Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
SOaAS
psot.repository
Commits
15f4a749
Commit
15f4a749
authored
Feb 27, 2017
by
Lukas Jelonek
Browse files
Added --result and --output options to json converter scripts
parent
9945d113
Changes
2
Hide whitespace changes
Inline
Side-by-side
bin/convert_blast_swissprot.py
View file @
15f4a749
#!/usr/bin/python3
import
sys
import
json
import
argparse
filename
=
sys
.
argv
[
1
]
parser
=
argparse
.
ArgumentParser
(
description
=
'Convert blast results to json documents'
)
parser
.
add_argument
(
'--result'
,
'-r'
,
required
=
True
,
help
=
'The blast result file in outfmt 7 format (tsv with headers)'
)
parser
.
add_argument
(
'--output'
,
'-o'
,
required
=
True
,
help
=
'The converted results json file'
)
args
=
parser
.
parse_args
()
filename
=
args
.
result
documents
=
{}
with
open
(
filename
)
as
f
:
header
=
None
...
...
@@ -44,6 +50,6 @@ with open(filename) as f:
results
.
append
(
result
)
for
key
in
documents
:
print
(
json
.
dump
s
(
documents
[
key
])
)
output_filename
=
args
.
output
with
open
(
output_filename
,
'w'
)
as
o
:
json
.
dump
(
documents
,
o
)
bin/convert_signalp.py
View file @
15f4a749
#!/usr/bin/python3
import
sys
import
json
import
argparse
filename
=
sys
.
argv
[
1
]
parser
=
argparse
.
ArgumentParser
(
description
=
'Convert signalp results to json documents'
)
parser
.
add_argument
(
'--result'
,
'-r'
,
required
=
True
,
help
=
'The signalp result file'
)
parser
.
add_argument
(
'--output'
,
'-o'
,
required
=
True
,
help
=
'The converted results json file'
)
args
=
parser
.
parse_args
()
filename
=
args
.
result
documents
=
{}
with
open
(
filename
)
as
f
:
tool
=
None
...
...
@@ -29,5 +35,6 @@ with open(filename) as f:
'version'
:
split
[
1
].
split
(
'-'
)[
1
],
'mode'
:
split
[
2
]}
for
key
in
documents
:
print
(
json
.
dumps
(
documents
[
key
]))
output_filename
=
args
.
output
with
open
(
output_filename
,
'w'
)
as
o
:
json
.
dump
(
documents
,
o
)
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment