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comparison change_o/makedb.sh @ 0:8a5a2abbb870 draft default tip

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author davidvanzessen
date Mon, 29 Aug 2016 05:36:10 -0400
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-1:000000000000 0:8a5a2abbb870
1 #!/bin/bash
2 dir="$(cd "$(dirname "$0")" && pwd)"
3
4 input=$1
5 noparse=$2
6 scores=$3
7 regions=$4
8 output=$5
9
10 if [ "true" == "$noparse" ] ; then
11 noparse="--noparse"
12 else
13 noparse=""
14 fi
15
16 if [ "true" == "$scores" ] ; then
17 scores="--scores"
18 else
19 scores=""
20 fi
21
22 if [ "true" == "$regions" ] ; then
23 regions="--regions"
24 else
25 regions=""
26 fi
27
28 mkdir $PWD/outdir
29
30 echo "makedb: $PWD/outdir"
31
32 python3 $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
33 #/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
34 #/home/galaxy/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
35
36 mv $PWD/outdir/output_db-pass.tab $output
37
38 rm -rf $PWD/outdir/