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SOaAS
psot.repository
Commits
ebb26a4a
Commit
ebb26a4a
authored
Dec 05, 2017
by
Lukas Jelonek
Browse files
Merge branch 'hmmscan-empty-results' into 'develop'
Hmmscan empty results See merge request SOaAS/psot!4
parents
f67b0373
f404a49c
Changes
2
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Inline
Side-by-side
scripts/convert_hmmer.py
View file @
ebb26a4a
...
...
@@ -9,6 +9,11 @@ parser.add_argument('--output', '-o', required=True, help='The converted results
parser
.
add_argument
(
'--dbxref'
,
'-d'
,
required
=
True
,
help
=
'The dbxref prefix that will be prepended to the accession or id'
)
args
=
parser
.
parse_args
()
query_file
=
args
.
result
+
"/queries.json"
queries
=
[]
with
open
(
query_file
)
as
f
:
queries
=
json
.
load
(
f
)
filename
=
args
.
result
+
"/domtblout.tsv"
documents
=
{}
tool
=
{
'name'
:
None
,
'version'
:
None
,
'database'
:
None
}
...
...
@@ -30,7 +35,11 @@ with open(filename) as f:
query_id
=
split
[
3
]
if
not
query_id
in
documents
:
documents
[
query_id
]
=
{
"id"
:
query_id
,
"computations"
:
[{
'tool'
:
tool
,
'results'
:[]}]}
results
=
documents
[
query_id
][
'computations'
][
0
][
"results"
]
try
:
queries
.
remove
(
query_id
)
except
ValueError
:
print
(
'HMMER converter: Query ID "'
+
query_id
+
'" not found among initial queries!'
)
results
=
documents
[
query_id
][
'computations'
][
0
][
"results"
]
results
.
append
({
'target'
:
{
...
...
@@ -48,6 +57,10 @@ with open(filename) as f:
}
})
for
query_id
in
queries
:
if
not
query_id
in
documents
:
documents
[
query_id
]
=
{
"id"
:
query_id
,
"computations"
:
[{
'tool'
:
tool
,
'results'
:[]}]}
output_filename
=
args
.
output
with
open
(
output_filename
,
'w'
)
as
o
:
json
.
dump
(
documents
,
o
)
scripts/run_hmmer.py
View file @
ebb26a4a
#!/usr/bin/env python3
import
env
import
argparse
import
json
from
psot
import
config
from
os
import
system
,
makedirs
...
...
@@ -17,8 +18,20 @@ makedirs(args.output, exist_ok=True)
system
(
hmmscan_tool
+
" -E "
+
args
.
evalue
+
" -o "
+
args
.
output
+
"/hmmscan.out "
+
" -o "
+
args
.
output
+
"/hmmscan.out "
+
" --tblout "
+
args
.
output
+
"/tblout.tsv "
+
" --domtblout "
+
args
.
output
+
"/domtblout.tsv "
+
" --pfamtblout "
+
args
.
output
+
"/pfamtblout.tsv "
+
args
.
database
+
" "
+
args
.
fasta
)
# Provide a list of all query sequence names for conversion process
queries
=
[]
with
open
(
args
.
fasta
)
as
f
:
for
line
in
f
:
if
line
.
startswith
(
'>'
):
queries
.
append
(
line
.
split
()[
0
].
strip
().
lstrip
(
'>'
))
query_file
=
args
.
output
+
'/queries.json'
with
open
(
query_file
,
'w'
)
as
o
:
json
.
dump
(
queries
,
o
)
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