Mercurial > repos > drosofff > msp_oases

diff oases_optimiser.sh @ 0:eedbe32980bb draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Sun, 21 Jun 2015 14:38:06 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/oases_optimiser.sh	Sun Jun 21 14:38:06 2015 -0400
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+min_k=$1
+max_k=$2
+input=$3
+job_dir=$4
+
+for i in `seq $min_k 2 $max_k`
+do
+     velveth $job_dir/outputFolder_$i $i $input
+     velvetg $job_dir/outputFolder_$i -read_trkg yes
+     oases $job_dir/outputFolder_$i
+done
+
+velveth $job_dir/MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa
+velvetg $job_dir/MergedAssemblyFolder -read_trkg yes -conserveLong yes
+oases $job_dir/MergedAssemblyFolder -merge yes
+