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SOaAS
psot.repository
Commits
5e73cabf
Commit
5e73cabf
authored
Dec 12, 2017
by
Lukas Jelonek
Browse files
Merge branch 'fix-include-sequence' into 'develop'
Fix loss of last fasta entry. Solves #31 See merge request SOaAS/psot!7
parents
639c784e
171d47d8
Changes
1
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scripts/convert_fasta.py
View file @
5e73cabf
#!/usr/bin/python3
import
sys
import
json
import
argparse
parser
=
argparse
.
ArgumentParser
(
description
=
'Convert a fasta file into a json document'
)
parser
.
add_argument
(
'--result'
,
'-r'
,
required
=
True
,
help
=
'The fasta file
result directory
'
)
parser
.
add_argument
(
'--result'
,
'-r'
,
required
=
True
,
help
=
'The fasta file'
)
parser
.
add_argument
(
'--output'
,
'-o'
,
required
=
True
,
help
=
'The json file'
)
args
=
parser
.
parse_args
()
documents
=
{}
with
open
(
args
.
result
)
as
f
:
# second scan for data
entry
=
None
id
=
None
for
line
in
f
:
if
line
.
startswith
(
">"
):
id
=
line
.
split
()[
0
][
1
:]
if
entry
is
not
None
:
documents
[
entry
[
'id'
]]
=
entry
entry
=
{
'id'
:
id
,
'sequence'
:
''
}
else
:
entry
[
'sequence'
]
=
entry
[
'sequence'
]
+
line
.
strip
()
id
=
line
.
split
()[
0
][
1
:]
documents
[
id
]
=
{
'id'
:
id
,
'sequence'
:
''
}
elif
id
is
not
None
:
documents
[
id
][
'sequence'
]
+=
line
.
strip
()
output_filename
=
args
.
output
with
open
(
output_filename
,
'w'
)
as
o
:
...
...
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