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 |
|---|---|
| date | Tue, 07 Jun 2011 17:41:37 -0400 |
| parents | |
| children |
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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 |