Mercurial > repos > ulfschaefer > phemost
changeset 0:9a2a4e1a4a8e draft
Uploaded
| author | ulfschaefer |
|---|---|
| date | Fri, 08 Jul 2016 10:10:30 -0400 |
| parents | |
| children | d85171c5a776 |
| files | MOST.sh |
| diffstat | 1 files changed, 29 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MOST.sh Fri Jul 08 10:10:30 2016 -0400 @@ -0,0 +1,29 @@ +#!/bin/bash + +echo $@ + +FWDFILE=$1 +shift +REVFILE=$1 +shift +OUTXML=$1 +shift +OUTCSV=$1 +shift +ORGANISM=$1 + +OUTFOLDER=$(mktemp -d --tmpdir tmpMOST_XXXXXXXXXXXXXXXXXXXX) +rm -rf $OUTFOLDER # MOST insists on creating the folder itself + +CMD="MOST.py -1 $FWDFILE -2 $REVFILE -o $OUTFOLDER -st $ORGANISM" + +echo $CMD +eval $CMD + +STEM=$(basename $FWDFILE) +STEM="${STEM%.*}" + +mv $OUTFOLDER"/"$STEM"_MLST_result.csv" $OUTCSV +mv "$OUTFOLDER/$STEM.results.xml" $OUTXML + +rm -rf $OUTFOLDER