From shameer at ncbs.res.in  Tue Aug  7 03:39:49 2007
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Tue, 7 Aug 2007 11:39:49 +0400 (RET)
Subject: [BioRuby] Ruby Newbie
Message-ID: <39717.192.168.1.186.1186472389.squirrel@mail.ncbs.res.in>

Dear All,

I am a Ruby/Bio-Ruby newbie. Please direct me to some good resource to
start learning Ruby by using Bio-Ruby classes.

cheers,
-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in


From ngoto at gen-info.osaka-u.ac.jp  Thu Aug  9 10:40:18 2007
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 9 Aug 2007 23:40:18 +0900
Subject: [BioRuby] Ruby Newbie
In-Reply-To: <39717.192.168.1.186.1186472389.squirrel@mail.ncbs.res.in>
References: <39717.192.168.1.186.1186472389.squirrel@mail.ncbs.res.in>
Message-ID: <20070809144018.57D9B1CBC558@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Tue, 7 Aug 2007 11:39:49 +0400 (RET)
"Shameer Khadar" <shameer at ncbs.res.in> wrote:

> Dear All,
> 
> I am a Ruby/Bio-Ruby newbie. Please direct me to some good resource to
> start learning Ruby by using Bio-Ruby classes.

BioRuby in Anger
http://dev.bioruby.org/wiki/en/?BioRuby+in+Anger

Tutorial.rd (bundled with bioruby-X.X.X.tar.gz)
http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/doc/Tutorial.rd?rev=HEAD&cvsroot=bioruby&content-type=text/plain

Tutorial.rd on Bioruby Wiki (older than above, and
parse error occurred?)
http://dev.bioruby.org/wiki/en/?Tutorial.rd

However, above documents may be too difficult for newbies
who don't know Ruby. If so, you may also want to read
introductions and tutorials of Ruby itself, for example,
http://tryruby.hobix.com/ (interactive tutorial of Ruby is available)

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
Department of Genome Informatics, Genome Information Research Center,
Research Institute for Microbial Diseases, Osaka University, Japan

From ngoto at gen-info.osaka-u.ac.jp  Thu Aug  9 12:15:45 2007
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Fri, 10 Aug 2007 01:15:45 +0900
Subject: [BioRuby] Wu-blast report parsing issue
In-Reply-To: <4702CF45-61F8-43CF-B758-083EA59AD10B@unil.ch>
References: <4702CF45-61F8-43CF-B758-083EA59AD10B@unil.ch>
Message-ID: <20070809161545.D4A971CBC3F7@idnmail.gen-info.osaka-u.ac.jp>

Hello,

I'm sorry it's too late.

It seems this error occurred in the line 29 of your xml file
         <Hit_def></Hit_def>
The content of the Hit_def is empty.
 
For sequences with no definition, NCBI BLAST outputs
          <Hit_def>No definition line found</Hit_def>
and the content of the Hit_def is not empty.

This means the output of WU-BLAST xml is sometimes
incompatible with the NCBI BLAST.

However, because this is very small difference,
I think this can be covered with BioRuby.


I can repeat the same error with the following data:

(saved as database.fst)
--------------------------------------------------------------
>lcl|EXAMPLE
AGACATAACCCAAACAGAATAACCTGAAAGAGACCCACGACCATGCAGGGGACCTGGATG
GTGCTGTTGGCACTGATATTGGGCACCTTCGGGGAGCTTGCTATGGCCTTACAGTGCTAC
ACCTGTGCGAATCCTGTGAGTGCATCCAACTGTGTCACCACCACCCACTGCCACATCAAT
GAAACCATGTGCAAGACTACGCTCTACTCCCTGGAGATTGTTTTCCCTTTCCTGGGGGAC
TCCACGGTGACCAAGTCCTGCGCCAGCAAGTGTGAGCCTTCGGATGTGGATGGCATTGGG
CAAACCCGGCCAGTGTCCTGCTGCAATTCTGACCTATGCAACGTGGATGGGGCACCCAGC
CTGGGCAGTCCTGGTGGCCTGCTCCTTGCCCTGGCACTTTTCTTGCTCTTGGGTGTCCTG
CTGTAAAGCCATGGCCATCTAGCTCCACTCCCTTGTCCCTGACATCCCAGTTCCCTAATG
CCTAGAAGAAATACAATGGCCATCTGC
--------------------------------------------------------------

(saved as query.fst)
--------------------------------------------------------------
>Contig1
AGACATAACCCAAACAGAATAACCTGAAAGAGACCCACGACCATGCAGGGGACCTGGATG
GTGCTGTTGGCACTGATATTGGGCACCTTCGGGGAGCTTGCTATGGCCTTACAGTGCTAC
ACCTGTGCGAATCCTGTGAGTGCATCCAACTGTGTCACCACCACCCACTGCCACATCAAT
GAAACCATGTGCAAGACTACGCTCTACTCCCTGGAGATTGTTTTCCCTTTCCTGGGGGAC
TCCACGGTGACCAAGTCCTGCGCCAGCAAGTGTGAGCCTTCGGATGTGGATGGCATTGGG
CAAACCCGGCCAGTGTCCTGCTGCAATTCTGACCTATGCAACGTGGATGGGGCACCCAGC
CTGGGCAGTCCTGGTGGCCTGCTCCTTGCCCTGGCACTTTTCTTGCTCTTGGGTGTCCTG
CTGTAAAGCCATGGCCATCTAGCTCCACTCCCTTGTCCCTGACATCCCAGTTCCCTAATG
CCTAGAAGAAATACAATGGCCATCTGC
--------------------------------------------------------------
The sequence of query.fst is completely the same as database.fst.
Only definition line is different.

commands for WU BLAST:
% xdformat -n database.fst
% wu-blastall -p blastn -i query.fst -d database.fst \
  -o wu-blastn.xml -e 1e-10 -m 7 -F F

commands for NCBI BLAST:
% formatdb -i database.fst -p F -o
% blastall -p blastn -i query.fst -d database.fst \
  -o ncbi-blastn.xml -e 1e-10 -m 7 -F F

Report of WU BLAST:
          <Hit_num>1</Hit_num>
          <Hit_id>lcl|EXAMPLE</Hit_id>
          <Hit_def></Hit_def>
          <Hit_accession>EXAMPLE</Hit_accession>
          <Hit_len>507</Hit_len>

Report of NCBI BLAST:
          <Hit_num>1</Hit_num>
          <Hit_id>lcl|EXAMPLE</Hit_id>
          <Hit_def>No definition line found</Hit_def>
          <Hit_accession>EXAMPLE</Hit_accession>
          <Hit_len>507</Hit_len>

The Hit_def line of WU-BLAST is incompatible with NCBI BLAST
for sequences with no definitions.

The versions of WU BLAST and NCBI BLAST were:
2.0MP-WashU [04-May-2006] [linux26-i786-ILP32F64 2006-05-09T12:19:58]
blastn 2.2.15 [Oct-15-2006]


> I've tried feeding my script normal (-m0) wublast output too. It  
> doesn't crash - but @reportsArray.length == 0).

Bio::Blast.reports can only be used for XML output.
For normal format,

49:		@reportsArray = Bio::FlatFile.new(nil, @file).to_a

would work.

Thank you,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


On Tue, 24 Apr 2007 21:03:56 +0200
Yannick Wurm <Yannick.Wurm at unil.ch> wrote:

> Hello,
> 
> I've generated a blast report using wu-blastall with -m7 to get xml  
> output.
> It should be easy to get this into ruby, but I'm having a hard time.
> 
> Here's the error I get:
> #~/ruby/dotGraphOfStrongHits.rb simple.xml simple.xml.dot 1.0e-5
> /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/xmlparser.rb:158:in  
> `clone': can't clone NilClass (TypeError)
>          from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/xmlparser.rb: 
> 158:in `xmlparser_parse_hit'
>          from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/xmlparser.rb: 
> 72:in `xmlparser_parse'
>          from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/xmlparser.rb: 
> 41:in `xmlparser_parse'
>          from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/report.rb: 
> 66:in `auto_parse'
>          from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/report.rb: 
> 89:in `initialize'
>          from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast.rb:115:in  
> `reports'
>          from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast.rb:109:in  
> `reports'
>          from /Users/yannickwurm/ruby/wublastReportParser.rb:49:in  
> `loadBlastReport'
>          from /Users/yannickwurm/ruby/dotGraphOfStrongHits.rb:30:in  
> `parseFile'
>          from /Users/yannickwurm/ruby/dotGraphOfStrongHits.rb:61
> 
> The corresponding lines of wublastReportParser.rb are:
> 48:		@file = File.open(@blast_report, IO::RDONLY)
> 49:		@reportsArray = Bio::Blast.reports(@file)
> 
> 
> Does wublast not respect the standard blast xml output?
> I've tried feeding my script normal (-m0) wublast output too. It  
> doesn't crash - but @reportsArray.length == 0).
> 
> My xml-ed blast report is here:
> http://wwwpeople.unil.ch/yannick.wurm/simple.xml
> 
> 
> What am I doing wrong? Do you have ideas how to solve this issue?
> 
> 
> My version info:
> 	wu-blastall 2.2.6
> 	ruby 1.8.4 (2005-12-24) [powerpc-darwin]
> 	bio.rb,v 1.84 2007/04/05
> 
> Thanks in advance for any pointers!
> yannick
> 
> --------------------------------------------
>           yannick . wurm @ unil . ch
> Ant Genomics, Ecology & Evolution @ Lausanne
>    http://www.unil.ch/dee/page28685_fr.html
> 
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From jan.aerts at bbsrc.ac.uk  Tue Aug 14 10:36:32 2007
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Tue, 14 Aug 2007 15:36:32 +0100
Subject: [BioRuby] ruby API to ensembl core database
Message-ID: <1F16910BB8546C4DA5526FABB0C98D093C09F3@ebre2ksrv1.ebrc.bbsrc.ac.uk>

All,

I've released a ruby API to the Ensembl core database, similar to the
one available for perl. Mitsuteru already wrote a very useful interface
to the ExportView functionality of the Ensembl website, but this API is
linked to the underlying mysql database and attempts to copy the
functionality of the full-blown perl API. This includes slices,
projections and transformations. A tutorial for the API is available at
the homepage where you can also download the gem (for the Ensembl core
people: 'gem' refers to a type of file, not to a developer who lost
touch with reality).

I've tested quite a bit, and hope there are no bugs left in the code...
If you find any: let me know.

For more information, see http://bioruby-annex.rubyforge.org and
http://saaientist.blogspot.com

If you have any suggestions, please don't hesitate to contact me. And if
anyone would be interested to help me in the future development of this
API, I'd be very happy.

Big big thanks to the Ensembl core team for helping me (and being my
hosts as a Geek for a Week).

Dr Jan Aerts
Bioinformatics Group
Roslin Institute
Roslin EH25 9PS
Scotland, UK
tel: +44 131 527 4198
skype: aerts_ri

----...and the obligatory disclaimer----
Roslin Institute is a company limited by guarantee, registered in
Scotland (registered number SC157100) and a Scottish Charity (registered
number SC023592). Our registered office is at Roslin, Midlothian, EH25
9PS. VAT registration number 847380013.

The information contained in this e-mail (including any attachments) is
confidential and is intended for the use of  the addressee only. The
opinions expressed within this e-mail (including any attachments) are
the opinions of the sender and do not necessarily constitute those of
Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
Institute.


From ktemme at gmail.com  Thu Aug 16 23:54:26 2007
From: ktemme at gmail.com (Karsten Temme)
Date: Thu, 16 Aug 2007 20:54:26 -0700
Subject: [BioRuby] Parse string containing GenBenk file?
Message-ID: <67c2cfda0708162054v6295dc25x881db2a50a51a6ec@mail.gmail.com>

Can anyone point me to a method for creating a Bio object from a
string that contains a Genbank file?

For example, I have a Genbank file and its contents have been read
into a single string.  I am unable to use Bio::FlatFile.auto(string)
to create a Bio object.

Thanks for the help,
Karsten

From ngoto at gen-info.osaka-u.ac.jp  Fri Aug 17 00:30:27 2007
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto)
Date: Fri, 17 Aug 2007 13:30:27 +0900
Subject: [BioRuby] Parse string containing GenBenk file?
In-Reply-To: <67c2cfda0708162054v6295dc25x881db2a50a51a6ec@mail.gmail.com>
References: <67c2cfda0708162054v6295dc25x881db2a50a51a6ec@mail.gmail.com>
Message-ID: <20070817131318.6647.NGOTO@gen-info.osaka-u.ac.jp>

Hi,

If you have a string with single GenBank entry,
you can use Bio::GenBank.new(string).
For example,

  require "bio"
  str = <<__EOF__
LOCUS       A00001                   335 bp    DNA     linear   PAT 11-MAY-2001
DEFINITION  Cauliflower mosaic virus satellite cDNA.
ACCESSION   A00001
VERSION     A00001.1  GI:58418
KEYWORDS    .
SOURCE      Cauliflower mosaic virus
  ORGANISM  Cauliflower mosaic virus
            Viruses; Retro-transcribing viruses; Caulimoviridae; Caulimovirus.
REFERENCE   1  (bases 1 to 335)
  AUTHORS   Baulcombe,D.C., Mayo,M.A., Harrison,B.D. and Bevan,M.W.
  TITLE     Modification of plant viruses or their effects
  JOURNAL   Patent: EP 0242016-A 1 21-OCT-1987;
            AGRICULTURAL GENETICS COMPANY LIMITED
FEATURES             Location/Qualifiers
     source          1..335
                     /organism="Cauliflower mosaic virus"
                     /mol_type="unassigned DNA"
                     /db_xref="taxon:10641"
     misc_feature    1..335
                     /note="satellite DNA"
ORIGIN
        1 gttttgtttg atggagaatt gcgcagaggg gttatatctg cgtgaggatc tgtcactcgg
       61 cggtgtggga tacctccctg ctaaggcggg ttgagtgatg ttccctcgga ctggggaccg
      121 ctggcttgcg agctatgtcc gctactctca gtactacact ctcatttgag cccccgctca
      181 gtttgctagc agaacccggc acatggttcg ccgataccat ggaatttcga aagaaacact
      241 ctgttaggtg gtatgagtca tgacgcacgc agggagaggc taaggcttat gctatgctga
      301 tctccgtgaa tgtctatcat tcctacacag gaccc
//
__EOF__
  
  gb = Bio::GenBank.new(str)
  p gb


If you have a string with multiple entries,
or the string might be other than GenBank (e.g. EMBL.),
using StringIO is better.

  require 'stringio'
  Bio::FlatFile.auto(StringIO.new(string))


Regards,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


> Can anyone point me to a method for creating a Bio object from a
> string that contains a Genbank file?
> 
> For example, I have a Genbank file and its contents have been read
> into a single string.  I am unable to use Bio::FlatFile.auto(string)
> to create a Bio object.
> 
> Thanks for the help,
> Karsten
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From raoul.bonnal at itb.cnr.it  Wed Aug 29 05:21:09 2007
From: raoul.bonnal at itb.cnr.it (Raoul Jean Pierre Bonnal)
Date: Wed, 29 Aug 2007 11:21:09 +0200
Subject: [BioRuby] Blast Format8 hsps' patch
Message-ID: <1188379270.9964.6.camel@localhost>

Hi Guys, 
I found a bug in the parser. Take this example:


contig00002     gi|15902044|ref|NC_003098.1|    99.71   1399    4
0       5       1403    414678  416076  0.0     2742
contig00002     gi|118090026|ref|NC_003028.2|   98.25   858     5
1       556     1403    448891  449748  0.0     1592
contig00003     gi|116515308|ref|NC_008533.1|   99.67   2997    7
2       1       2994    423818  426814  0.0     5848
contig00003     gi|15902044|ref|NC_003098.1|    99.67   2997    7
2       1       2994    416288  419284  0.0     5848
contig00003     gi|118090026|ref|NC_003028.2|   99.60   2997    9
2       1       2994    449959  452955  0.0     5832
contig00004     gi|118090026|ref|NC_003028.2|   98.08   2238    40
3       5       2242    453000  455234  0.0     4072
contig00004     gi|116515308|ref|NC_008533.1|   97.94   2238    43
3       5       2242    426859  429093  0.0     4048
contig00004     gi|15902044|ref|NC_003098.1|    97.94   2238    43
3       5       2242    419329  421563  0.0     4048


about last contig00003 the parser create an hit with 2 hsps, putting
togheter results from last contig00003 and first contig00004, this is
wrong. The code check only if the target is different from the prev one,
in this case the target is the same but the query is different. 

In attach the patch to solve the problem, I put a chk on the query too.

Actually I don't know if the problem is present with other parsers.

Best regards.

--
Ra