Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

For #2064 - Added check for pipe in gene symbol #666

Merged
merged 1 commit into from
Feb 8, 2024
Merged

For #2064 - Added check for pipe in gene symbol #666

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion ontobio/io/gafparser.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -393,7 +393,10 @@ def to_association(gaf_line: List[str], report=None, group="unknown", dataset="u
return assocparser.ParseResult(source_line, [], True, report=report)
if gaf_line[DB_OBJECT_SYMBOL] == "":
report.error(source_line, Report.INVALID_ID, "EMPTY", "col3 is empty", taxon=gaf_line[TAXON_INDEX], rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
return assocparser.ParseResult(source_line, [], True, report=report)
if '|' in gaf_line[DB_OBJECT_SYMBOL]:
report.error(source_line, Report.INVALID_SYMBOL, gaf_line[4], "Pipes are not allowed in gene symbol", taxon=gaf_line[TAXON_INDEX], rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
if gaf_line[REFERENCE_INDEX] == "":
report.error(source_line, Report.INVALID_ID, "EMPTY", "reference column 6 is empty", taxon=gaf_line[TAXON_INDEX], rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
Expand Down
6 changes: 6 additions & 0 deletions tests/test_gafparser.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -421,6 +421,12 @@ def test_bad_date():
assert assoc_result.skipped == True
assert assoc_result.associations == []

def test_bad_gene_symbol():
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\ta|pipeisnotallowed\t\tGO:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20231110\tPomBase\tfoo(X:1)")
assert assoc_result.skipped == True
assert assoc_result.associations == []

def test_bad_go_id():
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tINVALID:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20231110\tPomBase\tfoo(X:1)")
Expand Down
Loading