Mercurial > repos > rhpvorderman > shm_csr

annotate change_o/makedb.sh @ 6:ea9d5fc4c001 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 9ada186a78831ca2618ec817a23a77de6adf1a5d"
author rhpvorderman
date Wed, 22 Dec 2021 11:29:16 +0000
parents 64d74ba01a7c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
1 #!/bin/bash
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
2 dir="$(cd "$(dirname "$0")" && pwd)"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
3
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
4 input=$1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
5 noparse=$2
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
6 scores=$3
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
7 regions=$4
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
8 output=$5
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
9
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
10 if [ "true" == "$noparse" ] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
11 noparse="--noparse"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
12 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
13 noparse=""
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
14 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
15
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
16 if [ "true" == "$scores" ] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
17 scores="--scores"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
18 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
19 scores=""
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
20 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
21
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
22 if [ "true" == "$regions" ] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
23 regions="--regions"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
24 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
25 regions=""
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
26 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
27
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
28 mkdir $PWD/outdir
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
29
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
30 echo "makedb: $PWD/outdir"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
31
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
32 MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
33
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
34 mv $PWD/outdir/output_db-pass.tab $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
35
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
36 rm -rf $PWD/outdir/