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SOaAS
psot.repository
Commits
c0db9a40
Commit
c0db9a40
authored
Dec 07, 2017
by
lmueller
Browse files
adapted resolve_dbxrefs.py to input format
parent
9d4265ae
Changes
3
Expand all
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Inline
Side-by-side
scripts/resolve_dbxrefs.py
View file @
c0db9a40
...
...
@@ -7,7 +7,7 @@ import sys
parser
=
argparse
.
ArgumentParser
(
description
=
'Resolve dbxrefs from json file'
)
parser
.
add_argument
(
'--input'
,
'-i'
,
required
=
True
,
help
=
'The json input document'
)
parser
.
add_argument
(
'--retriever'
,
'-s'
,
required
=
True
,
help
=
'Location of retriever'
)
parser
.
add_argument
(
'--output'
,
'-o'
,
required
=
True
,
help
=
'Name of the output document'
)
#
parser.add_argument('--output', '-o', required=True, help='Name of the output document')
args
=
parser
.
parse_args
()
basename
=
args
.
retriever
.
replace
(
'scripts/'
,
''
)
...
...
@@ -18,13 +18,16 @@ from retriever import retrieve
json_file
=
open
(
args
.
input
).
read
()
j
=
json
.
loads
(
json_file
)
di
=
[]
#
di = []
for
c
in
j
[
'computations'
]:
for
r
in
c
[
'results'
]:
di
=
retrieve
(
r
[
'informations'
],
basename
)
output_filename
=
args
.
output
with
open
(
output_filename
,
'w'
)
as
o
:
json
.
dump
(
di
,
o
)
if
'target'
in
r
and
'dbxref'
in
r
[
'target'
]:
di
=
retrieve
([
r
[
'target'
][
'dbxref'
]],
basename
)
r
[
'target'
][
'dbxref'
]
=
{
'dbxref'
:
r
[
'target'
][
'dbxref'
],
'informations'
:
di
[
0
]}
#output_filename = args.output
#with open(output_filename, 'w') as o:
with
open
(
args
.
input
,
'w'
)
as
o
:
json
.
dump
(
j
,
o
)
testfiles/resolver_test.json
View file @
c0db9a40
...
...
@@ -9,21 +9,186 @@
},
"results"
:
[
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"informations"
:
[
"UniProtKB/Swiss-Prot:Q5XI95"
,
"UniProtKB/Swiss-Prot:Q70UN9"
,
"GO:0008270"
,
"GO:0004024"
,
"GO:0004930"
,
"EC:1.1.1.1"
,
"EC:2.2.1.1"
,
"PFAM:PF00002"
,
"PFAM:PF08240"
,
"SO:0000022"
,
"SO:0000714"
]
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"UniProtKB/Swiss-Prot:Q5XI95"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"UniProtKB/Swiss-Prot:Q70UN9"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"GO:0008270"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"GO:0004024"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"GO:0004930"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"EC:1.1.1.1"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"EC:2.2.1.1"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"PFAM:PF00002"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"PFAM:PF08240"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"SO:0000022"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"SO:0000714"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"GO:0005737"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"GO:0004022"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"GO:0008270"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"Pfam:PF08240"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"SO:0000380"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"SO:0000026"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"SO:0000020"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"UniProtKB/Swiss-Prot:P09370"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"UniProtKB/Swiss-Prot:P22246"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"UniProtKB/Swiss-Prot:P08843"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"GO:001"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"EC:2.1"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"Pfam:PF040"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"SO:020"
}
},
{
"target"
:
{
"score"
:
"42"
,
"alignment"
:
"|||||||||||||||||||||||||||"
,
"dbxref"
:
"UniProtKB/Swiss-Prot:P09"
}
}
]
}
...
...
testfiles/resolver_test2.json
View file @
c0db9a40
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