be parsed by
>>>>>> BioJava so you should be able to push it straight into your program &
>>>>>> let it handle it.
>>>>>>
>>>>>> Andy
>>>>>>
>>>>>> Ashika Umanga Umagiliya wrote:
>>>>>>
>>>>>>>
>>>>>>> Greetings all,
>>>>>>>
>>>>>>> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
>>>>>>> image 2 (end of graph): ?http://i44.tinypic.com/2vt4iu8.png
>>>>>>>
>>>>>>>
>>>>>>> As shown in image (1) , I draw the basecall sequences of AB1 file,by
>>>>>>> parsing the ACE file generated by Phrap.That is ,for upper part I
>>>>>>> do not
>>>>>>> read AB1 file.Only read values from ACE file.(values under 'RD' tag
>>>>>>> in
>>>>>>> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
>>>>>>> 'sampleA-S-F.AB1'.
>>>>>>>
>>>>>>> For the bottom part- that is to draw Chromatogram, I use Biojavas
>>>>>>> 'ChromatogramGraphic' class.
>>>>>>>
>>>>>>> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
>>>>>>> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so
>>>>>>> on...(like
>>>>>>> in ChromasPro).
>>>>>>>
>>>>>>> But I noticed that basecall sequence of 'ChromatogramGraphic' is
>>>>>>> totally
>>>>>>> different than that of from ACE file.
>>>>>>> Refer to image (2) ; you can see the two sequences generated by
>>>>>>> same AB1
>>>>>>> file is different in lenght also.
>>>>>>>
>>>>>>> What could be the problem here? Any suggestions please
>>>>>>>
>>>>>>> thanks in advance.
>>>>>>> umanga
>>>>>>> _______________________________________________
>>>>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From aumanga at biggjapan.com  Thu Jun 18 02:51:44 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Thu, 18 Jun 2009 11:51:44 +0900
Subject: [Biojava-l] SCF Parser issues with gaps and unread peak values ?
Message-ID: <4A39ABC0.8090503@biggjapan.com>

Greetings all,

Please refer to image at:  http://i43.tinypic.com/sfdjs6.png

As shown in Figure1 , I am drawing bases using Phrap ACE file and 
drawing chromatographs using
Biojava 'ChromatoGraphics' . I use .SCF file generated by phrep.

As can be seen in Figure 1 , the alignment breaks from the 'Magenta 
callbase-box'.The reason is may be the 'SCF parser' has ignored one of 
the peaks which should be a 'T'.


Figure 2 : Shows what need to be happen.If somehow if I can fill it with 
a T (or may be sometimes a Gap) I can save the alignment between sequences.

Figure 3 : Shows the same Chromatograph using ChromasPro , It has 
identified the peak as a T.

I went throught the biojavas SCF  parser , I noticed that it finally 
creates a 'SimpleAlignment'.Can I utilize 'GappedSymbolList' and fix this?
Is there a way to read the gaps (or incases like this , the correct base 
T) and make these two align.

Thanks in advance,
Umanga


From aumanga at biggjapan.com  Fri Jun 19 01:28:56 2009
From: aumanga at biggjapan.com (Ashika Umanga Umagiliya)
Date: Fri, 19 Jun 2009 10:28:56 +0900
Subject: [Biojava-l] SCF Parser issues with gaps and unread peak values ?
In-Reply-To: <4A3A163A.6080304@ebi.ac.uk>
References: <4A39ABC0.8090503@biggjapan.com> <4A3A163A.6080304@ebi.ac.uk>
Message-ID: <4A3AE9D8.108@biggjapan.com>

Hi Andy,

Thank you for the help.
Yes,looking at the trace the bases has to be TGTTGTTAGG as you said.

I get Chromatogram using SCF parse like :

Chromatogram chroma = SCF.create(scfFile);

then when I print the bases using

chroma.getBaseCalls()

It shows the bases sequence "TGTTGTAGG" (T is missing).
So I put a System.out.println() to the decode method in SCF parser class 
, that ie at :


 static class DefaultUncertaintyDecoder implements  
BaseCallUncertaintyDecoder {
        public DefaultUncertaintyDecoder() { }

        public Symbol decode(byte call) throws IllegalSymbolException {
            char c = (char) call;
            System.out.print(""+c);
..
..


But here also it showed "TGTTGTAGG" (with missubg T).

So I thought this is not an issue with rendering logic, but in the parser.


Thanks again,
Umanga




Andy Yates wrote:
> Hi Umanga,
>
> Looking at your graphic the SCF parser hasn't missed out the T. Looking
> at the trace I can read the bases to be TGTTGTTAGGG. What I think has
> happened is the callboxes are assuming a more uniformed trace since the
> G has bled a bit too much into the previous T.
>
> My knowledge of the callbox code is non-existent as my previous work on
> these types of graphics did not call for this kind of rendering (we
> didn't use any base calls as we were looking for variation in samples
> with varying copy numbers so they were quite subtle). Have a look in the
> options for the call box rendering & see if there is anything which can
> limit the size of a callbox & the bounds it is rendered to. Also looking
> at the basecalled positions might be a good idea as that would give a
> clue about what the graphics are attempting to do WRT this data
>
> Hope that helps.
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Greetings all,
>>
>> Please refer to image at:  http://i43.tinypic.com/sfdjs6.png
>>
>> As shown in Figure1 , I am drawing bases using Phrap ACE file and
>> drawing chromatographs using
>> Biojava 'ChromatoGraphics' . I use .SCF file generated by phrep.
>>
>> As can be seen in Figure 1 , the alignment breaks from the 'Magenta
>> callbase-box'.The reason is may be the 'SCF parser' has ignored one of
>> the peaks which should be a 'T'.
>>
>>
>> Figure 2 : Shows what need to be happen.If somehow if I can fill it with
>> a T (or may be sometimes a Gap) I can save the alignment between sequences.
>>
>> Figure 3 : Shows the same Chromatograph using ChromasPro , It has
>> identified the peak as a T.
>>
>> I went throught the biojavas SCF  parser , I noticed that it finally
>> creates a 'SimpleAlignment'.Can I utilize 'GappedSymbolList' and fix this?
>> Is there a way to read the gaps (or incases like this , the correct base
>> T) and make these two align.
>>
>> Thanks in advance,
>> Umanga
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>     



From abdul.qaddos at gmail.com  Fri Jun 19 06:52:38 2009
From: abdul.qaddos at gmail.com (Abdul Qaddus)
Date: Fri, 19 Jun 2009 11:52:38 +0500
Subject: [Biojava-l] Need help for resolving the issue args[0]
In-Reply-To: <a6b292990906182350q4c0a6fc4u8783bd8b021c8321@mail.gmail.com>
References: <a6b292990906182350q4c0a6fc4u8783bd8b021c8321@mail.gmail.com>
Message-ID: <a6b292990906182352k1168b1e2l611c3cb7b941b7b8@mail.gmail.com>

 Hello Support,
I am a new developer of biojava, I have a good knowledge about java and bio,
but this is new tool for me, I have some problem while working in this
tools, below I have write down the code for reading the Gen Bank file and
then convert into "DNA", "RNA" or "Protein". I have already add the biojava
library into my source code. When I have read this code I have come to know
from your arguments portion for the execution of this code, I have need
three argument, one for the filename, second for the file type and third is
the alphabet.
Now the problem is that how I will pass these three parameter values into
source code for args[0], args[1] and args[2]. When I have passed these
values by using the string pattern then this code generte a errors, "illegel
statement". Please help me out how I can fixed this problem, I will be very
thankful to you if you will reply me soon


package biojava;
import java.io.*;

import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;

public class ReadFasta2 {

 /**
  * This program will read any file supported by SeqIOTools it takes three
  * arguments, the first is the file name the second is the name of
  * a file format supported by SeqIOTools. eg fasta, genbank etc.
  * The third argument is the alphabet (eg dna, rna, protein).
  *
  * Both the format and alphabet names are case insensitive.
  *
  */
 public static void main(String[] args) {
   try {
     //prepare a BufferedReader for file io
     BufferedReader br = new BufferedReader(new FileReader(args[0]));

     String format = args[1];
     String alphabet = args[2];

     /*
      * get a Sequence Iterator over all the sequences in the file.
      * SeqIOTools.fileToBiojava() returns an Object. If the file read
      * is an alignment format like MSF and Alignment object is returned
      * otherwise a SequenceIterator is returned.
      */
     SequenceIterator iter =
         (SequenceIterator)SeqIOTools.fileToBiojava(format,alphabet, br);
   }
   catch (FileNotFoundException ex) {
     //can't find file specified by args[0]
     ex.printStackTrace();
   }catch (BioException ex) {
     //error parsing requested format
     ex.printStackTrace();
   }
 }
}
--




-- 
Abdul Qaddus
www.futurelinkers.com
Cell No:- +92-3336540863


From mark.schreiber at novartis.com  Fri Jun 19 06:57:09 2009
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 19 Jun 2009 14:57:09 +0800
Subject: [Biojava-l] Need help for resolving the issue args[0]
In-Reply-To: <a6b292990906182352k1168b1e2l611c3cb7b941b7b8@mail.gmail.com>
Message-ID: <OF3E1E7BF7.498CFB66-ON482575DA.00262486-482575DA.002631AC@ah.novartis.com>

Can you post the stack trace?



biojava-l-bounces at lists.open-bio.org wrote on 06/19/2009 02:52:38 PM:

>  Hello Support,
> I am a new developer of biojava, I have a good knowledge about java and 
bio,
> but this is new tool for me, I have some problem while working in this
> tools, below I have write down the code for reading the Gen Bank file 
and
> then convert into "DNA", "RNA" or "Protein". I have already add the 
biojava
> library into my source code. When I have read this code I have come to 
know
> from your arguments portion for the execution of this code, I have need
> three argument, one for the filename, second for the file type and third 
is
> the alphabet.
> Now the problem is that how I will pass these three parameter values 
into
> source code for args[0], args[1] and args[2]. When I have passed these
> values by using the string pattern then this code generte a errors, 
"illegel
> statement". Please help me out how I can fixed this problem, I will be 
very
> thankful to you if you will reply me soon
> 
> 
> package biojava;
> import java.io.*;
> 
> import org.biojava.bio.*;
> import org.biojava.bio.seq.*;
> import org.biojava.bio.seq.io.*;
> 
> public class ReadFasta2 {
> 
>  /**
>   * This program will read any file supported by SeqIOTools it takes 
three
>   * arguments, the first is the file name the second is the name of
>   * a file format supported by SeqIOTools. eg fasta, genbank etc.
>   * The third argument is the alphabet (eg dna, rna, protein).
>   *
>   * Both the format and alphabet names are case insensitive.
>   *
>   */
>  public static void main(String[] args) {
>    try {
>      //prepare a BufferedReader for file io
>      BufferedReader br = new BufferedReader(new FileReader(args[0]));
> 
>      String format = args[1];
>      String alphabet = args[2];
> 
>      /*
>       * get a Sequence Iterator over all the sequences in the file.
>       * SeqIOTools.fileToBiojava() returns an Object. If the file read
>       * is an alignment format like MSF and Alignment object is returned
>       * otherwise a SequenceIterator is returned.
>       */
>      SequenceIterator iter =
>          (SequenceIterator)SeqIOTools.fileToBiojava(format,alphabet, 
br);
>    }
>    catch (FileNotFoundException ex) {
>      //can't find file specified by args[0]
>      ex.printStackTrace();
>    }catch (BioException ex) {
>      //error parsing requested format
>      ex.printStackTrace();
>    }
>  }
> }
> --
> 
> 
> 
> 
> -- 
> Abdul Qaddus
> www.futurelinkers.com
> Cell No:- +92-3336540863
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

_________________________

CONFIDENTIALITY NOTICE

The information contained in this e-mail message is intended only for the 
exclusive use of the individual or entity named above and may contain 
information that is privileged, confidential or exempt from disclosure 
under applicable law. If the reader of this message is not the intended 
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dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this communication in error, please 
notify the sender immediately by e-mail and delete the material from any 
computer.  Thank you.


From ayates at ebi.ac.uk  Fri Jun 19 15:37:10 2009
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 19 Jun 2009 16:37:10 +0100
Subject: [Biojava-l] SCF Parser issues with gaps and unread peak values ?
In-Reply-To: <4A3AE9D8.108@biggjapan.com>
References: <4A39ABC0.8090503@biggjapan.com> <4A3A163A.6080304@ebi.ac.uk>
	<4A3AE9D8.108@biggjapan.com>
Message-ID: <4A3BB0A6.2070202@ebi.ac.uk>

Hi Umanga,

That does sound like a problem with the decoder. It's been quite a bit
of time since I last looked at the SCF code. Maybe Franklin who posted
to this list recently (whom I'm guessing is a bit more used to SCF file
formats at the moment) could help if he would be so willing :)

Andy

Ashika Umanga Umagiliya wrote:
> Hi Andy,
> 
> Thank you for the help.
> Yes,looking at the trace the bases has to be TGTTGTTAGG as you said.
> 
> I get Chromatogram using SCF parse like :
> 
> Chromatogram chroma = SCF.create(scfFile);
> 
> then when I print the bases using
> 
> chroma.getBaseCalls()
> 
> It shows the bases sequence "TGTTGTAGG" (T is missing).
> So I put a System.out.println() to the decode method in SCF parser class
> , that ie at :
> 
> 
> static class DefaultUncertaintyDecoder implements 
> BaseCallUncertaintyDecoder {
>        public DefaultUncertaintyDecoder() { }
> 
>        public Symbol decode(byte call) throws IllegalSymbolException {
>            char c = (char) call;
>            System.out.print(""+c);
> ..
> ..
> 
> 
> But here also it showed "TGTTGTAGG" (with missubg T).
> 
> So I thought this is not an issue with rendering logic, but in the parser.
> 
> 
> Thanks again,
> Umanga
> 
> 
> 
> 
> Andy Yates wrote:
>> Hi Umanga,
>>
>> Looking at your graphic the SCF parser hasn't missed out the T. Looking
>> at the trace I can read the bases to be TGTTGTTAGGG. What I think has
>> happened is the callboxes are assuming a more uniformed trace since the
>> G has bled a bit too much into the previous T.
>>
>> My knowledge of the callbox code is non-existent as my previous work on
>> these types of graphics did not call for this kind of rendering (we
>> didn't use any base calls as we were looking for variation in samples
>> with varying copy numbers so they were quite subtle). Have a look in the
>> options for the call box rendering & see if there is anything which can
>> limit the size of a callbox & the bounds it is rendered to. Also looking
>> at the basecalled positions might be a good idea as that would give a
>> clue about what the graphics are attempting to do WRT this data
>>
>> Hope that helps.
>>
>> Andy
>>
>> Ashika Umanga Umagiliya wrote:
>>  
>>> Greetings all,
>>>
>>> Please refer to image at:  http://i43.tinypic.com/sfdjs6.png
>>>
>>> As shown in Figure1 , I am drawing bases using Phrap ACE file and
>>> drawing chromatographs using
>>> Biojava 'ChromatoGraphics' . I use .SCF file generated by phrep.
>>>
>>> As can be seen in Figure 1 , the alignment breaks from the 'Magenta
>>> callbase-box'.The reason is may be the 'SCF parser' has ignored one of
>>> the peaks which should be a 'T'.
>>>
>>>
>>> Figure 2 : Shows what need to be happen.If somehow if I can fill it with
>>> a T (or may be sometimes a Gap) I can save the alignment between
>>> sequences.
>>>
>>> Figure 3 : Shows the same Chromatograph using ChromasPro , It has
>>> identified the peak as a T.
>>>
>>> I went throught the biojavas SCF  parser , I noticed that it finally
>>> creates a 'SimpleAlignment'.Can I utilize 'GappedSymbolList' and fix
>>> this?
>>> Is there a way to read the gaps (or incases like this , the correct base
>>> T) and make these two align.
>>>
>>> Thanks in advance,
>>> Umanga
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>     
> 
> 


From jp at javaclass.co.uk  Fri Jun 19 17:37:38 2009
From: jp at javaclass.co.uk (JP)
Date: Fri, 19 Jun 2009 18:37:38 +0100
Subject: [Biojava-l] Simple Question - Creating a Java object (some form of
	Tree) from a Newick format file
Message-ID: <4adc29060906191037u53cb1622p2e982543f5c22cba@mail.gmail.com>

Does anyone know of a tool to create a tree by parsing a Newick Tree format
file in Java ?
Is there anything in biojava to read this ?

Many Thanks
JP


From holland at eaglegenomics.com  Fri Jun 19 17:56:15 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Fri, 19 Jun 2009 18:56:15 +0100
Subject: [Biojava-l] Simple Question - Creating a Java object (some form
 of Tree) from a Newick format file
In-Reply-To: <4adc29060906191037u53cb1622p2e982543f5c22cba@mail.gmail.com>
References: <4adc29060906191037u53cb1622p2e982543f5c22cba@mail.gmail.com>
Message-ID: <1245434175.8158.6.camel@buzzybee>

Biojava has a parser which understands Nexus files, including the
embedded Newick tree data. You could probably extract and modify the
Newick bits to run standalone. The Nexus code is written up here:

http://biojava.org/wiki/BioJava:PhyloSOC07_doc
http://www.biojava.org/docs/api/org/biojavax/bio/phylo/io/nexus/package-summary.html
http://www.mail-archive.com/biojava-l at lists.open-bio.org/msg00892.html

cheers,
Richard


On Fri, 2009-06-19 at 18:37 +0100, JP wrote:
> Does anyone know of a tool to create a tree by parsing a Newick Tree format
> file in Java ?
> Is there anything in biojava to read this ?
> 
> Many Thanks
> JP
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From andreas at sdsc.edu  Sat Jun 20 16:45:51 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 20 Jun 2009 09:45:51 -0700
Subject: [Biojava-l] BioJava user meeting at ISMB/BOSC
Message-ID: <59a41c430906200945q598503ccj52717cf708b67083@mail.gmail.com>

Hi,

Next week the ISMB and BOSC conferences will take place in Stockholm,
Sweden. As has become kind of a tradition, we will have a BioJava user
meeting around BOSC.

If you are in Stockholm at the time please join us on Sunday, late
afternoon. We will meet during the "Birds of a Feather" session.
http://open-bio.org/wiki/BOSC_2009/Birds-of-a-Feather

Looking forward to meeting you there,
Andreas


From mcolosimo at mitre.org  Mon Jun 22 13:19:01 2009
From: mcolosimo at mitre.org (Colosimo, Marc E.)
Date: Mon, 22 Jun 2009 09:19:01 -0400
Subject: [Biojava-l] Simple Question - Creating a Java object
In-Reply-To: <mailman.11.1245513607.22652.biojava-l@lists.open-bio.org>
References: <mailman.11.1245513607.22652.biojava-l@lists.open-bio.org>
Message-ID: <2A8C361000E22F4895ACA58412E8F06CF4DB53CF@IMCMBX3.MITRE.ORG>

If you just want to view a tree, try TreeViewJ <http://sourceforge.net/projects/treeviewj/>. The GUI can read in newick and phyloXML trees and import trees from Nexus files. It can export back out to newick and phyloXML or as SVG or JPEG images. I have more code that I'll be checking in soon. 

Best,
Marc


From: Richard Holland <holland at eaglegenomics.com>
Subject: Re: [Biojava-l] Simple Question - Creating a Java object
	(some form of Tree) from a Newick format file
To: JP <jp at javaclass.co.uk>
Cc: biojava-l at biojava.org
Message-ID: <1245434175.8158.6.camel at buzzybee>
Content-Type: text/plain

Biojava has a parser which understands Nexus files, including the
embedded Newick tree data. You could probably extract and modify the
Newick bits to run standalone. The Nexus code is written up here:

http://biojava.org/wiki/BioJava:PhyloSOC07_doc
http://www.biojava.org/docs/api/org/biojavax/bio/phylo/io/nexus/package-summary.html
http://www.mail-archive.com/biojava-l at lists.open-bio.org/msg00892.html

cheers,
Richard


On Fri, 2009-06-19 at 18:37 +0100, JP wrote:
> Does anyone know of a tool to create a tree by parsing a Newick Tree format
> file in Java ?
> Is there anything in biojava to read this ?
> 
> Many Thanks
> JP
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From jp at javaclass.co.uk  Mon Jun 22 15:32:58 2009
From: jp at javaclass.co.uk (JP)
Date: Mon, 22 Jun 2009 16:32:58 +0100
Subject: [Biojava-l] Reading a newick format tree file
	(getTreeAsWeightedJGraphT) generates an
	ArrayIndexOutOfBoundsException in TreeBlock
Message-ID: <4adc29060906220832i3e64b699u3b842122df400cb0@mail.gmail.com>

I have tried to use the getTreeAsWeightedJGraphT functionality in TreesBlock
as highlighted in the wikipedia page:

My code for completeness sake (a direct and lazy copy and paste)

String newickFileContents = FileUtils.readTextFile(treeFile, false);  //
> reads the text file without newlines
> WeightedGraph<String, DefaultWeightedEdge> jg = new
> SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
> TreesBlock sample_tree = new TreesBlock();
> TreesBlock.NewickTreeString s = new TreesBlock.NewickTreeString();
> s.setTreeString(newickFileContents);
> sample_tree.addTree("test", s);
> jg = sample_tree.getTreeAsWeightedJGraphT("test");
> System.out.println(newickFileContents);
> System.out.println(jg.toString());
>

The data file is attached (newwick format), and this is the returned error
message...

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 79169
>     at
> org.biojavax.bio.phylo.io.nexus.TreesBlock.getTreeAsWeightedJGraphT(TreesBlock.java:562)
>     at
> edu.imperial.msc.multiglass.tree.TreeBuilder.<init>(TreeBuilder.java:50)
>     at
> edu.imperial.msc.multiglass.launcher.MultiGlassLauncher.main(MultiGlassLauncher.java:59)


Any idea why this is so ?


The data file:

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From ranjithkurungadam at gmail.com  Wed Jun 24 09:29:39 2009
From: ranjithkurungadam at gmail.com (ranjith kurungadam)
Date: Wed, 24 Jun 2009 14:59:39 +0530
Subject: [Biojava-l] : prob in reading sequence
Message-ID: <f31c43780906240229i5a2f4f32v8f5989c2a48ad69b@mail.gmail.com>

hello
//rof :  m new to this community..
going on wit my final semester M.Sc project work. m trying to do some
nucleotide sequence manipulation using biojava.

//rof : while trying to read different bio formats i found that the method
SeqIOTools.readEmbl( ) method instantiates the SequenceIterator object with
some unknown values wen a genbank format is read, but its ok wen a fasta is
read as stream.hasnext( ) gives Exception.
i got confused as this is not the case wit other methods readFastaDNA( ) and
readGenbank( )..

//Expecting ur support


From holland at eaglegenomics.com  Wed Jun 24 09:36:34 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 24 Jun 2009 10:36:34 +0100
Subject: [Biojava-l] : prob in reading sequence
In-Reply-To: <f31c43780906240229i5a2f4f32v8f5989c2a48ad69b@mail.gmail.com>
References: <f31c43780906240229i5a2f4f32v8f5989c2a48ad69b@mail.gmail.com>
Message-ID: <1245836195.4184.18.camel@buzzybee>

readEmbl() is for reading EMBL format files. It's not suprising it
causes problems if you use it to try to read Genbank or FASTA!

Also, SeqIOTools is deprecated and not really supported any more. You
should take a look at RichSequence.IOTools instead:

http://www.biojava.org/docs/api15b/org/biojavax/bio/seq/RichSequence.IOTools.html

cheers,
Richard

On Wed, 2009-06-24 at 14:59 +0530, ranjith kurungadam wrote:
> hello
> //rof :  m new to this community..
> going on wit my final semester M.Sc project work. m trying to do some
> nucleotide sequence manipulation using biojava.
> 
> //rof : while trying to read different bio formats i found that the method
> SeqIOTools.readEmbl( ) method instantiates the SequenceIterator object with
> some unknown values wen a genbank format is read, but its ok wen a fasta is
> read as stream.hasnext( ) gives Exception.
> i got confused as this is not the case wit other methods readFastaDNA( ) and
> readGenbank( )..
> 
> //Expecting ur support
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From andreas at sdsc.edu  Thu Jun 25 05:37:25 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 24 Jun 2009 22:37:25 -0700
Subject: [Biojava-l] BOSC presentation
Message-ID: <59a41c430906242237o45f0c6c6o2de4f3f0ad7f28a1@mail.gmail.com>

Hi,

Here the slides I prepared for the BioJava talk at BOSC on Sunday.

http://biojava.org/wiki/BOSC2009_Presentation

Andreas


From noreply at netlogmail.com  Thu Jun 25 18:47:30 2009
From: noreply at netlogmail.com (Saulo)
Date: Thu, 25 Jun 2009 14:47:30 -0400
Subject: [Biojava-l] Visit my Netlog profile
Message-ID: <200906251847.n5PIlU26006722@portal.open-bio.org>

Hey,

I have created a Netlog profile with my pictures, videos, blogs and events and I want to add you as a friend so you can see it. You first need to register on Netlog! When you log in, you can create your own profile.

Take a look:
http://en.netlog.com/go/mailurl/type=invite_1&mailid=342282513&id=1&url=-L2dvL3JlZ2lzdGVyL2lkPTExMjQ2MTU3OTMmaT10OTE_

Greetings,
Saulo

----------------------------------------------------------------
Don't want to receive invitations from your friends anymore?
http://en.netlog.com/go/mailurl/type=invite_1&mailid=342282513&id=2&url=-L2dvL25vbWFpbHMvaW52aXRlL2VtYWlsPS1ZbWx2YW1GMllTMXNRR3hwYzNSekxtOXdaVzR0WW1sdkxtOXlad19fJmNvZGU9MDE1MzI3MDYmaWQ9MTEyNDYxNTc5MyZpPXQ5Mg__


From jp at javaclass.co.uk  Mon Jun 22 15:05:31 2009
From: jp at javaclass.co.uk (JP)
Date: Mon, 22 Jun 2009 15:05:31 -0000
Subject: [Biojava-l] Reading a newick format tree file generates an
	ArrayIndexOutOfBoundsException (TreeBlock, getTreeAsWeightedJGraphT)
Message-ID: <4adc29060906220805t16e3f7c3k84f1f306c3861c39@mail.gmail.com>

I have tried to use the getTreeAsWeightedJGraphT functionality in TreesBlock
as highlighted in the wikipedia page:

My code for completeness sake (a direct and lazy copy and paste)

String newickFileContents = FileUtils.readTextFile(treeFile, false);  //
> reads the text file without newlines
> WeightedGraph<String, DefaultWeightedEdge> jg = new
> SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
> TreesBlock sample_tree = new TreesBlock();
> TreesBlock.NewickTreeString s = new TreesBlock.NewickTreeString();
> s.setTreeString(newickFileContents);
> sample_tree.addTree("test", s);
> jg = sample_tree.getTreeAsWeightedJGraphT("test");
> System.out.println(newickFileContents);
> System.out.println(jg.toString());
>

The data file is attached (newwick format), and this is the returned error
message...

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 79169
>     at
> org.biojavax.bio.phylo.io.nexus.TreesBlock.getTreeAsWeightedJGraphT(TreesBlock.java:562)
>     at
> edu.imperial.msc.multiglass.tree.TreeBuilder.<init>(TreeBuilder.java:50)
>     at
> edu.imperial.msc.multiglass.launcher.MultiGlassLauncher.main(MultiGlassLauncher.java:59)


Any idea why this is so ?
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