Hi All,
does any one know how to convert .sra files into .csfasata?
does any one know how to convert .sra files into .csfasata?
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#!/usr/bin/perl use warnings; use strict; my ($infile,$outfile) = @ARGV; die "Usage is fix_csfasta.pl [input file] [output file]\n" unless ($outfile); open (IN,$infile) or die "Can't read $infile: $!"; open (OUT,'>',$outfile) or die "Can't write to $outfile: $!"; while (<IN>) { if (/^>/) { my $header = $_; chomp $header; $header =~ s/[\r\n]//g; $header =~ s/[^>\w_\. ]//g; my $seq = <IN>; chomp $seq; $seq =~ s/[\r\n]//g; unless ($seq =~ /^T[0123\.]+$/) { warn "Skipping odd looking sequence '$seq'\n"; next; } print OUT "$header\n$seq\n"; } else { warn "Skipping unexpected line : $_"; } }
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