Mercurial > repos > konradpaszkiewicz > oasesoptimiser
comparison 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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-1:000000000000 | 0:53e887dda799 |
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1 #!/bin/bash | |
2 | |
3 min_k=$1 | |
4 max_k=$2 | |
5 input=$3 | |
6 args=$# | |
7 if [$args -gt 3]; then | |
8 velvetoptions=$4 | |
9 oasesoptions=$5 | |
10 else | |
11 velvetoptions='' | |
12 oasesoptions='' | |
13 fi | |
14 | |
15 for i in `seq $min_k 2 $max_k` | |
16 do | |
17 velveth . $i $input | |
18 velvetg . -read_trkg yes | |
19 oases . $oasesoptions | |
20 mv transcripts.fa transcripts_$i.fa | |
21 done | |
22 | |
23 velveth . $max_k -long transcripts_*.fa $input | |
24 velvetg . -read_trkg yes $velvetoptions | |
25 oases . -amos_file yes -unused_reads yes $oasesoptions | |
26 |