Mercurial > repos > ulfschaefer > phemost
comparison MOST.sh @ 0:653407a0018e draft default tip
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| author | ulfschaefer |
|---|---|
| date | Wed, 13 Jul 2016 06:12:58 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:653407a0018e |
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| 1 #!/bin/bash | |
| 2 | |
| 3 echo $@ | |
| 4 | |
| 5 FWDFILE=$1 | |
| 6 shift | |
| 7 REVFILE=$1 | |
| 8 shift | |
| 9 OUTXML=$1 | |
| 10 shift | |
| 11 OUTCSV=$1 | |
| 12 shift | |
| 13 ORGANISM=$1 | |
| 14 | |
| 15 OUTFOLDER=$(mktemp -d --tmpdir tmpMOST_XXXXXXXXXXXXXXXXXXXX) | |
| 16 rm -rf $OUTFOLDER # MOST insists on creating the folder itself | |
| 17 | |
| 18 CMD="MOST.py -1 $FWDFILE -2 $REVFILE -o $OUTFOLDER -st $ORGANISM" | |
| 19 | |
| 20 echo $CMD | |
| 21 eval $CMD | |
| 22 | |
| 23 STEM=$(basename $FWDFILE) | |
| 24 STEM="${STEM%.*}" | |
| 25 | |
| 26 mv $OUTFOLDER"/"$STEM"_MLST_result.csv" $OUTCSV | |
| 27 mv "$OUTFOLDER/$STEM.results.xml" $OUTXML | |
| 28 | |
| 29 rm -rf $OUTFOLDER |