Mercurial > repos > jampradinuk > repo_testing
changeset 0:ba3bec698d3a draft
First upload.
| author | jampradinuk |
|---|---|
| date | Thu, 10 May 2012 16:34:08 -0400 |
| parents | |
| children | 028cfb1b807b |
| 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, 87 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/my_tools/fastq_paired_reads_convention.pl Thu May 10 16:34:08 2012 -0400 @@ -0,0 +1,50 @@ +#! /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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/my_tools/fastq_paired_reads_convention.xml Thu May 10 16:34:08 2012 -0400 @@ -0,0 +1,37 @@ +<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>