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-rw-r--r--r_qtl/r_qtl2.py30
-rw-r--r--tests/r_qtl/test_r_qtl2_map_files.py40
-rw-r--r--tests/r_qtl/test_r_qtl2_pheno.py20
3 files changed, 55 insertions, 35 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index d3a3805..d8231bb 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -48,12 +48,26 @@ def with_non_transposed(zfile: ZipFile,
def not_comment_line(line):
return not line.startswith(cdata.get("comment.char", "#"))
+ sep = cdata.get("sep", ",")
with zfile.open(cdata[member_key]) as innerfile:
- reader = csv.DictReader(
- filter(not_comment_line, io.TextIOWrapper(innerfile)),
- delimiter=cdata.get("sep", ","))
+ wrapped_file = io.TextIOWrapper(innerfile)
+ firstrow = tuple(
+ field.strip() for field in
+ next(filter(not_comment_line, wrapped_file)).strip().split(sep))
+ id_key = firstrow[0]
+ wrapped_file.seek(0)
+ reader = csv.DictReader(filter(not_comment_line, wrapped_file),
+ delimiter=sep)
for row in reader:
- yield process_value(row)
+ processed = process_value(row)
+ yield {
+ "id": processed[id_key],
+ **{
+ key: value
+ for key, value in processed.items()
+ if key != id_key
+ }
+ }
def __make_organise_by_id__(id_key):
"""Return a function to use with `reduce` to organise values by some
@@ -101,7 +115,13 @@ def with_transposed(zfile: ZipFile,
for line in batch
for row in process_value(id_key, headers, line)),
{}).items():
- yield row
+ yield {
+ "id": row[id_key],
+ **{
+ key: value
+ for key, value in row.items()
+ if key != id_key
+ }}
except StopIteration:
pass
diff --git a/tests/r_qtl/test_r_qtl2_map_files.py b/tests/r_qtl/test_r_qtl2_map_files.py
index 5c8ca6a..3427ffb 100644
--- a/tests/r_qtl/test_r_qtl2_map_files.py
+++ b/tests/r_qtl/test_r_qtl2_map_files.py
@@ -11,32 +11,32 @@ from r_qtl import r_qtl2 as rqtl2
"relpath,mapfiletype,expected",
(("tests/r_qtl/test_files/test_gmap.zip",
"gmap",
- ({"marker": "PVV4", "chr": "1", "pos": "0.000000"},
- {"marker": "AXR-1", "chr": "1", "pos": "6.250674"},
- {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
- {"marker": "EC.480C", "chr": "1", "pos": "12.577629"},
- {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})),
+ ({"id": "PVV4", "chr": "1", "pos": "0.000000"},
+ {"id": "AXR-1", "chr": "1", "pos": "6.250674"},
+ {"id": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
+ {"id": "EC.480C", "chr": "1", "pos": "12.577629"},
+ {"id": "EC.66C", "chr": "1", "pos": "18.392830"})),
("tests/r_qtl/test_files/test_gmap_transposed.zip",
"gmap",
- ({"marker": "PVV4", "chr": "1", "pos": "0.000000"},
- {"marker": "AXR-1", "chr": "1", "pos": "6.250674"},
- {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
- {"marker": "EC.480C", "chr": "1", "pos": "12.577629"},
- {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})),
+ ({"id": "PVV4", "chr": "1", "pos": "0.000000"},
+ {"id": "AXR-1", "chr": "1", "pos": "6.250674"},
+ {"id": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
+ {"id": "EC.480C", "chr": "1", "pos": "12.577629"},
+ {"id": "EC.66C", "chr": "1", "pos": "18.392830"})),
("tests/r_qtl/test_files/test_pmap.zip",
"pmap",
- ({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"},
- {"marker": "D1Mit80", "chr": "1", "pos": "86.377953"},
- {"marker": "D1Mit17", "chr": "1", "pos": "189.571337"},
- {"marker": "D2Mit379", "chr": "2", "pos": "37.451062"},
- {"marker": "D2Mit75", "chr": "2", "pos": "80.584782"})),
+ ({"id": "D1Mit18", "chr": "1", "pos": "52.418656"},
+ {"id": "D1Mit80", "chr": "1", "pos": "86.377953"},
+ {"id": "D1Mit17", "chr": "1", "pos": "189.571337"},
+ {"id": "D2Mit379", "chr": "2", "pos": "37.451062"},
+ {"id": "D2Mit75", "chr": "2", "pos": "80.584782"})),
("tests/r_qtl/test_files/test_pmap_transposed.zip",
"pmap",
- ({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"},
- {"marker": "D1Mit80", "chr": "1", "pos": "86.377953"},
- {"marker": "D1Mit17", "chr": "1", "pos": "189.571337"},
- {"marker": "D2Mit379", "chr": "2", "pos": "37.451062"},
- {"marker": "D2Mit75", "chr": "2", "pos": "80.584782"}))))
+ ({"id": "D1Mit18", "chr": "1", "pos": "52.418656"},
+ {"id": "D1Mit80", "chr": "1", "pos": "86.377953"},
+ {"id": "D1Mit17", "chr": "1", "pos": "189.571337"},
+ {"id": "D2Mit379", "chr": "2", "pos": "37.451062"},
+ {"id": "D2Mit75", "chr": "2", "pos": "80.584782"}))))
def test_parse_map_files(relpath, mapfiletype, expected):
"""
GIVEN: A path to a zip file, `relpath` and the type of the map file,
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
index 66850a0..a7de675 100644
--- a/tests/r_qtl/test_r_qtl2_pheno.py
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -36,17 +36,17 @@ def test_parse_pheno_files(filepath, expected):
@pytest.mark.parametrize(
"filepath,expected",
(("tests/r_qtl/test_files/test_phenocovar.zip",
- ({"pheno": "T0", "time (hrs)": "0"},
- {"pheno": "T2", "time (hrs)": "0.0333333333333333"},
- {"pheno": "T4", "time (hrs)": "0.0666666666666667"},
- {"pheno": "T6", "time (hrs)": "0.1"},
- {"pheno": "T8", "time (hrs)": "0.133333333333333"})),
+ ({"id": "T0", "time (hrs)": "0"},
+ {"id": "T2", "time (hrs)": "0.0333333333333333"},
+ {"id": "T4", "time (hrs)": "0.0666666666666667"},
+ {"id": "T6", "time (hrs)": "0.1"},
+ {"id": "T8", "time (hrs)": "0.133333333333333"})),
("tests/r_qtl/test_files/test_phenocovar_transposed.zip",
- ({"pheno": "T0", "time (hrs)": "0"},
- {"pheno": "T2", "time (hrs)": "0.0333333333333333"},
- {"pheno": "T4", "time (hrs)": "0.0666666666666667"},
- {"pheno": "T6", "time (hrs)": "0.1"},
- {"pheno": "T8", "time (hrs)": "0.133333333333333"}))))
+ ({"id": "T0", "time (hrs)": "0"},
+ {"id": "T2", "time (hrs)": "0.0333333333333333"},
+ {"id": "T4", "time (hrs)": "0.0666666666666667"},
+ {"id": "T6", "time (hrs)": "0.1"},
+ {"id": "T8", "time (hrs)": "0.133333333333333"}))))
def test_parse_phenocovar_files(filepath, expected):
"""Test parsing of 'phenocovar' files from the R/qtl2 bundle.
generated by cgit v1.2.3 (git 2.44.0) at 2024-08-22 08:32:45 +0000