Mercurial > repos > ulfschaefer > phemost

comparison MOST.sh @ 0:653407a0018e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ulfschaefer
date Wed, 13 Jul 2016 06:12:58 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:653407a0018e
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