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SOaAS
psot.repository
Commits
d47a4529
Commit
d47a4529
authored
8 years ago
by
Lukas Jelonek
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Added configuration file for the whole system
parent
a6cb14bf
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bin/module_signalp.py
+20
-1
20 additions, 1 deletion
bin/module_signalp.py
config.yaml
+2
-0
2 additions, 0 deletions
config.yaml
with
22 additions
and
1 deletion
bin/module_signalp.py
+
20
−
1
View file @
d47a4529
#!/usr/bin/env python3
import
argparse
import
yaml
import
os
from
os
import
system
def
get_config_file
():
"""
Finds the config file, that is located in the directory above script
"""
script_path
=
os
.
path
.
realpath
(
__file__
)
script_dir
=
os
.
path
.
dirname
(
script_path
)
config_dir
=
os
.
path
.
dirname
(
script_dir
)
config_file
=
os
.
path
.
join
(
config_dir
,
'
config.yaml
'
)
return
config_file
def
get_signalp_tool
():
"""
Extracts the configuration entry for signalp. If it is not present, it defaults to signalp
"""
tool
=
None
with
open
(
get_config_file
())
as
f
:
config
=
yaml
.
load
(
f
)
tool
=
config
[
'
tools
'
].
get
(
'
signalp
'
,
'
signalp
'
)
return
tool
parser
=
argparse
.
ArgumentParser
(
description
=
'
Find signal peptides in amino acid sequences
'
)
parser
.
add_argument
(
'
--fasta
'
,
'
-f
'
,
required
=
True
,
help
=
'
A fasta file with aminoacid sequences
'
)
parser
.
add_argument
(
'
--organism
'
,
'
-o
'
,
choices
=
[
'
euk
'
,
'
gram+
'
,
'
gram-
'
],
default
=
'
euk
'
,
help
=
'
The organism type
'
)
args
=
parser
.
parse_args
()
system
(
"
/vol/biotools/bin/signalp
-t
"
+
args
.
organism
+
"
"
+
args
.
fasta
)
system
(
get_signalp_tool
()
+
"
-t
"
+
args
.
organism
+
"
"
+
args
.
fasta
)
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config.yaml
0 → 100644
+
2
−
0
View file @
d47a4529
tools
:
signalp
:
'
/vol/biotools/bin/signalp'
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