Hi,
have a large file containing more than 10 contigs of different length.
Input:
seq_1 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAACGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC
seq_2 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAATGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC
seq_3 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGACCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
seq_4 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
seq_5 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
seq_6 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAACGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC
seq_7 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAATGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC
seq_8 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGACCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
seq_9 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
seq_10 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
I would like to merge some of the fasta sequences based on IDs
Output:
seq_1_seq_2 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAACGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTCAAGGGTTTAGAAAAAAACCAAACAAACAATCGAAATGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC
seq_3 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGACCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
seq_4 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
seq_5 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
seq_6_seq_7 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAACGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTCAAGGGTTTAGAAAAAAACCAAACAAACAATCGAAATGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC
seq_8_seq_9_seq_10 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGACCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTTTTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTTTTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT
Thank you
•
written
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K •
1 answer
Here is a perl script I am using to join sequences from multiple fasta files by their sequence id.
Usage:
combineFasta.pl -out outputfile.fasta -in file1.fasta file2.fasta .... <more files>
Perl code:
#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Bio::SeqIO;
use File::Basename qw(basename);
my @inputs = ();
my $out;
GetOptions ("out=s" => \$out, "in=s{1,}" => \@inputs);
my %h = ();
FILE: foreach my $f (@inputs) {
print $f,"\n";
my $in = Bio::SeqIO->new(-file => $f);
while (my $seq = $in->next_seq) {
my $gid = $seq->display_id;
if (! ref $h{$gid}) {
$h{$gid} = $seq;
} else {
$h{$gid}->seq ($h{$gid}->seq . $seq->seq);
}
}
}
print "finished reading input \n";
my $out = Bio::SeqIO->new(-format => 'fasta', -file => ">$out");
while (my ($k, $v) = each %h ) {
$out->write_seq($v);
}
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What have you tried? Are you hoping someone will just give you a complete script?