seqsero2: libs/split_interleaved

annotate libs/split_interleaved_fastq.pl @ 16:ed79f56d2184 draft default tip

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

author	charles_s_test
date	Thu, 30 Nov 2017 16:58:25 -0500
parents	6895de35a263
children

rev	line source
0 6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	1 #!/usr/bin/perl-w
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	2
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	3 use strict;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	4
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	5 use warnings;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	6
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	7 use Getopt::Long;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	8
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	9 use Pod::Usage;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	10
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	11 use File::Basename;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	12
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	13 # Date: 14-05-2010
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	14
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	15 # This program takes a fastq file containing paired-end reads in interleaved format as input and returns two separate files containing read 1 and read 2 in the correct order.
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	16
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	17 # Author: Ram Vinay Pandey
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	18
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	19
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	20
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	21 # Define the variables
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	22
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	23 my $input="";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	24
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	25 my $output="";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	26
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	27 my $help=0;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	28
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	29 my $test=0;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	30
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	31 my $verbose=1;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	32
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	33
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	34
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	35 my $usage="perl $0 --input interleaved_fastq_file.fastq --output output.fastq\n";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	36
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	37
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	38
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	39 GetOptions(
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	40
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	41 "input=s" =>\$input,
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	42
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	43 "output=s" =>\$output,
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	44
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	45 "test" =>\$test,
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	46
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	47 "help" =>\$help
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	48
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	49 ) or pod2usage(-msg=>"Wrong options",-verbose=>1);
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	50
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	51
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	52
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	53 pod2usage(-verbose=>2) if $help;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	54
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	55 Test::runTests() if $test;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	56
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	57
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	58
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	59 pod2usage(-msg=>"\n\tProvide an input file!!\n\n\t\t$usage\n\n",-verbose=>1) unless -e $input;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	60
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	61 pod2usage(-msg=>"\n\tProvide an output file!!\n\n\t\t$usage\n\n",-verbose=>1) unless $output;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	62
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	63
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	64
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	65
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	66
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	67 my ( $name, $path, $extension ) = File::Basename::fileparse ( $output, '\..*' );
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	68
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	69 my $output1 = $name."-read1.fastq";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	70
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	71 my $output2 = $name."-read2.fastq";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	72
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	73
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	74
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	75 open my $ofh1, ">$output1" or die "Could not open output file";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	76
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	77 open my $ofh2, ">$output2" or die "Could not open output file";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	78
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	79
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	80
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	81
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	82
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	83 open (IN, "<$input") or die ("Could not open file $input for reading\n");
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	84
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	85
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	86
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	87 while (<IN>) {
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	88
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	89 chomp;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	90
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	91 s/\r/\n/g;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	92
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	93 # discard blank line
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	94
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	95 if (m/^\s*$/g) {
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	96
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	97 next;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	98
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	99 }
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	100
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	101 else {
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	102
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	103 # Reading all lines for read 1
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	104
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	105 if (m/^\s\@.1$/) {
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	106
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	107
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	108
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	109 print $ofh1 "$_\n";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	110
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	111 my $ct=0;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	112
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	113 while(my $l = <IN>) {
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	114
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	115
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	116
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	117 $ct++;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	118
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	119 chomp $l;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	120
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	121 s/\r/\n/g;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	122
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	123 print $ofh1 "$l\n";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	124
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	125
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	126
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	127 last if($ct ==3);
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	128
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	129
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	130
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	131 }
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	132
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	133
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	134
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	135 }
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	136
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	137 # Reading all lines for read 2
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	138
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	139 if (m/^\s\@.2$/) {
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	140
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	141
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	142
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	143 print $ofh2 "$_\n";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	144
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	145 my $ct=0;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	146
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	147 while(my $l = <IN>) {
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	148
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	149
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	150
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	151 $ct++;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	152
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	153 chomp $l;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	154
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	155 s/\r/\n/g;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	156
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	157 print $ofh2 "$l\n";
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	158
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	159
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	160
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	161 last if($ct ==3);
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	162
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	163 }
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	164
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	165
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	166
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	167
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	168
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	169 }
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	170
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	171
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	172
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	173 }
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	174
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	175 }
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	176
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	177
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	178
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	179 close IN;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	180
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	181 close $ofh1;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	182
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	183 close $ofh2;
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	184
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	185
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	186
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	187
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	188
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	189
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	190
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	191 =head1 NAME
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	192
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	193
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	194
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	195 split-interleaved-fastq.pl - TThis program takes a fastq file containing paired-end reads in interleaved format as input and returns two separate files containing read 1 and read 2 in the correct order.
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	196
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	197
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	198
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	199 =head1 SYNOPSIS
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	200
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	201
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	202
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	203 perl split-interleaved-fastq.pl --input interleaved_fastq_file.fastq --output output.fastq
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	204
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	205
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	206
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	207 =head1 OPTIONS
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	208
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	209
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	210
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	211 =over 4
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	212
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	213
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	214
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	215 =item B<--input>
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	216
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	217
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	218
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	219 The input file which contains read1 and read2 in a single file in FASTQ format. Mandatory parameter
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	220
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	221
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	222
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	223 =item B<--output>
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	224
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	225
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	226
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	227 The output file. Mandatory parameter
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	228
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	229
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	230
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	231 =item B<--help>
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	232
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	233
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	234
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	235 Display help for this script
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	236
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	237
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	238
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	239 =back
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	240
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	241
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	242
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	243 =head1 Details
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	244
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	245
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	246
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	247 =head2 Input
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	248
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	249
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	250
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	251 The paired-end reads in interleaved format; input file looks like following:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	252
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	253
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	254
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	255 @fc_HWUSI-EAS613R:1:1:4:682#CATA/1
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	256
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	257 TTGTANGATTTCGTCCAGACTTATCTGGAGCATCCGGACGGTCGGGTGAAGCTCAATCCTCAGCTGGTGTTG
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	258
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	259 +fc_HWUSI-EAS613R:1:1:4:682#CATA/1
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	260
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	261 baaa\DVbbbbaaaaa`[`abaaaab`b`]aab]_aaa``Z^`a[SN^QR^`]___aXK[a\T\[UTWWMZV
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	262
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	263 @fc_HWUSI-EAS613R:1:1:4:682#CATA/2
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	264
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	265 TCGACAGCTGCTGCTCCGTATTGAGGTACGGATCGTTCACGATCATATACGCCCTCTCTTTCAAAAACCTCA
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	266
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	267 +fc_HWUSI-EAS613R:1:1:4:682#CATA/2
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	268
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	269 bbbY`[`a\S_Y][XPaUDZ__LLL]TZPWXBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	270
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	271
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	272
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	273 =head2 Output
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	274
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	275
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	276
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	277 The output looks like as following for reads 1:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	278
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	279
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	280
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	281 @fc_HWUSI-EAS613R:1:1:4:682#CATA/1
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	282
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	283 TTGTANGATTTCGTCCAGACTTATCTGGAGCATCCGGACGGTCGGGTGAAGCTCAATCCTCAGCTGGTGTTG
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	284
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	285 +fc_HWUSI-EAS613R:1:1:4:682#CATA/1
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	286
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	287 baaa\DVbbbbaaaaa`[`abaaaab`b`]aab]_aaa``Z^`a[SN^QR^`]___aXK[a\T\[UTWWMZV
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	288
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	289
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	290
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	291 The output looks like as following for reads 2:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	292
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	293
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	294
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	295 @fc_HWUSI-EAS613R:1:1:4:682#CATA/2
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	296
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	297 TCGACAGCTGCTGCTCCGTATTGAGGTACGGATCGTTCACGATCATATACGCCCTCTCTTTCAAAAACCTCA
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	298
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	299 +fc_HWUSI-EAS613R:1:1:4:682#CATA/2
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	300
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	301 bbbY`[`a\S_Y][XPaUDZ__LLL]TZPWXBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	302
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	303
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	304
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	305
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	306
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	307 =head1 AUTHORS
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	308
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	309
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	310
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	311 Ram vinay pandey
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	312
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	313
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	314
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	315 =cut
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	316
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	317

Mercurial > repos > charles_s_test > seqsero2

annotate libs/split_interleaved_fastq.pl @ 16:ed79f56d2184 draft default tip