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June 3, 2011 18:13
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trim2.pl (QSEQ)
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# !/usr/bin/perl -w | |
# | |
# Trim2_Illumina.pl | |
# Written by: David B. Crabb | |
# Eric Triplett's Group | |
# University of Florida | |
# Last Modified: November 30, 2010 | |
################################################### | |
# | |
# Parameters: | |
# -a raw illumina input file read 1 | |
# -b raw illumina input file read 2 | |
# | |
################################################### | |
$LENGTH_CUTOFF = 70; | |
$QUALITY_CUTOFF = 20; | |
$TRUNCATE = 11; | |
# If Length < 70; throw out. | |
# If throw out 1; then throw out both. | |
# Delete first 11 on both sides | |
# Number of reads in each barcode | |
# Number thrown out | |
use Getopt::Std; | |
use File::Basename; | |
# PARSE ARGUMENTS | |
my %parameters; | |
getopts( 'a:b:', \%parameters ); #Takes parameters | |
unless ( $parameters{a} && $parameters{b} ) { | |
print "Usage: perl trim2.pl | |
-a raw illumina input file read 1 | |
-b raw illumina input file read 2\n"; | |
exit; | |
} | |
$read1 = $parameters{a}; | |
$read2 = $parameters{b}; | |
unless ( open( READ1, "$read1" ) ) { | |
print "Unable to open $read1\n"; | |
exit; | |
} | |
unless ( open( READ2, "$read2" ) ) { | |
print "Unable to open $read2\n"; | |
exit; | |
} | |
@split_out1 = split( /\./, $prefix ); | |
$out_dir = dirname($read1); | |
$prefix = basename($read1); | |
# Make Singletons Directory | |
system("mkdir -p $out_dir/singletons/"); | |
open SINGLETONS, ">$out_dir/singletons/$prefix" . "_trim_single.txt" or die $!; | |
while ( $read1_line = <READ1> ) { | |
chomp($read1_line); | |
chomp( $read2_line = <READ2> ); | |
@line1 = split( /\t/, $read1_line ); | |
@line2 = split( /\t/, $read2_line ); | |
$line1[8] =~ s/\./N/g; | |
$line2[8] =~ s/\./N/g; | |
$line1[8] = trim( $line1[8], $line1[9] ); | |
$line2[8] = trim( $line2[8], $line2[9] ); | |
$line1[9] = ""; | |
$line2[9] = ""; | |
next if ( ( $line1[8] eq "0" ) && ( $line2[8] eq "0" ) ); | |
# Print Singletons | |
if ( $line1[8] eq "0" ) { | |
print SINGLETONS join( "\t", @line2 ) . "\n"; | |
} | |
elsif ( $line2[8] eq "0" ) { | |
print SINGLETONS join( "\t", @line1 ) . "\n"; | |
} | |
# Or, print entire thing (interleaved QSEQ) | |
else { | |
# Print in QSEQ format, uncomment (and comment FASTQ line) | |
# print join( "\t", @line1 ) . "\n" . join( "\t", @line2 ) . "\n"; | |
# Print in FASTQ (interleaved) format: | |
# TODO shorten this! | |
$header = join(':', @line1[0..7]); | |
$sequence_quality = @line1[8]; | |
@sq = split( /\t/, $sequence_quality); | |
$sequence = @sq[0]; | |
$quality = @sq[1]; | |
print "\@$header:A\n$sequence\n\+$header:A\n$quality\n"; | |
$header = join(':', @line2[0..7]); | |
$sequence_quality = @line2[8]; | |
@sq = split( /\t/, $sequence_quality); | |
$sequence = @sq[0]; | |
$quality = @sq[1]; | |
print "\@$header:B\n$sequence\n\+$header:B\n$quality\n"; | |
} | |
} | |
close SINGLE1; | |
close SINGLE2; | |
# trim($seq, $qual); | |
sub trim() { | |
$seq = shift; | |
$qual = shift; | |
#trim off primer | |
$seq = substr( $seq, $TRUNCATE ); | |
$qual = substr( $qual, $TRUNCATE ); | |
$max = 0; | |
$sum = 0; | |
$first = 0; | |
$start = 0; | |
$end = 0; | |
@qualities = split( //, $qual ); | |
$size = scalar @qualities; | |
for ( $a = 0 ; $a < $size ; $a++ ) { | |
$sum += ( ord( $qualities[$a] ) - 64 - $QUALITY_CUTOFF ); | |
if ( $sum > $max ) { | |
$max = $sum; | |
$end = $a; | |
$start = $first; | |
} | |
if ( $sum < 0 ) { | |
$sum = 0; | |
$first = $a; | |
} | |
} | |
$seq = substr( $seq, $start, $end - $start ); | |
return 0 if ( length($seq) < $LENGTH_CUTOFF ); | |
$seq = $seq . "\t" . substr( $qual, $start, $end - $start ); | |
return $seq; | |
} |
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