Hey guys I'm back with another question. I'm trying to split a fasta into individual .seq files. So far I have this... 
use strict;
use warnings;

$/ = ">";

my $fastafile = 'j:\summer\begomo_genomes2.fasta';
my ($OUT, $IN);

print "Input: $fastafile\n";
open my $ifh, "<", $fastafile or die "cannot open $fastafile: $!\n";

while (my $chunk = <$ifh>){
   $chunk = lc $chunk;  
         my ($accession) = $chunk =~ /gi\|(\d+)/;
         my ($acronym) = $chunk =~ /\|\s+(.*),/;
            $acronym =~ s/\[|\]|\:|\d+|\-\///g;
            $acronym =~ s/\s/_/g; 
            $acronym =~ s/dnaa/dna_a/g;
            $acronym =~ s/dnab/dna_b/g;
         my ($sequence) = $chunk =~ /([a|c|t|g]+)\s+/;

   my $outfile = "j:\\summer\\begomo\\${accession}_${acronym}.seq";

open my $ofh, ">", $outfile or die "cannot open $outfile: $!\n";

print "Creating $outfile\n";

print $ofh "$accession $acronym\n^^\n$sequence";

close $ofh;

}

[download]
One of my problems is my ($sequence) = $chunk =~ /([a|c|t|g]+)\s+/; I know this isn't right, but I have gone through a lot of different syntax's for this to no avail. What's the best way to parse the sequence out?

My other problem is that $chunk is only the first line, why is it doing this?

Here is a sample of the file I am working with...
>gi|9626081|ref|NC_001359.1| Pepper huasteco yellow vein virus DNA A, 
+complete sequence
GGCCATCCGTTATAATATTACCGGATGGCCGACCGCTTACCTTATCTATCCGTACTGCTTTATTTGAATT
AAAGATGTTACTTTTATGCTATCCAATGAAGCGTAGCGTCTGGGAAGCTTAGTTATCAGTTCCAGACGTG
GGGACCAAGTAGTGTATGACCACTTTATTGACTGTCAGCTTTATAAATTGAAATTAAAACATAAGTGGTC
CATGTACCTTTAATTCAAAATGCCTAAGCGTGATGCTCCTTGGCGATTAACGGCGGGGACCGCCAAGATT
AGCCGAACTGGCAATAATTCACGGGCTCTTATCATGGGCCCGAGTACTAGCAGGGCCTCAGCTTGGGTTA
ATCGCCCAATGTACAGGAAGCCCCGGATTTATCGTATGTACAGAACTCCGGATGTGCCGAAAGGTTGTGA
AGGTCCCTGTAAGGTTCAATCGTTTGAACAACGACATGACGTCTCTCATGTTGGTAAGGTTATTTGTATA
TCCGACGTAACTCGTGGTAATGGTATTACCCATCGTGTTGGCAAACGATTCTGCGTTAAGTCTGTCTATA
TTCTGGGCAAAATCTGGATGGATGAAAATATTAAGTTGAAGAACCATACCAACAGTGTCATGTTTTGGTT
GGTTAGGGATAGGAGACCCTACGGTACGCCTATGGATTTTGGCCAAGTCTTTAACATGTATGACAACGAG
CCCAGTACCGCTACTGTGAAGAACGATCTTCGGGATCGTTATCAAGTTATGCATAGATTCTATGCTAAGG
TCACTGGTGGGCAATATGCAAGCAACGAGCAAGCCTTGGTTAGGCGTTTCTGGAAGGTGAACAACCATGT
TGTGTATAACCATCAAGAAGCTGGGAAATATGAGAACCACACGGAGAATGCGCTGTTATTGTATATGGCA
TGTACTCATGCATCTAATCCCGTGTATGCAACACTCAAAATTCGGGTCTATTTTTATGACTCGATAATGA
ATTAATAAAGTTTGTATATTATTTCATGATTCTCAAGTACAGCATTGACATAACGTTTGTCTGTAGCAAA
CGAAACAGCCCTAATTACATTGTTAACTGAAATAAGACCTAAGTTATCTAGATAAAACATGACAAGCAAT
TTAAATCTATTTAAGTAAATCTGCCCAGAAATCGTCGTCAACGTCGTCCAGACTTGGAAGTTGAAGTAGG
CTTTGTGGAGACCCAACGCTGTCCTCATGTTGTGGTTTGCTCTGACTTGAATGTGAAATACCCGGCTGCG
TGTGTACATTGGCGTCTCCACTAGCCGTATTTTGAAATATAGGGGATTTCGAAGCTCCCAGATAAAAACG
CCATTCGCTGCTTGAGCTGCAGTGATGGGTACCCCGGTGCGTAAATCCATTGTTAACACAGTTAATATGT
ATATAAATTGAACAGCCGCAAGCGAGATCAATCCTTCTACGTCGTATCTGTCTCTTTGCAAATCTATGGC
GAAGTTTGACTTCCGGTGGTGAAGATAGCTTCTTCGATGGTGACGTAGATGGCGTTTTTTTGGACCCAGT
CATTGAGGCTCCTATTTTTCTCTTCGCTGAGGTAGTCTTTATAGGAAGACTGGGGGCCCGGATTGCAAAG
AAAGATAGTGGGTATCCCACCTTTAATTTGAATTGGTTTGCCGTATTTGCAGTTTGATTGCCAATCCCGT
TGGGCCCCCATAAACTCTTTAAAGTGCTTAACATAATGCGGAGGGATGTCATCAATGACGTTATACCATG
CATTATTGGAGTAGATTTTTGGGCTGAGATCCATATGACCACATATGTAATTGTGTGGGCCGAGACTTCG
GGCCCATAATGTTTTGCCTGTCCGTGAAGGACCCTCGACCACTAATGACAATGGTCTCATTGGCCGCGCA
GCGGCATCACATACATTATCAGACACCCATTGTGTCATTATTGCAGGCACATTATTAAAGGACGCCTGTT
GAAATGGAGGAACCCACGGTTCCGGGGGAGTTTGGAATATCCGATTAGCGTTTGACACAATGTTATGAAA
TTGGAGGAAGAAATGCTGAGGTTGTTCTTCCTTTATGATCTGCAGAGCTTCTTCTGCAGATGCTGAATTT
AACGCCTTAGCATATGTGTCATTAGCAGACTGCTGTCCTCCTCTAGCAGATCTGCCGTCTATTTGGAATT
CTCCCCATTCTACGGTATCGCCGTCTTTGTCGATGTACGTCTTGACGTCGGAGCTTGATTTAGCTCCCTG
AATGTTCGGATGGAAATGTGCTGATCTGGTAGAGGATACGAGGTCAAAGAATCGGTTGTTCGTGCATTGG
TATTTTCCTTCGAACTGAATAAGCACGTGCAGATGAGGTTGCCCATCTTCATGAGATTCTTTGCAAATTT
TGATGTACTTCTTGTTTACCGGCGTCGAGAGGTTTTGTAGTTGAGCGAGACGCTCTTCTTTGGAAATGGA
ACATTGTGGATAGGTGAGGAAATAATTCTTGGCATTTAAACGAAATCGTTTAGGTAATGGCATATTTGTA
ATAAGAGAGGTGTACACCGATTGGAGCTCTTTAACCTGGGCTTATTGTATCGGTGTATTGGTAGCCAATA
TATAGTATATGGGAGTTATCTAGGATCTTCGTACACGTGAG

>gi|9626131|ref|NC_001369.1| Pepper huasteco yellow vein virus DNA B, 
+complete sequence
GGCCATCCGTTATAATATTACCGGATGGCCGACCGCTTCCACTCTCTTTCCTTTGGGACAGCTGGCGCGC
ACTATGTATTATGTTTACGTGGCATCATGTGGGTCGTTGGATGAATTCAATCGCGCGCCTTCATTTCAAA
TTAAAGTGTGTGTCCATACATCGAGAAATGTGTAATGACGTGGAGCGTTCTCCACCATTCCTGAATCGTT
AGATAATTGTTTGACCAGGACCACAGCTGTCATTTGGGACCACACGTCCTTTGGGACCACCACTATAATG
ATAATGTTTCCTGTTATTGCGGTCCACGTGGTCCAATTAAATTGCACCTCGCGAGTCTACATATCCACAA
TTTTGAATATCCTATTCTATAAAATGGCTTCCATTTTTATATTCAAAATTATATTCACATCTCTTTTAAT
ATATATTTATCTTTAAGCAATTTAATATGTATTCTACTAGATTTAGACGTGGGTTATCCTATGTTCCACG
GCGTTATAATCCACGTAATTATGGTTTTAAACGTACATTCGTCGTTAAACGTGGTGATGCTAAACGACGT
CAGACTCAAGTGAAGAAACTAACAGAAGATGTTAAAATGTCATCACAACGCATCCATGAAAATCAATATG
GTCCAGAATTTGTCATGGCGCATAATACAGCAATATCTACATTCATCAATTATCCCCAACTGTGTAAGAC
TCAGCCCAATCGTAGTAGGTCATATATTAAGTTAAAATCGTTACATTTTAAGGGAACCTTAAAGATCGAA
CGTGTTGGGTCTGAGGTAAATATGGCTGGGTTAAATCCGAAGATTGAGGGTGTGTTTACTGTGGTTTTAG
TTGTTGACCGTAAGCCACATTTGAATCCTACTGGTAACTTGCTACAGTTTGACGAGTTATTTGGTGCAAG
AATTCACAGTCTAGGGAACTTAGCCGTTACCCCGGCGTTGAAAGAACGGTTCTACATACTGCATGTGTTG
AAGCGAGTTATCTCCGTTGAGAAGGATAGTATGATGCTGGACCTAGAAGGATCCACTTGTCTCTCTAGTC
GGCGTTATAATTGTTGGTCTACATTTAAGGACCTTGATCCTTCGTCATGTAACGGCGTCTATGATAATAT
AAGCAAAAACGCCATATTAGTTTATTATTGTTGGATGTCGGATGCTATGTCTAAGGCATCCACATTTGTA
TCATTTGATTTGGACTATTTTGGTTAAGAAATAATTGACTTGCGTAGTTTGCTCATATTTGTATTTTGTC
ACAAAATAAAATATTATTATCTTAGCGACTTCGGTTGTGTCGGATTACAATTACTGTTAATACATTCATG
GACCGTAGTCCTTACAAGCTCATTCAACTGGGCCAAGGACATAGTTATATTTGATTGAGAGCGTGTTAGA
CCCACTTGTGATGCTGAATCACCTGGGTCCAAAACACTTCCGCCTAACTGATGAAGATCTTTATACGGAT
GTAATGCGCTATGTCCTTGGTTGTCAGCATCTGTGTGAGTGGTTCCTATGGTGCTTCTACAAGCCCAGGA
TTCACCTGGTTTTAATTCAATTGGGCCTGTAATGCCGAACCTTGACATGGATGCTGACCTCAATGGTTTT
CTCTCCCACCTGCCGTAGTCCACATGTGTAAAGTCCACATCGTTATGGGTGAACTGTTTCGATAAAATCT
TCACCGTCGGAGCCCGGAAAGGTATATCCACGGAGTGTTTAGCTGTGGACAACTTCAATTTCCCTTTGAA
CTTGGCAAAATGGGTGTTCTGATGTACGTTAGTATCGGAGACTCTGTAATATAGCTTCCAGGGTATGGGG
TCCTTCAAGGAGAAGAAGGATGCTGAGAAATAATGGAGATCGATGTTACATCTTAGTGGAAATGTCCAAG
AAGCTTGTAATGATTCATTGTCTGTCATTCGTTTGTCATGGATTTCCACTATGACCGACCCAGTGGCGTT
TATCGGAACTTGCTGTCTATACTCGATAACGCAATGGTCAATTTTCATACAGCTACGACTAAGTCTGGCA
GCGTACTGCGACGCCGTTGACGGAAATTGAAGTATTATCTCCGTTAAGTCATGAGAGAGCTGATATTCAT
CTCTATGTGACTCTATATAATTGAATGCGCTAGGAGGATTCGCCAACCATGAATCCATATATGAAAATTT
GGCAGCGCACGTGAAGGCTTACGGAGTCTGAATCTGGTAATAAGAAGCTATACCTAACAATGTTAATGGT
AATGAAAATGACAAATTACTATTTGCTGAAAGAGTTCAAAAATAAATGCTTACTTAGTTATTAAGATATT
GCTATTAGCAGCAACAATATATGAGGAAACCGGTGAGGATGAAAGCAAAAGCGTCTTCAGAAGACAGAGC
AGAAAGAATTGGTATGAATAATTAAATGAACAGGCAGTGTCGTTATATAGAAGATCATTGTGTTTTAGAG
AGAGAAAATTTTGCAGTGGCATTTGTGTAATATGGAGGGGTACACCGATTGGAGCTCTTTAACCTGGGCT
TATTGTATCGGTGTATTGGTAGCCAATATATAGTATATGGGAGTTATCTAGGATCTTCGTACACGTGGA

[download]

In reply to FASTA Splitter by perl_n00b

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.