Created
September 8, 2019 21:05
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fa2fastq
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#!/usr/bin/perl -w | |
# perl fa2fastq.pl input.fa > output.fastq | |
# Contact: Shicheng Guo | |
# Version 1.3 | |
# Update: 2019-09-08 | |
use strict; | |
die USAGE() if scalar(@ARGV)<1; | |
my $file = $ARGV[0]; | |
open FILE, $file; | |
my ($header, $sequence, $sequence_length, $sequence_quality); | |
while(<FILE>) { | |
chomp $_; | |
if ($_ =~ /^>(.+)/) { | |
if($header ne "") { | |
print "\@".$header."\n"; | |
print $sequence."\n"; | |
print "+"."\n"; | |
print $sequence_quality."\n"; | |
} | |
$header = $1; | |
$sequence = ""; | |
$sequence_length = ""; | |
$sequence_quality = ""; | |
} | |
else { | |
$sequence .= $_; | |
$sequence_length = length($_); | |
for(my $i=0; $i<$sequence_length; $i++) {$sequence_quality .= "I"} | |
} | |
} | |
close FILE; | |
print "\@".$header."\n"; | |
print $sequence."\n"; | |
print "+"."\n"; | |
print $sequence_quality."\n"; | |
sub USAGE{ | |
print "\nUSAGE: perl $0 input.fa > output.fastq\n\n"; | |
} | |
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