annotate change_o/makedb.sh @ 61:275e759e7985 draft

Uploaded
author davidvanzessen
date Fri, 18 Aug 2017 10:43:31 -0400
parents c33d93683a09
children c787e79e8b90
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
1 #!/bin/bash
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
2 dir="$(cd "$(dirname "$0")" && pwd)"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
3
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
4 input=$1
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
5 noparse=$2
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
6 scores=$3
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
7 regions=$4
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
8 output=$5
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
9
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
10 if [ "true" == "$noparse" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
11 noparse="--noparse"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
12 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
13 noparse=""
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
14 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
15
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
16 if [ "true" == "$scores" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
17 scores="--scores"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
18 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
19 scores=""
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
20 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
21
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
22 if [ "true" == "$regions" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
23 regions="--regions"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
24 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
25 regions=""
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
26 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
27
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
28 mkdir $PWD/outdir
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
29
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
30 echo "makedb: $PWD/outdir"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
31
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
32 python3 $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
33 #/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
34 #/home/galaxy/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
35
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
36 mv $PWD/outdir/output_db-pass.tab $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
37
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
38 rm -rf $PWD/outdir/