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Mutalyzer
mutalyzer2
Commits
36428807
Commit
36428807
authored
Dec 09, 2019
by
Mihai
Browse files
Fix erroneous message for mtDNA m. coordinate system
- including other fixes for NC coordinate systems.
parent
07807486
Changes
1
Hide whitespace changes
Inline
Side-by-side
mutalyzer/nc_db.py
View file @
36428807
...
...
@@ -59,13 +59,6 @@ def get_nc_record(record_id, parsed_description, output):
if
not
_configuration_check
(
output
):
return
None
if
parsed_description
.
RefType
in
[
'p'
,
'm'
,
'n'
]:
output
.
addMessage
(
__file__
,
4
,
'ECHROMCOORD'
,
'Could not retrieve information for '
'the provided {}. coordinate system.'
.
format
(
parsed_description
.
RefType
))
return
None
# Get the accession
accession
,
version
=
get_accession_version
(
record_id
)
...
...
@@ -93,10 +86,13 @@ def get_nc_record(record_id, parsed_description, output):
", "
.
join
(
versions
)))
return
None
if
parsed_description
.
RefType
==
'g'
:
# Example: NC_000001.11:g.111501128del
if
parsed_description
.
RefType
in
[
'g'
,
''
]:
# Examples:
# - NC_000001.11:g.111501128del
# - NC_000001.11:62825del
p_s
,
p_e
=
_get_description_boundary_positions
(
parsed_description
)
elif
parsed_description
.
RefType
==
'c'
:
elif
parsed_description
.
RefType
in
[
'c'
,
'n'
]
or
\
parsed_description
.
Gene
or
parsed_description
.
AccNoTransVar
:
if
parsed_description
.
Gene
:
# Example: 'NC_000001.11(OR4F5_v001):c.101del'
transcripts
=
Transcript
.
query
.
\
...
...
@@ -127,12 +123,9 @@ def get_nc_record(record_id, parsed_description, output):
p_s
=
transcript
.
transcript_start
p_e
=
transcript
.
transcript_stop
else
:
# Example: 'NC_000001.11:62825del'
return
_record_with_genes_only
(
reference
)
# db_transcripts = Transcript.query.\
# filter_by(reference_id=reference.id).all()
else
:
return
None
return
_record_with_genes_only
(
reference
)
db_transcripts
=
_get_transcripts
(
reference
,
p_s
,
p_e
)
...
...
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