Mercurial > repos > konradpaszkiewicz > oasesoptimiser
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/oases_optimiser.sh Tue Jun 07 17:41:37 2011 -0400 @@ -0,0 +1,26 @@ +#!/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 +