Mercurial > repos > takakoron > fastq2fasta
changeset 0:eeb91602f5e9
commit
| author | takakoron <tm@nig.ac.jp> |
|---|---|
| date | Tue, 16 Feb 2016 17:47:23 +0900 |
| parents | |
| children | 0d2b0feee15b |
| files | fastq2fasta.pl fastq2fasta.xml |
| diffstat | 2 files changed, 61 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq2fasta.pl Tue Feb 16 17:47:23 2016 +0900 @@ -0,0 +1,47 @@ +#!/usr/bin/perl + +#*--<<Definision>>-----------------------------------------* +#PGID fastq2fastq.pl +#Kind of PG Main PG +#Create Date 2011/02/01 +# +# Comandline Input File(fasta) +# Output File(fastq) +#*---------------------------------------------------------* + +#*********************************************************** +# use?錾 +#*********************************************************** +use 5.8.0; +use utf8; +use strict; +#*********************************************************** +# +#*********************************************************** +my $input; +my $output; +my $line; +#*********************************************************** +# Main Coading +#*********************************************************** +$input = $ARGV[0]; +$output = $ARGV[1]; + +open(OUTPUT, ">$output"); +open(INPUT, "<$input") || die "\nThe input file does not exist.\n\n"; +my $index = 0; +while ($line = <INPUT>) { + $index++; + if($index == 1){ + my $name = substr($line,1); + print OUTPUT ">"; + print OUTPUT "$name"; + }elsif($index == 2){ + print OUTPUT "$line"; + } + if($index == 4){ + $index = 0; + } +} +close OUTPUT; +close INPUT;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq2fasta.xml Tue Feb 16 17:47:23 2016 +0900 @@ -0,0 +1,14 @@ +<tool id="fastq2fastq" name="Convert FASTQ into FASTA" version="0.0.1"> + <description>for Testing</description> + <command interpreter="perl"> + fastq2fasta.pl $fastq $fastq + </command> + <inputs> + <param name="fastq" format="fastq" type="data" value="" label="FASTQ format file" /> + </inputs> + <outputs> + <data format="fasta" name="fasta" label="${tool.name} on ${on_string}" /> + </outputs> + <help> + </help> +</tool>