lomSpace has asked for the wisdom of the Perl Monks concerning the following question:
Hello,
I am using BioPerl to parse a file with two fasta sequences.
The separator is '>'.
Any ideas?
I am using BioPerl to parse a file with two fasta sequences.
The separator is '>'.
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Data::Dumper; my $file = "C:/Documents and Settings/mydir/fasta.contigs"; my $seqIO = Bio::SeqIO->new({-file=>'$file', -format=>'fasta'}); while (my $seq = $seqIO->next_seq()) { my $out = Bio::SeqIO->new( -file => ">$file"."_fasta", -format => 'Fasta'); $out->write_seq($seq); } __DATA__ >i:/13414 Ccl9 (88)/sequencing/13414_fasta.Contig1 TTTCTCCGGCCCCCTCCTCCCGCGGGGGAAAAAACCCGGGGAGCAGTCGG GCAGGGGTTTTTTGGTTTTTTCAAAATAAAAAGGGGTGCCCGTTGGGGGGcd GGGGGGGTGCAGGTTTCAACCCCCCCCCCCAAAGAAAAAAAAATTTTGGG GAATTTTTGGGGGGCTCCACCAGTTTTCGGGGTTTTTGGGCCTTTTCAGA AGGTAGGTTGGACGCGGATTGGGCAATAAACCACCCCGCTTCATCGGATA ATTTTCCCCGGCCGAAAAGGGCCGCGGGGCCGGTGGGCGGCCTTGGGTTT >i:/13414 Ccl9 (88)/sequencing/13414_fasta.Contig2 TAAACCCAAGGCCCCCCAGGTAAAAAAAAAACCGGCCAGGGGGGGGGGGG TAAAAAAAACCAAGTGTCACCCAGGGTGGAGATCCCCGGAAAAGGAAAAG GGGGGTTTTTTATTCGAAACGGGGAAAACTTTCACAAAATTTTGGAAGAA TCCCCTTTAATGTTTTCTTTTCAAAAGGGGGTAAAAAAACCACCTTTAAA AAGAAGTCTACCTTGGGAAAAAATAATTTTTGGGAAAATTTAAAAATTGA
Any ideas?
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Replies are listed 'Best First'. | |
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Re: splitting fasta file into individual fasta files
by BrowserUk (Patriarch) on May 06, 2009 at 21:39 UTC | |
Re: splitting fasta file into individual fasta files
by moritz (Cardinal) on May 06, 2009 at 21:32 UTC | |
by lomSpace (Scribe) on May 06, 2009 at 21:57 UTC | |
by moritz (Cardinal) on May 06, 2009 at 22:07 UTC | |
by citromatik (Curate) on May 07, 2009 at 09:13 UTC | |
by lomSpace (Scribe) on May 07, 2009 at 16:06 UTC | |
Re: splitting fasta file into individual fasta files
by bichonfrise74 (Vicar) on May 07, 2009 at 00:53 UTC | |
by citromatik (Curate) on May 07, 2009 at 09:02 UTC | |
by lomSpace (Scribe) on May 07, 2009 at 16:30 UTC |
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