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SOaAS
psot.repository
Commits
ab4892f2
Commit
ab4892f2
authored
Jul 26, 2017
by
Lukas Jelonek
Browse files
Add configuration whether the id or the accession should be used to blastp runner
parent
95dd1a8d
Changes
1
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Inline
Side-by-side
bin/run_blastp.py
View file @
ab4892f2
...
...
@@ -11,9 +11,16 @@ parser.add_argument('--database', '-d', required=True, help='Database to search
parser
.
add_argument
(
'--output'
,
'-o'
,
required
=
True
,
help
=
'The result file'
)
parser
.
add_argument
(
'--evalue'
,
'-e'
,
default
=
'0.0001'
,
help
=
'Evalue cutoff'
)
parser
.
add_argument
(
'--alignment'
,
'-a'
,
action
=
'store_true'
,
help
=
'Include alignments in btop format'
)
parser
.
add_argument
(
'--use_accession'
,
'-x'
,
action
=
'store_true'
,
help
=
'Output the subject accession instead of the whole subject id'
)
args
=
parser
.
parse_args
()
format
=
'7 qseqid sseqid pident qstart qend sstart send evalue bitscore'
format
=
'7 qseqid'
if
args
.
use_accession
:
format
+=
' saccver'
else
:
format
+=
' sseqid'
format
+=
' pident qstart qend sstart send evalue bitscore'
if
args
.
alignment
:
format
+=
' btop'
...
...
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