From p.j.a.cock at googlemail.com  Tue Jan  3 09:44:03 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 3 Jan 2012 14:44:03 +0000
Subject: [Biopython-dev] Installing Bio.Geography
In-Reply-To: <1325600614.87653.YahooMailNeo@web160904.mail.bf1.yahoo.com>
References: <mailman.1514.1325559336.3027.biopython-dev@lists.open-bio.org>
	<FBD94D55-5EAC-4C7D-884B-A96880BE11DE@yahoo.com>
	<CAKVJ-_6S2spq6crnqqkEpiE0oGZTT+TXXbOQk2STq94n5iuAHQ@mail.gmail.com>
	<1325600614.87653.YahooMailNeo@web160904.mail.bf1.yahoo.com>
Message-ID: <CAKVJ-_78=9eunF2=bcD_6428Le5x6_=nPijPxpAtQEP_WRGqmA@mail.gmail.com>

On Tue, Jan 3, 2012 at 2:23 PM, JOSE SERGIO HLEAP <sergiohleap at yahoo.com> wrote:
> Thanks for your quick answer Peter... I already went
> trough?http://biopython.org/wiki/BioGeography?at the?Nick Matzke's github. I
> dowloaded the enrire branch in a zip, then build, test and install, using
> the setup... but still does not work. When in a python console I type:
>
>>>> from Bio import Geography
>
> Give me the following taceback:
> ...
> ImportError: cannot import name Geography
>
> ...
>
> am I doing something wrong??
>
> Thanks again for any help you can provide me!
>
> Sergio

Hi again.

My guess is you got the (default) master branch from
Nick's repository, not the Geography branch:
https://github.com/nmatzke/biopython/branches

Try something like this before installing,

git clone https://github.com/nmatzke/biopython.git
cd biopython
git checkout Geography

Peter


From eric.talevich at gmail.com  Tue Jan  3 11:42:51 2012
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 3 Jan 2012 11:42:51 -0500
Subject: [Biopython-dev] Installing Bio.Geography
In-Reply-To: <CAKVJ-_78=9eunF2=bcD_6428Le5x6_=nPijPxpAtQEP_WRGqmA@mail.gmail.com>
References: <mailman.1514.1325559336.3027.biopython-dev@lists.open-bio.org>
	<FBD94D55-5EAC-4C7D-884B-A96880BE11DE@yahoo.com>
	<CAKVJ-_6S2spq6crnqqkEpiE0oGZTT+TXXbOQk2STq94n5iuAHQ@mail.gmail.com>
	<1325600614.87653.YahooMailNeo@web160904.mail.bf1.yahoo.com>
	<CAKVJ-_78=9eunF2=bcD_6428Le5x6_=nPijPxpAtQEP_WRGqmA@mail.gmail.com>
Message-ID: <CAMC681kwmFRMtUk8coN+8VpkKLAawLUfpgWNKmUSXLp0mDDp-A@mail.gmail.com>

On Tue, Jan 3, 2012 at 9:44 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Tue, Jan 3, 2012 at 2:23 PM, JOSE SERGIO HLEAP <sergiohleap at yahoo.com>
> wrote:
> > Thanks for your quick answer Peter... I already went
> > trough http://biopython.org/wiki/BioGeography at the Nick Matzke's
> github. I
> > dowloaded the enrire branch in a zip, then build, test and install, using
> > the setup... but still does not work. When in a python console I type:
> >
> >>>> from Bio import Geography
> >
> > Give me the following taceback:
> > ...
> > ImportError: cannot import name Geography
> >
> > ...
> >
> > am I doing something wrong??
> >
> > Thanks again for any help you can provide me!
> >
> > Sergio
>
> Hi again.
>
> My guess is you got the (default) master branch from
> Nick's repository, not the Geography branch:
> https://github.com/nmatzke/biopython/branches
>
> Try something like this before installing,
>
> git clone https://github.com/nmatzke/biopython.git
> cd biopython
> git checkout Geography
>
> Peter
>
>
Also, for the sub-package to be installed via setup.py, you'll need to add
Bio.Geography to the list of installed packages. In setup.py, around line
207,  you'll see a global variable PACKAGES and a list of module names as
strings. Try adding "Bio.Geography" to this list.

-Eric

From redmine at redmine.open-bio.org  Thu Jan  5 19:53:33 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Fri, 6 Jan 2012 00:53:33 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] (New) Parsing Stockholm
	files fails with some sequence IDs
Message-ID: <redmine.issue-3317.20120106005333@redmine.open-bio.org>


Issue #3317 has been reported by Connor McCoy.

----------------------------------------
Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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From redmine at redmine.open-bio.org  Thu Jan  5 19:53:34 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Fri, 6 Jan 2012 00:53:34 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] (New) Parsing Stockholm
	files fails with some sequence IDs
Message-ID: <redmine.issue-3317.20120106005333@redmine.open-bio.org>


Issue #3317 has been reported by Connor McCoy.

----------------------------------------
Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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From carlcrott at gmail.com  Mon Jan  9 09:36:00 2012
From: carlcrott at gmail.com (carl crott)
Date: Mon, 9 Jan 2012 09:36:00 -0500
Subject: [Biopython-dev] GFF file parsing and error handling
Message-ID: <CAE2MQmCRSBhJ5O1LxAW-BPyFetaCNc_t0R4cR+ZpFkSDwvfL-w@mail.gmail.com>

Hey all,

I'm posting here because I know there has been talk about GFF file parsing
and I'd love to code a bit as soon as I comprehend whats going on with
these files.


I've got this GFF file ( placed in a spreadsheet for readability )

https://docs.google.com/spreadsheet/ccc?key=0AtOqyz8P_fJ0dGVOMzNSM29qUVdjZmZ4emdIQ3U2OUE&hl=en_US#gid=0

line 178 + 179 are the problematic lines

what is going on here?

I know that these genes are listed in reverse order and that a sequence of:
    stop_codon
    CDS
    CDS
    start_codon

the above is a normal gene arrangement.

BUT my guesses as to what happening ( between 178 and 179 ):
1) the gene stretches from the end of one chromosome to another?
2) simply a stop_codon with no attached CDS or start_codon ?

I've successfully managed to parse out the gene intervals and now I'm
working on the error handling.

Thanks,
Carl

-- 
Carl Crott
Web Applications Engineer
www.black-glass.com
412-610-0600

From chapmanb at 50mail.com  Tue Jan 10 11:21:17 2012
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 10 Jan 2012 11:21:17 -0500
Subject: [Biopython-dev] GFF file parsing and error handling
In-Reply-To: <CAE2MQmCRSBhJ5O1LxAW-BPyFetaCNc_t0R4cR+ZpFkSDwvfL-w@mail.gmail.com>
References: <CAE2MQmCRSBhJ5O1LxAW-BPyFetaCNc_t0R4cR+ZpFkSDwvfL-w@mail.gmail.com>
Message-ID: <87boqb5y0y.fsf@fastmail.fm>



Carl;

> I've got this GFF file ( placed in a spreadsheet for readability )
> 
> https://docs.google.com/spreadsheet/ccc?key=0AtOqyz8P_fJ0dGVOMzNSM29qUVdjZmZ4emdIQ3U2OUE&hl=en_US#gid=0
> 
> line 178 + 179 are the problematic lines
> 
> what is going on here?

I'm not sure I understand exactly what is giving you problems. There are
two different genes:

- gene_id 000014 on segment human.ENr12. This has two exons and an
  annotated start and stop codon.

- gene_id 000001 on segment human.ENr13. This has an exon and a start
  codon, but no annotated stop codon.

Does that help?
Brad

From redmine at redmine.open-bio.org  Mon Jan 16 04:30:37 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 16 Jan 2012 09:30:37 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] Parsing Stockholm files
	fails with some sequence IDs
References: <redmine.issue-3317.20120106005333@redmine.open-bio.org>
Message-ID: <redmine.journal-14752.20120116093037@redmine.open-bio.org>


Issue #3317 has been updated by Peter Cock.


Patch cherry-picked and applied to master,
https://github.com/biopython/biopython/commit/ca86f1a27e7af20b4c692cbbe9d54f08e0c65906

Do you fancy preparing a little unit test as well?

Thanks.
----------------------------------------
Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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From redmine at redmine.open-bio.org  Wed Jan 18 17:32:35 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Wed, 18 Jan 2012 22:32:35 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] Parsing Stockholm files
	fails with some sequence IDs
References: <redmine.issue-3317.20120106005333@redmine.open-bio.org>
Message-ID: <redmine.journal-14753.20120118223235@redmine.open-bio.org>


Issue #3317 has been updated by Connor McCoy.


Sure: I added an example of the previously failing sequence to the existing `Tests/Stockholm/funny.sth` file.

https://github.com/cmccoy/biopython/commit/7e9f697c38f0132952b50482fddfea77ce800536

If there's a better place, please let me know.

All tests pass for me.
----------------------------------------
Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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From redmine at redmine.open-bio.org  Thu Jan 19 13:11:10 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Thu, 19 Jan 2012 18:11:10 +0000
Subject: [Biopython-dev] [Biopython - Bug #3318] (New)
	Bio.GenBank.LocationParserError on RefSeq files
Message-ID: <redmine.issue-3318.20120119181110@redmine.open-bio.org>


Issue #3318 has been reported by John Eppley.

----------------------------------------
Bug #3318: Bio.GenBank.LocationParserError on RefSeq files
https://redmine.open-bio.org/issues/3318

Author: John Eppley
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


I get the following error trying to parse a file from NCBI RefSeq:
<pre>
Traceback (most recent call last):
  File "/Users/jmeppley/work/delong/projects/scripts/getSequencesFromGbk.py", line 62, in main
    translateStream(instream,options.formatIn,outstream, options.formatOut, options.cds, options.translate)
  File "/Users/jmeppley/work/delong/projects/scripts/getSequencesFromGbk.py", line 87, in translateStream
    for record in records:
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/SeqIO/__init__.py", line 532, in parse
    for r in i:
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/Scanner.py", line 440, in parse_records
    record = self.parse(handle, do_features)
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/Scanner.py", line 423, in parse
    if self.feed(handle, consumer, do_features):
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/Scanner.py", line 395, in feed
    self._feed_feature_table(consumer, self.parse_features(skip=False))
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/Scanner.py", line 347, in _feed_feature_table
    consumer.location(location_string)
  File "/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/__init__.py", line 975, in location
    raise LocationParserError(location_line)
LocationParserError: join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)
</pre>

The file can be found here (release 51):

The relevant section is:
<pre>
     gene            join(complement(149815..150200),
                     complement(293787..295573),NC_016402.1:6618..6676,
                     181647..181905)
                     /gene="nad1"
                     /trans_splicing
                     /note="exons 1, 2, 3, and 5 on chromosome 1 are
                     trans-spliced with exon 4 on chromosome 3 to form the
                     complete coding region"
                     /db_xref="GeneID:11447159"
</pre>

I think the underscore in the sequence name is confounding the regular expressions in Bio/GenBank/__init__.py. I was able to stop the error by making the following change (first line is mine, second is original):
<pre>
99c99
< _complex_location = r"([a-zA-z][a-zA-Z0-9_]*(\.[a-zA-Z0-9]+)?\:)?(%s|%s|%s|%s|%s)" \
---
> _complex_location = r"([a-zA-z][a-zA-Z0-9]*(\.[a-zA-Z0-9]+)?\:)?(%s|%s|%s|%s|%s)" \
</pre>

I haven't really tested it to see if the output is correct, though. It does pass the doctests.


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From p.j.a.cock at googlemail.com  Fri Jan 20 05:46:18 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 20 Jan 2012 10:46:18 +0000
Subject: [Biopython-dev] NCBI adoption of AGP v2.0 and new qualifiers in
	GenBank/EMBL
Message-ID: <CAKVJ-_68TGz776oFFDtTNwtS3L6EDJjiW2cZDQN=-rTSo0_3OQ@mail.gmail.com>

Dear all,

I just spotted this via the @NCBI twitter feed,
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/agp_spec_change.shtml

In addition to the NCBI switch from AGP v1.1 to v2.0, the INSDC have
recently added a new feature type called "assembly_gap", and the
associated qualifiers "gap_type" and "linkage_evidence" to the INSDC
Feature Table Definitons.

Quoting from version 10.0, dated Dec 2011
http://www.insdc.org/documents/feature_table.html#7.2
> Feature Key           assembly_gap
>
>
> Definition            gap between two components of a CON record that is
> 		      part of a genome assembly;
>
> Mandatory qualifiers  /estimated_length=unknown or <integer>
> 		      /gap_type="TYPE"
>                       /linkage_evidence="TYPE" (Note: Mandatory only if the
>                       /gap_type is "within scaffold" or "repeat within
>                       scaffold".If there are multiple types of linkage_evidence
>                       they will appear as multiple /linkage_evidence="TYPE"
>                       qualifiers. For all other types of assembly_gap
>                       features, use of the /linkage_evidence qualifier is
>                       invalid.)
>
> Comment               the location span of the assembly_gap feature for an
> 		      unknown gap is 100 bp, with the 100 bp indicated as
> 		      100 "n"'s in sequence.
>

i.e. DDBJ, ENA & GenBank flat-files will start to use the "assembly_gap"
features to display information derived from version 2.0 AGP files from
10th Feb 2012. Probably this will affect the XML variants as well.

Unless any of the parsers/writers for GenBank or EMBL flat files use a white
list approach, the new feature key and qualifiers shouldn't cause a problem.

Peter

From chapmanb at 50mail.com  Tue Jan 24 21:14:58 2012
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 24 Jan 2012 21:14:58 -0500
Subject: [Biopython-dev] Bug in Bio.Blast.NCBIWWW ?
In-Reply-To: <4F1F0E020200009500004335@gwsmtp2.uni-regensburg.de>
References: <4F1F0E020200009500004335@gwsmtp2.uni-regensburg.de>
Message-ID: <87vco0wmsd.fsf@fastmail.fm>


Micheal;
Thanks for the e-mail and problem report. For Biopython issues, the best
approach is to e-mail the development list (cc'ed here). Since it's a
community project, there are a wide variety of contributors that can
provide help and expertise.

In this particular case, I am not especially familiar with python 3 as
I'm still a python 2 user myself. Peter, Eric and other folks have been
doing a lot of work on this, so hopefully they can confirm or provide
additional details.

Thanks again,
Brad

> Dear Mr. Chapman,
> 
> I perhaps found a bug in the Bio.Blast.NCBIWWW module.
> But since I'm using Python 3.2.2 and didn't test this with Python2.x, I don't know if this is a Python2/Python3 issue.
> 
> When I try to execute the following line of code (where contig is a string):
> 
>     resultHandle = NCBIWWW.qblast('blastn', 'nr', contig)
> 
> I get the following error message:
> 
> Traceback (most recent call last):
>   File "/home/michael/python/gb/sheet11/ex80_all-contigs.py", line 575, in <module>
>     blastContig(contigs[i])
>   File "/home/michael/python/gb/sheet11/ex80_all-contigs.py", line 441, in blastContig
>     resultHandle = NCBIWWW.qblast('blastn', 'nr', contig, hitlist_size=1)
>   File "/usr/local/lib/python3.2/dist-packages/Bio/Blast/NCBIWWW.py", line 122, in qblast
>     handle = urllib.request.urlopen(request)
>   File "/usr/lib/python3.2/urllib/request.py", line 138, in urlopen
>     return opener.open(url, data, timeout)
>   File "/usr/lib/python3.2/urllib/request.py", line 367, in open
>     req = meth(req)
>   File "/usr/lib/python3.2/urllib/request.py", line 1066, in do_request_
>     raise TypeError("POST data should be bytes"
> TypeError: POST data should be bytes or an iterable of bytes. It cannot be str.
> 
> 
> After trying different things, I found that this can be fixed by replacing
> 
>     message = urllib.parse.urlencode(query)
> 
> in lines 113 and 145 in the NCBIWWW.py script by
> 
>     message = urllib.parse.urlencode(query, encoding='ascii')
>     message = bytes(message, 'ascii')
> 
> If this is not a Python2/Python3 thing, you perhaps want to use this fix for the next version of Biopython.
> 
> Yours sincerely,
> Michael Grauvogl
> 
> 
Non-text part: text/html

From p.j.a.cock at googlemail.com  Wed Jan 25 08:13:59 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 25 Jan 2012 13:13:59 +0000
Subject: [Biopython-dev] Bug in Bio.Blast.NCBIWWW ?
In-Reply-To: <87vco0wmsd.fsf@fastmail.fm>
References: <4F1F0E020200009500004335@gwsmtp2.uni-regensburg.de>
	<87vco0wmsd.fsf@fastmail.fm>
Message-ID: <CAKVJ-_7wwx_GpYbrNG+LzQ92aHMDz0HQKNAHyYF3GEJpuR0ptA@mail.gmail.com>

On Wed, Jan 25, 2012 at 2:14 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Micheal;
> Thanks for the e-mail and problem report. For Biopython issues, the best
> approach is to e-mail the development list (cc'ed here). Since it's a
> community project, there are a wide variety of contributors that can
> provide help and expertise.
>
> In this particular case, I am not especially familiar with python 3 as
> I'm still a python 2 user myself. Peter, Eric and other folks have been
> doing a lot of work on this, so hopefully they can confirm or provide
> additional details.
>
> Thanks again,
> Brad

Hi all,

Yes, as you guessed Michael, this is a Python 3 problem. This
should work now - doing something similar to your suggestion:
https://github.com/biopython/biopython/commit/7bd519e68974185c7b489e2415c9ee3b6f1d7ac4

Thanks for the reminder - there are still a few things to fix under
in Biopython under Python 3.

Peter

From redmine at redmine.open-bio.org  Mon Jan 30 10:59:43 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 30 Jan 2012 15:59:43 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] (Resolved) Parsing
	Stockholm files fails with some sequence IDs
References: <redmine.issue-3317.20120106005333@redmine.open-bio.org>
Message-ID: <redmine.journal-14756.20120130155943@redmine.open-bio.org>


Issue #3317 has been updated by Peter Cock.

Status changed from New to Resolved
% Done changed from 0 to 100

Thanks,
https://github.com/biopython/biopython/commit/d439ba5c6a5a501ba859cce02c746f7d75b2914e
----------------------------------------
Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: Resolved
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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From p.j.a.cock at googlemail.com  Tue Jan  3 14:44:03 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 3 Jan 2012 14:44:03 +0000
Subject: [Biopython-dev] Installing Bio.Geography
In-Reply-To: <1325600614.87653.YahooMailNeo@web160904.mail.bf1.yahoo.com>
References: <mailman.1514.1325559336.3027.biopython-dev@lists.open-bio.org>
	<FBD94D55-5EAC-4C7D-884B-A96880BE11DE@yahoo.com>
	<CAKVJ-_6S2spq6crnqqkEpiE0oGZTT+TXXbOQk2STq94n5iuAHQ@mail.gmail.com>
	<1325600614.87653.YahooMailNeo@web160904.mail.bf1.yahoo.com>
Message-ID: <CAKVJ-_78=9eunF2=bcD_6428Le5x6_=nPijPxpAtQEP_WRGqmA@mail.gmail.com>

On Tue, Jan 3, 2012 at 2:23 PM, JOSE SERGIO HLEAP <sergiohleap at yahoo.com> wrote:
> Thanks for your quick answer Peter... I already went
> trough?http://biopython.org/wiki/BioGeography?at the?Nick Matzke's github. I
> dowloaded the enrire branch in a zip, then build, test and install, using
> the setup... but still does not work. When in a python console I type:
>
>>>> from Bio import Geography
>
> Give me the following taceback:
> ...
> ImportError: cannot import name Geography
>
> ...
>
> am I doing something wrong??
>
> Thanks again for any help you can provide me!
>
> Sergio

Hi again.

My guess is you got the (default) master branch from
Nick's repository, not the Geography branch:
https://github.com/nmatzke/biopython/branches

Try something like this before installing,

git clone https://github.com/nmatzke/biopython.git
cd biopython
git checkout Geography

Peter



From eric.talevich at gmail.com  Tue Jan  3 16:42:51 2012
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 3 Jan 2012 11:42:51 -0500
Subject: [Biopython-dev] Installing Bio.Geography
In-Reply-To: <CAKVJ-_78=9eunF2=bcD_6428Le5x6_=nPijPxpAtQEP_WRGqmA@mail.gmail.com>
References: <mailman.1514.1325559336.3027.biopython-dev@lists.open-bio.org>
	<FBD94D55-5EAC-4C7D-884B-A96880BE11DE@yahoo.com>
	<CAKVJ-_6S2spq6crnqqkEpiE0oGZTT+TXXbOQk2STq94n5iuAHQ@mail.gmail.com>
	<1325600614.87653.YahooMailNeo@web160904.mail.bf1.yahoo.com>
	<CAKVJ-_78=9eunF2=bcD_6428Le5x6_=nPijPxpAtQEP_WRGqmA@mail.gmail.com>
Message-ID: <CAMC681kwmFRMtUk8coN+8VpkKLAawLUfpgWNKmUSXLp0mDDp-A@mail.gmail.com>

On Tue, Jan 3, 2012 at 9:44 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Tue, Jan 3, 2012 at 2:23 PM, JOSE SERGIO HLEAP <sergiohleap at yahoo.com>
> wrote:
> > Thanks for your quick answer Peter... I already went
> > trough http://biopython.org/wiki/BioGeography at the Nick Matzke's
> github. I
> > dowloaded the enrire branch in a zip, then build, test and install, using
> > the setup... but still does not work. When in a python console I type:
> >
> >>>> from Bio import Geography
> >
> > Give me the following taceback:
> > ...
> > ImportError: cannot import name Geography
> >
> > ...
> >
> > am I doing something wrong??
> >
> > Thanks again for any help you can provide me!
> >
> > Sergio
>
> Hi again.
>
> My guess is you got the (default) master branch from
> Nick's repository, not the Geography branch:
> https://github.com/nmatzke/biopython/branches
>
> Try something like this before installing,
>
> git clone https://github.com/nmatzke/biopython.git
> cd biopython
> git checkout Geography
>
> Peter
>
>
Also, for the sub-package to be installed via setup.py, you'll need to add
Bio.Geography to the list of installed packages. In setup.py, around line
207,  you'll see a global variable PACKAGES and a list of module names as
strings. Try adding "Bio.Geography" to this list.

-Eric


From redmine at redmine.open-bio.org  Fri Jan  6 00:53:33 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Fri, 6 Jan 2012 00:53:33 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] (New) Parsing Stockholm
	files fails with some sequence IDs
Message-ID: <redmine.issue-3317.20120106005333@redmine.open-bio.org>


Issue #3317 has been reported by Connor McCoy.

----------------------------------------
Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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From redmine at redmine.open-bio.org  Fri Jan  6 00:53:34 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Fri, 6 Jan 2012 00:53:34 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] (New) Parsing Stockholm
	files fails with some sequence IDs
Message-ID: <redmine.issue-3317.20120106005333@redmine.open-bio.org>


Issue #3317 has been reported by Connor McCoy.

----------------------------------------
Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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From carlcrott at gmail.com  Mon Jan  9 14:36:00 2012
From: carlcrott at gmail.com (carl crott)
Date: Mon, 9 Jan 2012 09:36:00 -0500
Subject: [Biopython-dev] GFF file parsing and error handling
Message-ID: <CAE2MQmCRSBhJ5O1LxAW-BPyFetaCNc_t0R4cR+ZpFkSDwvfL-w@mail.gmail.com>

Hey all,

I'm posting here because I know there has been talk about GFF file parsing
and I'd love to code a bit as soon as I comprehend whats going on with
these files.


I've got this GFF file ( placed in a spreadsheet for readability )

https://docs.google.com/spreadsheet/ccc?key=0AtOqyz8P_fJ0dGVOMzNSM29qUVdjZmZ4emdIQ3U2OUE&hl=en_US#gid=0

line 178 + 179 are the problematic lines

what is going on here?

I know that these genes are listed in reverse order and that a sequence of:
    stop_codon
    CDS
    CDS
    start_codon

the above is a normal gene arrangement.

BUT my guesses as to what happening ( between 178 and 179 ):
1) the gene stretches from the end of one chromosome to another?
2) simply a stop_codon with no attached CDS or start_codon ?

I've successfully managed to parse out the gene intervals and now I'm
working on the error handling.

Thanks,
Carl

-- 
Carl Crott
Web Applications Engineer
www.black-glass.com
412-610-0600


From chapmanb at 50mail.com  Tue Jan 10 16:21:17 2012
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 10 Jan 2012 11:21:17 -0500
Subject: [Biopython-dev] GFF file parsing and error handling
In-Reply-To: <CAE2MQmCRSBhJ5O1LxAW-BPyFetaCNc_t0R4cR+ZpFkSDwvfL-w@mail.gmail.com>
References: <CAE2MQmCRSBhJ5O1LxAW-BPyFetaCNc_t0R4cR+ZpFkSDwvfL-w@mail.gmail.com>
Message-ID: <87boqb5y0y.fsf@fastmail.fm>



Carl;

> I've got this GFF file ( placed in a spreadsheet for readability )
> 
> https://docs.google.com/spreadsheet/ccc?key=0AtOqyz8P_fJ0dGVOMzNSM29qUVdjZmZ4emdIQ3U2OUE&hl=en_US#gid=0
> 
> line 178 + 179 are the problematic lines
> 
> what is going on here?

I'm not sure I understand exactly what is giving you problems. There are
two different genes:

- gene_id 000014 on segment human.ENr12. This has two exons and an
  annotated start and stop codon.

- gene_id 000001 on segment human.ENr13. This has an exon and a start
  codon, but no annotated stop codon.

Does that help?
Brad


From redmine at redmine.open-bio.org  Mon Jan 16 09:30:37 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 16 Jan 2012 09:30:37 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] Parsing Stockholm files
	fails with some sequence IDs
References: <redmine.issue-3317.20120106005333@redmine.open-bio.org>
Message-ID: <redmine.journal-14752.20120116093037@redmine.open-bio.org>


Issue #3317 has been updated by Peter Cock.


Patch cherry-picked and applied to master,
https://github.com/biopython/biopython/commit/ca86f1a27e7af20b4c692cbbe9d54f08e0c65906

Do you fancy preparing a little unit test as well?

Thanks.
----------------------------------------
Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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From redmine at redmine.open-bio.org  Wed Jan 18 22:32:35 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Wed, 18 Jan 2012 22:32:35 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] Parsing Stockholm files
	fails with some sequence IDs
References: <redmine.issue-3317.20120106005333@redmine.open-bio.org>
Message-ID: <redmine.journal-14753.20120118223235@redmine.open-bio.org>


Issue #3317 has been updated by Connor McCoy.


Sure: I added an example of the previously failing sequence to the existing `Tests/Stockholm/funny.sth` file.

https://github.com/cmccoy/biopython/commit/7e9f697c38f0132952b50482fddfea77ce800536

If there's a better place, please let me know.

All tests pass for me.
----------------------------------------
Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


-- 
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From redmine at redmine.open-bio.org  Thu Jan 19 18:11:10 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Thu, 19 Jan 2012 18:11:10 +0000
Subject: [Biopython-dev] [Biopython - Bug #3318] (New)
	Bio.GenBank.LocationParserError on RefSeq files
Message-ID: <redmine.issue-3318.20120119181110@redmine.open-bio.org>


Issue #3318 has been reported by John Eppley.

----------------------------------------
Bug #3318: Bio.GenBank.LocationParserError on RefSeq files
https://redmine.open-bio.org/issues/3318

Author: John Eppley
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


I get the following error trying to parse a file from NCBI RefSeq:
<pre>
Traceback (most recent call last):
  File "/Users/jmeppley/work/delong/projects/scripts/getSequencesFromGbk.py", line 62, in main
    translateStream(instream,options.formatIn,outstream, options.formatOut, options.cds, options.translate)
  File "/Users/jmeppley/work/delong/projects/scripts/getSequencesFromGbk.py", line 87, in translateStream
    for record in records:
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/SeqIO/__init__.py", line 532, in parse
    for r in i:
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/Scanner.py", line 440, in parse_records
    record = self.parse(handle, do_features)
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/Scanner.py", line 423, in parse
    if self.feed(handle, consumer, do_features):
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/Scanner.py", line 395, in feed
    self._feed_feature_table(consumer, self.parse_features(skip=False))
  File "/nfs/Isilon/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/Scanner.py", line 347, in _feed_feature_table
    consumer.location(location_string)
  File "/common/lib/python/2.6/biopython-1.57-py2.6-macosx-10.6-universal.egg/Bio/GenBank/__init__.py", line 975, in location
    raise LocationParserError(location_line)
LocationParserError: join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)
</pre>

The file can be found here (release 51):

The relevant section is:
<pre>
     gene            join(complement(149815..150200),
                     complement(293787..295573),NC_016402.1:6618..6676,
                     181647..181905)
                     /gene="nad1"
                     /trans_splicing
                     /note="exons 1, 2, 3, and 5 on chromosome 1 are
                     trans-spliced with exon 4 on chromosome 3 to form the
                     complete coding region"
                     /db_xref="GeneID:11447159"
</pre>

I think the underscore in the sequence name is confounding the regular expressions in Bio/GenBank/__init__.py. I was able to stop the error by making the following change (first line is mine, second is original):
<pre>
99c99
< _complex_location = r"([a-zA-z][a-zA-Z0-9_]*(\.[a-zA-Z0-9]+)?\:)?(%s|%s|%s|%s|%s)" \
---
> _complex_location = r"([a-zA-z][a-zA-Z0-9]*(\.[a-zA-Z0-9]+)?\:)?(%s|%s|%s|%s|%s)" \
</pre>

I haven't really tested it to see if the output is correct, though. It does pass the doctests.


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From p.j.a.cock at googlemail.com  Fri Jan 20 10:46:18 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 20 Jan 2012 10:46:18 +0000
Subject: [Biopython-dev] NCBI adoption of AGP v2.0 and new qualifiers in
	GenBank/EMBL
Message-ID: <CAKVJ-_68TGz776oFFDtTNwtS3L6EDJjiW2cZDQN=-rTSo0_3OQ@mail.gmail.com>

Dear all,

I just spotted this via the @NCBI twitter feed,
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/agp_spec_change.shtml

In addition to the NCBI switch from AGP v1.1 to v2.0, the INSDC have
recently added a new feature type called "assembly_gap", and the
associated qualifiers "gap_type" and "linkage_evidence" to the INSDC
Feature Table Definitons.

Quoting from version 10.0, dated Dec 2011
http://www.insdc.org/documents/feature_table.html#7.2
> Feature Key           assembly_gap
>
>
> Definition            gap between two components of a CON record that is
> 		      part of a genome assembly;
>
> Mandatory qualifiers  /estimated_length=unknown or <integer>
> 		      /gap_type="TYPE"
>                       /linkage_evidence="TYPE" (Note: Mandatory only if the
>                       /gap_type is "within scaffold" or "repeat within
>                       scaffold".If there are multiple types of linkage_evidence
>                       they will appear as multiple /linkage_evidence="TYPE"
>                       qualifiers. For all other types of assembly_gap
>                       features, use of the /linkage_evidence qualifier is
>                       invalid.)
>
> Comment               the location span of the assembly_gap feature for an
> 		      unknown gap is 100 bp, with the 100 bp indicated as
> 		      100 "n"'s in sequence.
>

i.e. DDBJ, ENA & GenBank flat-files will start to use the "assembly_gap"
features to display information derived from version 2.0 AGP files from
10th Feb 2012. Probably this will affect the XML variants as well.

Unless any of the parsers/writers for GenBank or EMBL flat files use a white
list approach, the new feature key and qualifiers shouldn't cause a problem.

Peter


From chapmanb at 50mail.com  Wed Jan 25 02:14:58 2012
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 24 Jan 2012 21:14:58 -0500
Subject: [Biopython-dev] Bug in Bio.Blast.NCBIWWW ?
In-Reply-To: <4F1F0E020200009500004335@gwsmtp2.uni-regensburg.de>
References: <4F1F0E020200009500004335@gwsmtp2.uni-regensburg.de>
Message-ID: <87vco0wmsd.fsf@fastmail.fm>


Micheal;
Thanks for the e-mail and problem report. For Biopython issues, the best
approach is to e-mail the development list (cc'ed here). Since it's a
community project, there are a wide variety of contributors that can
provide help and expertise.

In this particular case, I am not especially familiar with python 3 as
I'm still a python 2 user myself. Peter, Eric and other folks have been
doing a lot of work on this, so hopefully they can confirm or provide
additional details.

Thanks again,
Brad

> Dear Mr. Chapman,
> 
> I perhaps found a bug in the Bio.Blast.NCBIWWW module.
> But since I'm using Python 3.2.2 and didn't test this with Python2.x, I don't know if this is a Python2/Python3 issue.
> 
> When I try to execute the following line of code (where contig is a string):
> 
>     resultHandle = NCBIWWW.qblast('blastn', 'nr', contig)
> 
> I get the following error message:
> 
> Traceback (most recent call last):
>   File "/home/michael/python/gb/sheet11/ex80_all-contigs.py", line 575, in <module>
>     blastContig(contigs[i])
>   File "/home/michael/python/gb/sheet11/ex80_all-contigs.py", line 441, in blastContig
>     resultHandle = NCBIWWW.qblast('blastn', 'nr', contig, hitlist_size=1)
>   File "/usr/local/lib/python3.2/dist-packages/Bio/Blast/NCBIWWW.py", line 122, in qblast
>     handle = urllib.request.urlopen(request)
>   File "/usr/lib/python3.2/urllib/request.py", line 138, in urlopen
>     return opener.open(url, data, timeout)
>   File "/usr/lib/python3.2/urllib/request.py", line 367, in open
>     req = meth(req)
>   File "/usr/lib/python3.2/urllib/request.py", line 1066, in do_request_
>     raise TypeError("POST data should be bytes"
> TypeError: POST data should be bytes or an iterable of bytes. It cannot be str.
> 
> 
> After trying different things, I found that this can be fixed by replacing
> 
>     message = urllib.parse.urlencode(query)
> 
> in lines 113 and 145 in the NCBIWWW.py script by
> 
>     message = urllib.parse.urlencode(query, encoding='ascii')
>     message = bytes(message, 'ascii')
> 
> If this is not a Python2/Python3 thing, you perhaps want to use this fix for the next version of Biopython.
> 
> Yours sincerely,
> Michael Grauvogl
> 
> 
Non-text part: text/html


From p.j.a.cock at googlemail.com  Wed Jan 25 13:13:59 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 25 Jan 2012 13:13:59 +0000
Subject: [Biopython-dev] Bug in Bio.Blast.NCBIWWW ?
In-Reply-To: <87vco0wmsd.fsf@fastmail.fm>
References: <4F1F0E020200009500004335@gwsmtp2.uni-regensburg.de>
	<87vco0wmsd.fsf@fastmail.fm>
Message-ID: <CAKVJ-_7wwx_GpYbrNG+LzQ92aHMDz0HQKNAHyYF3GEJpuR0ptA@mail.gmail.com>

On Wed, Jan 25, 2012 at 2:14 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Micheal;
> Thanks for the e-mail and problem report. For Biopython issues, the best
> approach is to e-mail the development list (cc'ed here). Since it's a
> community project, there are a wide variety of contributors that can
> provide help and expertise.
>
> In this particular case, I am not especially familiar with python 3 as
> I'm still a python 2 user myself. Peter, Eric and other folks have been
> doing a lot of work on this, so hopefully they can confirm or provide
> additional details.
>
> Thanks again,
> Brad

Hi all,

Yes, as you guessed Michael, this is a Python 3 problem. This
should work now - doing something similar to your suggestion:
https://github.com/biopython/biopython/commit/7bd519e68974185c7b489e2415c9ee3b6f1d7ac4

Thanks for the reminder - there are still a few things to fix under
in Biopython under Python 3.

Peter


From redmine at redmine.open-bio.org  Mon Jan 30 15:59:43 2012
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 30 Jan 2012 15:59:43 +0000
Subject: [Biopython-dev] [Biopython - Bug #3317] (Resolved) Parsing
	Stockholm files fails with some sequence IDs
References: <redmine.issue-3317.20120106005333@redmine.open-bio.org>
Message-ID: <redmine.journal-14756.20120130155943@redmine.open-bio.org>


Issue #3317 has been updated by Peter Cock.

Status changed from New to Resolved
% Done changed from 0 to 100

Thanks,
https://github.com/biopython/biopython/commit/d439ba5c6a5a501ba859cce02c746f7d75b2914e
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Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

Author: Connor McCoy
Status: Resolved
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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