Re: splitting fasta file into individual fasta files

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Re^2: splitting fasta file into individual fasta files by lomSpace (Scribe) on May 06, 2009 at 21:57 UTC
How can I split a file __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 [download] based on the delimiter '>' and then print the lines in between '>' and the next '>' then continue until I have separate files like this file1: `>i:/13414 Ccl9 (88)/sequencing/13414_fasta.Contig1 TTTCTCCGGCCCCCTCCTCCCGCGGGGGAAAAAACCCGGGGAGCAGTCGG GCAGGGGTTTTTTGGTTTTTTCAAAATAAAAAGGGGTGCCCGTTGGGGGGcd GGGGGGGTGCAGGTTTCAACCCCCCCCCCCAAAGAAAAAAAAATTTTGGG GAATTTTTGGGGGGCTCCACCAGTTTTCGGGGTTTTTGGGCCTTTTCAGA AGGTAGGTTGGACGCGGATTGGGCAATAAACCACCCCGCTTCATCGGATA ATTTTCCCCGGCCGAAAAGGGCCGCGGGGCCGGTGGGCGGCCTTGGGTTT` [download] And file2: `>i:/13414 Ccl9 (88)/sequencing/13414_fasta.Contig2 TAAACCCAAGGCCCCCCAGGTAAAAAAAAAACCGGCCAGGGGGGGGGGGG TAAAAAAAACCAAGTGTCACCCAGGGTGGAGATCCCCGGAAAAGGAAAAG GGGGGTTTTTTATTCGAAACGGGGAAAACTTTCACAAAATTTTGGAAGAA TCCCCTTTAATGTTTTCTTTTCAAAAGGGGGTAAAAAAACCACCTTTAAA AAGAAGTCTACCTTGGGAAAAAATAATTTTTGGGAAAATTTAAAAATTGA` [download] I am running into some trouble with this code: #!/usr/bin/perl use warnings; use strict; use Data::Dumper; # # split a fasta file into separate sequence files # open( my $seqs, "C:/Documents and Settings/mydir/13063_fasta.contigs") +; open(my $seq_out,">C:/Documents and Settings/mydir/contig.fa" ); $/ = '\777'; # entire input to be read in one slurp $seqs = <>; # read input, assigning to single string while (<$seqs>){ if($seqs =~ m/^(>[^>]+)/mg) { # match indiv. sequences by '>'s push(my @seqs,$1); # and store in array } for (my @seqs) { # only allow characters A-Z,a-z,0-9,'_','-', and '.' in names; # change if you're more liberal /^> *([\w\-\.]+)/ && (my $seq_name = $1); if ($seq_name) { open($seq_out,">$seq_name"); print $seq_out "$_"; } else { warn "couldn't recognise the sequence name in \n$_"; } } } close($seqs); close($seq_out); [download] Sorry for not being specific enough :-)	[reply] [d/l] [select]
Re^3: splitting fasta file into individual fasta files by moritz (Cardinal) on May 06, 2009 at 22:07 UTC
Actually I was interested in what kinds of trouble you ran into, but anyway... There's a trick in Perl that makes that quite easy: you can set the input record separator to `'>'`, so that the `<DATA>` iterator gives you chunks splitted by `'>'`: use strict; use warnings; local $/ = '>'; my $c = 0; while (<DATA>) { chomp; next unless length; my $fn = "file" . ++$c; open my $handle, '>', $fn or die "Can't open `$fn' for writing: $! +"; print $handle '>', $_; close $handle or warn $!; } __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 [download]	[reply] [d/l] [select]
Re^3: splitting fasta file into individual fasta files by citromatik (Curate) on May 07, 2009 at 09:13 UTC
You can use Tie::File::AnyData::Bio::Fasta to facilitate this task. This script reads a multi-fasta file and splits it in multiple single-fasta files: `use strict; use warnings; use Tie::File::AnyData::Bio::Fasta; tie my @in,'Tie::File::AnyData::Bio::Fasta', shift @ARGV, or die $!; my $n = 0; for my $seq (@in){ tie my @out, 'Tie::File::AnyData::Bio::Fasta', "$n.fa" or die $!; $n++; @out = ($seq); untie @out; } untie @in;` [download] citromatik	[reply] [d/l]
Re^4: splitting fasta file into individual fasta files by lomSpace (Scribe) on May 07, 2009 at 16:06 UTC
citromatik, Thanks. I have installed the files into 'C:\Perl\site\lib' and 'C:\Perl\lib' on my windows system, but the error keeps stating that it 'Can't locate Tie/File/AnyData/Bio/Fasta.pm in @INC (@INC contains: C:/Perl/site/lib C:/Perl/lib .)' What could I be doing wrong?	[reply]