Mercurial > repos > konradpaszkiewicz > oasesoptimiser
view oases_optimiser.sh @ 0:53e887dda799 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | konradpaszkiewicz |
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date | Tue, 07 Jun 2011 17:41:37 -0400 |
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#!/bin/bash min_k=$1 max_k=$2 input=$3 args=$# if [$args -gt 3]; then velvetoptions=$4 oasesoptions=$5 else velvetoptions='' oasesoptions='' fi for i in `seq $min_k 2 $max_k` do velveth . $i $input velvetg . -read_trkg yes oases . $oasesoptions mv transcripts.fa transcripts_$i.fa done velveth . $max_k -long transcripts_*.fa $input velvetg . -read_trkg yes $velvetoptions oases . -amos_file yes -unused_reads yes $oasesoptions