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Gmane
From: Alexey Morozov <alexeymorozov1991 <at> gmail.com>
Subject: Re: Failure to merge two scripts
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 20th June 2013 02:11:04 UTC (over 3 years ago)
2013/6/12 

> I am a novice at PERL and came across a script to sort sequences in a
> mulitple sequence fasta file by name.  It does what it should.  However,
it
> does give the following error:
> "Replacement list is longer than search list at
> C:/Perl/site/lib/Bio/Range.pm line 251."
> I'm not too worried about this as it does work.
>
> I have another PERL script that takes uniprotkb fasta headers and trims
> them to just the organism name and strain.  I would like to run this
script
> and the sorting script together on a series of files and then concatenate
> the results.  I can run the scripts separately and they work.  I tried to
> put my trimming script before the sorting script in a single script, and
it
> no longer works.
>
> Could anyone take a look and see if there is something simple I am doing
> wrong?   Or, is there a better way to do this? I will need to do this
> repetitively on batches of 33 files. I am running PERL 5.12.2 on Windows
XP
> sp3 with BioPerl 1.6.1.
>
> Attached:
> L1.fasta - example Uniprot file to be trimmed and sorted
> L1ss.fasta - desired output from running the scripts in sequence
> fastaSortByName.pl - script from Naoki Takebayashi
> (
> http://raven.iab.alaska.edu/~ntakebay/teaching/programming/perl-scripts/perl-scripts.html
> )
> shortenIDs.pl - my fasta header trimming script
> shortsort.pl - my attempt at merging the two scripts above into a single
> one
>
> _______________________________________________
> Bioperl-l mailing list
> [email protected]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


To be honest, I'm to lazy to read your scripts, but have you tried glueing
them together with some bash?
Something like "Script 1 | Script 2" or "Script1 -foo; Script2 -bar" must
do the job. Plus, if you are novice (and willing to learn), it may be
useful for you to rewrite the whole thing from the scratch in a single
script, it seems to be about 50 lines of code at most.
-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
 
CD: 3ms