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Fixing sorting of numerical columns #230

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merged 6 commits into from
Mar 27, 2024
+14 −10
Merged

Fixing sorting of numerical columns #230

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a479398
fix sorting?
Phlya Mar 27, 2024
3a6bd32
pairs
Phlya Mar 27, 2024
8dd2621
intify positions in test
Phlya Mar 27, 2024
037ae7f
more ints
Phlya Mar 27, 2024
74b17cb
fix test merge?
Phlya Mar 27, 2024
ad0c87e
fix test scaling
Phlya Mar 27, 2024
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2 changes: 1 addition & 1 deletion pairtools/cli/sort.py
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Original file line number Diff line number Diff line change
Expand Up @@ -198,7 +198,7 @@ def sort_py(
for col in columns:
colindex = int(col) if col.isnumeric() else column_names.index(col) + 1
cols.append(
f"-k {colindex},{colindex}{'n' if isinstance(pairsam_format.DTYPES_PAIRSAM.get(column_names[colindex-1], str), int) else ''}"
f"-k {colindex},{colindex}{'n' if issubclass(pairsam_format.DTYPES_PAIRSAM.get(column_names[colindex-1], str), int) else ''}"
)
cols = " ".join(cols)
command = rf"""
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2 changes: 2 additions & 0 deletions tests/data/mock.pairsam
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Original file line number Diff line number Diff line change
Expand Up @@ -18,3 +18,5 @@ readid05 chr2 1 chr3 2 + + UU readid05129chr2160101Mchr320CGFFXS:i:0
readid06 ! 0 chr1 3 - + NU readid06129chr1160101Mchr130CGFFXS:i:0Yt:Z:NU readid0665chr1360101Mchr110ATIIXS:i:0Yt:Z:NU
readid07 ! 0 chr1 3 - + MU readid07129chr1160101Mchr130CGFFXS:i:0Yt:Z:NU readid0765chr1360101Mchr110ATIIXS:i:0Yt:Z:NU
readid08 ! 0 ! 0 - - WW readid08129chr1160101Mchr130CGFFXS:i:0Yt:Z:WW readid0865chr1360101Mchr110ATIIXS:i:0Yt:Z:WW
readid09 chr1 120 chr1 121 + + UU readid09129chr112060101Mchr11210CGFFXS:i:0Yt:Z:UU readid0965chr112160101Mchr11200ATIIXS:i:0Yt:Z:UU
readid10 chr1 13 chr1 14 + + UU readid10129chr11360101Mchr1140CGFFXS:i:0Yt:Z:UU readid1065chr11460101Mchr1130ATIIXS:i:0Yt:Z:UU
10 changes: 5 additions & 5 deletions tests/test_merge.py
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Expand Up @@ -90,11 +90,11 @@ def test_mock_pairsam(setup_sort_two):
if prev_pair is not None:
assert cur_pair[0] >= prev_pair[0]
if cur_pair[0] == prev_pair[0]:
assert cur_pair[1] >= prev_pair[1]
if cur_pair[1] == prev_pair[1]:
assert cur_pair[2] >= prev_pair[2]
if cur_pair[2] == prev_pair[2]:
assert cur_pair[3] >= prev_pair[3]
assert cur_pair[2] >= prev_pair[2]
if cur_pair[2] == prev_pair[2]:
assert int(cur_pair[1]) >= int(prev_pair[1])
if int(cur_pair[1]) == int(prev_pair[1]):
assert int(cur_pair[3]) >= int(prev_pair[3])

prev_pair = cur_pair

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4 changes: 3 additions & 1 deletion tests/test_scaling.py
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Expand Up @@ -22,4 +22,6 @@ def test_scaling():

output = pd.read_csv(io.StringIO(result), sep="\t", header=0)

assert output["n_pairs"].sum() == 7 # double unmapped pairs are currently ignored by lib.scaling
assert (
output["n_pairs"].sum() == 9
) # double unmapped pairs are currently ignored by lib.scaling
6 changes: 3 additions & 3 deletions tests/test_sort.py
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Expand Up @@ -56,8 +56,8 @@ def test_mock_pairsam():
if cur_pair[0] == prev_pair[0]:
assert cur_pair[2] >= prev_pair[2]
if cur_pair[2] == prev_pair[2]:
assert cur_pair[1] >= prev_pair[1]
if cur_pair[1] == prev_pair[1]:
assert cur_pair[3] >= prev_pair[3]
assert int(cur_pair[1]) >= int(prev_pair[1])
if int(cur_pair[1]) == int(prev_pair[1]):
assert int(cur_pair[3]) >= int(prev_pair[3])

prev_pair = cur_pair
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