Mercurial > repos > jampradinuk > repo_testing
changeset 1:028cfb1b807b draft
Deleted selected files
author | jampradinuk |
---|---|
date | Thu, 10 May 2012 16:34:41 -0400 |
parents | ba3bec698d3a |
children | 50905eb47f2d |
files | my_tools/.DS_Store my_tools/._.DS_Store my_tools/._fastq_paired_reads_convention.xml my_tools/fastq_paired_reads_convention.pl my_tools/fastq_paired_reads_convention.xml |
diffstat | 5 files changed, 0 insertions(+), 87 deletions(-) [+] |
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--- a/my_tools/fastq_paired_reads_convention.pl Thu May 10 16:34:08 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -#! /usr/bin/perl -w - -use strict; -use warnings; - -# fastq_paired_reads_convention2.pl [input file] [left output file] [right output file] - -die "Check arguments" unless @ARGV == 3; - -#open (LEFT, '>data/left2.fastq') or die "Cannot create $ARGV[1]: $!\n"; -#open (RIGHT, '>data/right2.fastq') or die "Cannot create $ARGV[2]: $!\n"; -#open (INPUT, '<data/interlaced.fastq') or die "Cannot open $ARGV[0]: $!\n"; - -open (LEFT, '>', $ARGV[1]) or die "Cannot create $ARGV[1]: $!\n"; -open (RIGHT, '>', $ARGV[2]) or die "Cannot create $ARGV[2]: $!\n"; -open (INPUT, '<', $ARGV[0]) or die "Cannot open $ARGV[0]: $!\n"; - -my $which = 0; -my $current_id; - -while(<INPUT>) { - chomp; - if(/ 1\S*/){ - $_ =~ s/ 1\S*//; - $_.='/1'; - $current_id = substr $_, 1; - $which = 1; - } - if(/ 2\S*/){ - $_ =~ s/ 2\S*//; - $_.='/2'; - $current_id = substr $_, 1; - $which = 2; - } - - if($_ eq '+'){ - $_.=$current_id; - } - - if($which == 1){ - print LEFT "$_\n"; - } - if($which == 2){ - print RIGHT "$_\n"; - } -} - -close (LEFT); -close (RIGHT); -close (INPUT); \ No newline at end of file
--- a/my_tools/fastq_paired_reads_convention.xml Thu May 10 16:34:08 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<tool id="FASTQPairedReadsConvention" name="Convert paired reads format"> - <description>to conventional (/1 and /2)</description> - <command interpreter="perl">fastq_paired_reads_convention.pl $input $left_out $right_out</command> - <inputs> - <param name="input" type="data" label="FASTQ file" format="fastqsanger, fastqcssanger"></param></inputs> - <outputs> - <data format="input" name="left_out"></data> - <data format="input" name="right_out"></data></outputs> - <help> - - **What it does** - - This tool takes a paired ends fastq file (with the first format below) and produces a left and right fastq file (with the second format below). - - ----- - - **Example** - - Data like this:: - - <![CDATA[ - @M00325:2:000000000-A0DG1:1:1:15761:1554 1:N:0:1 - NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG - + - #+14:A?DAD1<;EBD@C3C33:C0)))8'5::69=6';;;/58<>335'898(:0&&&0&070&&05085-55538<<-5>999-550--5&559>9<8<<(&&)&(+(((&&0&(+(&)&&&)(&((((((((+(&&((+++(((+((& - ]]> - - will produce an empty right file and a left file with one entry like this:: - - <![CDATA[ - @M00325:2:000000000-A0DG1:1:1:15761:1554/1 - NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG - +M00325:2:000000000-A0DG1:1:1:15761:1554/1 - #+14:A?DAD1<;EBD@C3C33:C0)))8'5::69=6';;;/58<>335'898(:0&&&0&070&&05085-55538<<-5>999-550--5&559>9<8<<(&&)&(+(((&&0&(+(&)&&&)(&((((((((+(&&((+++(((+((& - ]]> - - </help></tool>