[Bioperl-guts-l] [Bug 2392] New: Bio::Tools::Geneid - unable to parse target id using _target_id

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Nov 2 15:58:22 EDT 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2392

           Summary: Bio::Tools::Geneid - unable to parse target id using
                    _target_id
           Product: BioPerl
           Version: unspecified
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dschneid at bsd.uchicago.edu


I am trying to pull out the sequence ID from my FASTA files using the
Bio::Tools::Geneid _target_id module. This function ends up giving me nothing
since it is looking for a ">" FASTA header. I am currently using the latest
version of geneID, using the geneid (default) output format.

############

here is an example of a geneid output where I am trying to fetch DDB0232583


## date Fri Sep 28 18:48:00 2007
## source-version: geneid_v1.3 -- geneid at imim.es
# Sequence DDB0232583 - Length = 196197 bps
# Optimal Gene Structure. 84 genes. Score = 10080.86
# Gene 1 (Forward). 2 exons. 138 aa. Score = 22.55
   First      187      259      -4.24   + 0 1    8.34    9.35   -7.17    0.00AA
  1: 25 DDB0232583_1
Terminal     1778     2118      26.78   + 2 0   -4.01    5.49   71.08    0.00AA
 25:138 DDB0232583_1

# Gene 2 (Reverse). 5 exons. 679 aa. Score = 103.62
Terminal     3271     3542       9.96   - 2 0    2.20    5.13   31.58    0.00AA
589:679 DDB0232583_2
Internal     3840     4724      59.44   - 2 1    5.72    1.11   131.05   0.00AA
294:589 DDB0232583_2
Internal     4823     4946       4.39   - 0 1    2.56   12.21   13.01    0.00AA
253:294 DDB0232583_2
Internal     5261     5495      14.84   - 1 0    7.77   11.83   29.08    0.00AA
174:252 DDB0232583_2
   First     5632     6152      14.99   - 0 2    7.19    8.94   32.85    0.00AA
  1:174 DDB0232583_2

#################################


# in order to get this function to work properly I had to go in and make some
slight changes to the Geneid.pm file.


#first I added a new "or" statement 

if (/^>(\S+)\|GeneId/ or /^# Sequence (\S+)/)  ## ln 150


# also I removed "unless defined $self->_target_id;" inorder to continue 
# generating new sequence IDs in the case there are many outputs in one file

$self->_target_id($target_id) unless defined $self->_target_id;

# becomes

$self->_target_id($target_id);

###########

# patch file to be attached


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