Mercurial > repos > drosofff > msp_oases

comparison 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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-1:000000000000 0:eedbe32980bb
1 #!/bin/bash
2
3 min_k=$1
4 max_k=$2
5 input=$3
6 job_dir=$4
7
8 for i in `seq $min_k 2 $max_k`
9 do
10 velveth $job_dir/outputFolder_$i $i $input
11 velvetg $job_dir/outputFolder_$i -read_trkg yes
12 oases $job_dir/outputFolder_$i
13 done
14
15 velveth $job_dir/MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa
16 velvetg $job_dir/MergedAssemblyFolder -read_trkg yes -conserveLong yes
17 oases $job_dir/MergedAssemblyFolder -merge yes
18