Skip to content
GitLab
Menu
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
c48bce70
Commit
c48bce70
authored
Jul 31, 2017
by
Lukas Jelonek
Browse files
Add dbxref to ghostx converter. Adapt to blastp and hmmscan json format (Fixes #19)
parent
152c2c54
Changes
2
Hide whitespace changes
Inline
Side-by-side
bin/convert_ghostx.py
View file @
c48bce70
...
...
@@ -6,6 +6,9 @@ import argparse
parser
=
argparse
.
ArgumentParser
(
description
=
'Convert ghostx results to json documents'
)
parser
.
add_argument
(
'--result'
,
'-r'
,
required
=
True
,
help
=
'The ghostx result directory'
)
parser
.
add_argument
(
'--output'
,
'-o'
,
required
=
True
,
help
=
'The converted results json file'
)
parser
.
add_argument
(
'--dbxref'
,
'-d'
,
required
=
True
,
help
=
'The dbxref prefix that will be prepended to the accession or id'
)
parser
.
add_argument
(
'--acc_split'
,
'-s'
,
required
=
False
,
help
=
'The delimiter used to split the subject id (optional)'
)
parser
.
add_argument
(
'--acc_position'
,
'-p'
,
type
=
int
,
required
=
False
,
help
=
'The position of the accession after splitting the subject_id (optional)'
)
args
=
parser
.
parse_args
()
result_directory
=
args
.
result
...
...
@@ -27,11 +30,22 @@ with open(result_filename) as f:
results
=
documents
[
split
[
0
]][
'computations'
][
0
][
'results'
]
result
=
{}
result
[
"dbxref"
]
=
"UniProtKB/Swiss-Prot:"
+
split
[
1
].
split
(
"|"
)[
1
]
result
[
"percent_identity"
]
=
float
(
split
[
2
])
result
[
'qloc'
]
=
split
[
6
]
+
'-'
+
split
[
7
]
result
[
'sloc'
]
=
split
[
8
]
+
'-'
+
split
[
9
]
result
[
'evalue'
]
=
float
(
split
[
10
])
accession
=
split
[
1
]
if
args
.
acc_split
and
args
.
acc_position
:
accession
=
accession
.
split
(
args
.
acc_split
)[
args
.
acc_position
]
elif
args
.
acc_split
:
accession
=
acession
.
split
(
args
.
acc_split
)[
0
]
result
[
'query'
]
=
{
'start'
:
split
[
6
],
'end'
:
split
[
7
]
}
result
[
'target'
]
=
{
'dbxref'
:
args
.
dbxref
+
':'
+
accession
,
'start'
:
split
[
8
],
'end'
:
split
[
9
],
'evalue'
:
float
(
split
[
10
]),
'percent_identity'
:
float
(
split
[
2
])
}
results
.
append
(
result
)
...
...
modules/ghostx_vs_swissprot.yaml
View file @
c48bce70
...
...
@@ -17,4 +17,7 @@ analysis:
# result file from the analysis_script
converter
:
script
:
'
convert_ghostx.py'
parameters
:
dbxref
:
'
UniProtKB/Swiss-Prot'
acc_split
:
'
|'
acc_position
:
'
1'
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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