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SOaAS
psot.repository
Commits
8dbbeca4
Commit
8dbbeca4
authored
Nov 30, 2017
by
Lukas Jelonek
Browse files
Cleanup code
parent
ec72c85d
Changes
2
Hide whitespace changes
Inline
Side-by-side
scripts/convert_tmhmm.py
View file @
8dbbeca4
...
...
@@ -10,62 +10,62 @@ parser.add_argument('--output', '-o', required=True, help='The converted results
args
=
parser
.
parse_args
()
def
parse_topology
(
s
,
l
):
elements
=
[]
result
=
[]
flag
=
False
num
=
""
for
c
in
s
:
if
c
==
'i'
or
c
==
'o'
or
c
==
'-'
:
if
num
!=
""
:
elements
.
append
(
int
(
num
))
num
=
""
if
c
!=
'-'
:
elements
.
append
(
c
)
else
:
num
+=
c
if
num
!=
""
:
elements
.
append
(
int
(
num
))
for
i
in
range
(
len
(
elements
)):
if
flag
:
flag
=
False
else
:
if
elements
[
i
]
==
'i'
or
elements
[
i
]
==
'o'
:
location
=
""
if
elements
[
i
]
==
'i'
:
location
=
"inside"
else
:
location
=
"outside"
if
i
==
0
:
if
len
(
elements
)
==
1
:
result
.
append
({
'start'
:
1
,
'end'
:
l
,
'location'
:
location
})
else
:
result
.
append
({
'start'
:
1
,
'end'
:
elements
[
i
+
1
]
-
1
,
'location'
:
location
})
elif
i
+
1
==
len
(
elements
):
result
.
append
({
'start'
:
elements
[
i
-
1
]
+
1
,
'end'
:
l
,
'location'
:
location
})
else
:
result
.
append
({
'start'
:
elements
[
i
-
1
]
+
1
,
'end'
:
elements
[
i
+
1
]
-
1
,
'location'
:
location
})
else
:
result
.
append
({
'start'
:
elements
[
i
],
'end'
:
elements
[
i
+
1
]
,
'location'
:
'membrane'
})
flag
=
True
return
(
result
)
elements
=
[]
result
=
[]
flag
=
False
num
=
""
for
c
in
s
:
if
c
==
'i'
or
c
==
'o'
or
c
==
'-'
:
if
num
!=
""
:
elements
.
append
(
int
(
num
))
num
=
""
if
c
!=
'-'
:
elements
.
append
(
c
)
else
:
num
+=
c
if
num
!=
""
:
elements
.
append
(
int
(
num
))
for
i
in
range
(
len
(
elements
)):
if
flag
:
flag
=
False
else
:
if
elements
[
i
]
==
'i'
or
elements
[
i
]
==
'o'
:
location
=
""
if
elements
[
i
]
==
'i'
:
location
=
"inside"
else
:
location
=
"outside"
if
i
==
0
:
if
len
(
elements
)
==
1
:
result
.
append
({
'start'
:
1
,
'end'
:
l
,
'location'
:
location
})
else
:
result
.
append
({
'start'
:
1
,
'end'
:
elements
[
i
+
1
]
-
1
,
'location'
:
location
})
elif
i
+
1
==
len
(
elements
):
result
.
append
({
'start'
:
elements
[
i
-
1
]
+
1
,
'end'
:
l
,
'location'
:
location
})
else
:
result
.
append
({
'start'
:
elements
[
i
-
1
]
+
1
,
'end'
:
elements
[
i
+
1
]
-
1
,
'location'
:
location
})
else
:
result
.
append
({
'start'
:
elements
[
i
],
'end'
:
elements
[
i
+
1
]
,
'location'
:
'membrane'
})
flag
=
True
return
(
result
)
filename
=
args
.
result
documents
=
{}
with
open
(
filename
)
as
f
:
for
line
in
f
:
line_dic
=
{}
elements
=
line
.
rstrip
().
split
(
"
\t
"
)
for
i
in
range
(
1
,
len
(
elements
)):
key
=
elements
[
i
][:
elements
[
i
].
rfind
(
'='
)]
value
=
elements
[
i
][
elements
[
i
].
rfind
(
'='
)
+
1
:]
if
key
==
'Topology'
:
line_dic
[
'topology'
]
=
parse_topology
(
value
,
int
(
elements
[
i
-
4
][
elements
[
i
-
4
].
rfind
(
'='
)
+
1
:]))
elif
key
==
'PredHel'
:
line_dic
[
key
]
=
int
(
value
)
elif
not
key
==
'len'
:
line_dic
[
key
]
=
float
(
value
)
documents
[
elements
[
0
]]
=
{
'computations'
:
[{
'tool'
:
{
'name'
:
'TMHMM'
,
'version'
:
'2.0'
},
'results'
:
line_dic
}]}
for
line
in
f
:
line_dic
=
{}
elements
=
line
.
rstrip
().
split
(
"
\t
"
)
for
i
in
range
(
1
,
len
(
elements
)):
key
=
elements
[
i
][:
elements
[
i
].
rfind
(
'='
)]
value
=
elements
[
i
][
elements
[
i
].
rfind
(
'='
)
+
1
:]
if
key
==
'Topology'
:
line_dic
[
'topology'
]
=
parse_topology
(
value
,
int
(
elements
[
i
-
4
][
elements
[
i
-
4
].
rfind
(
'='
)
+
1
:]))
elif
key
==
'PredHel'
:
line_dic
[
key
]
=
int
(
value
)
elif
not
key
==
'len'
:
line_dic
[
key
]
=
float
(
value
)
documents
[
elements
[
0
]]
=
{
'computations'
:
[{
'tool'
:
{
'name'
:
'TMHMM'
,
'version'
:
'2.0'
},
'results'
:
line_dic
}]}
output_filename
=
args
.
output
with
open
(
output_filename
,
'w'
)
as
o
:
json
.
dump
(
documents
,
o
)
json
.
dump
(
documents
,
o
)
scripts/run_tmhmm.py
View file @
8dbbeca4
...
...
@@ -9,18 +9,6 @@ tmhmm_tool = config.load_config()['tools'].get('tmhmm', 'tmhmm')
parser
=
argparse
.
ArgumentParser
(
description
=
'Find transmembrane helices in amino acid sequences'
)
parser
.
add_argument
(
'--fasta'
,
'-f'
,
required
=
True
,
help
=
'A fasta file with aminoacid sequences'
)
#parser.add_argument('--workdir', '-workdir', help='Working directory')
#parser.add_argument('--wwwdir', '-wwwdir', help='The place where the www server looks for files')
#parser.add_argument('--serverhome', '-serverhome', help='') #
#parser.add_argument('--basedir', '-basedir', help='basis directory for TMHMM package')
#parser.add_argument('--bindir', '-bindir', help='Bin directory (defaults basedir/bin)')
#parser.add_argument('--scrdir', '-scrdir', help='Script directory (defaults basedir/bin)')
#parser.add_argument('--libdir', '-libdir', help='Library directory (defaults basedir/lib)')
#parser.add_argument('--html', '-html', help='Produce HTML output')
#parser.add_argument('--short', '-s', help='Short output format')
#parser.add_argument('--plot', '-p', help='Produce graphics')
#parser.add_argument('--version1', '-v1', help='Use old model (version 1)')
#parser.add_argument('--debugging', '-d', help='') #
parser
.
add_argument
(
'--output'
,
required
=
True
,
help
=
'The output file'
)
args
=
parser
.
parse_args
()
...
...
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