[Bioperl-l] Failure to merge two scripts

[tehanson at udel.edu]

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 
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