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Improve masking of domains overlapping bad bins #36

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merged 6 commits into from
Jun 19, 2024
Merged

Improve masking of domains overlapping bad bins #36

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bf52a1a
Let NCHG handle domain masking
robomics Jun 18, 2024
9fceac6
Update CI
robomics Jun 18, 2024
5e3f9e7
Format scripts and remove unused scripts
robomics Jun 18, 2024
70b3ce6
Fix typo
robomics Jun 18, 2024
de3a75f
Debugging
robomics Jun 18, 2024
265f33a
Bugfix
robomics Jun 18, 2024
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3 changes: 3 additions & 0 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -127,9 +127,12 @@ jobs:

- name: Test workflow
run: |
printf '%s\t%d\t%d' chr1 0 10000000 > mask.bed

nextflow run -c config/test.config \
--sample="test" \
--hic_file="data/$(basename "$TEST_DATASET_URL")" \
--mask=mask.bed \
--resolution=100000 \
--outdir=data/out \
--max_cpus=$(nproc) \
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238 changes: 0 additions & 238 deletions bin/extract_significant_trans_interactions.py
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75 changes: 0 additions & 75 deletions bin/fill_gaps_between_tads.py
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8 changes: 7 additions & 1 deletion bin/parse_samplesheet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,8 @@ def check_is_valid_bed3(path: pathlib.Path, strip_parent_dirs: bool = True):
path = file_uri_basename(str(path))
try:
df = pd.read_table(path, names=["chrom", "start", "end"], usecols=[0, 1, 2])
if len(df) == 0:
return
if df.isnull().values.any():
raise RuntimeError("found one or more null/nan value(s) in one of the first three columns")

Expand Down Expand Up @@ -127,6 +129,10 @@ def main():
if path != "":
check_is_valid_bed3(path)

for path in df["mask"].fillna(""):
if path != "":
check_is_valid_bed3(path)

paths = [uri.partition("::")[0] for uri in df["hic_file"]]

df["hic_file"] = paths
Expand All @@ -135,7 +141,7 @@ def main():


if __name__ == "__main__":
EXPECTED_COLUMNS = tuple(["sample", "hic_file", "resolution", "tads"])
EXPECTED_COLUMNS = tuple(["sample", "hic_file", "resolution", "tads", "mask"])
args = vars(make_cli().parse_args())
sample_sheet = args["tsv"]
detached = args["detached"]
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3 changes: 2 additions & 1 deletion bin/plot_maximal_clique_size_distribution.py
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Expand Up @@ -130,7 +130,8 @@ def plot_maximal_clique_sizes(cliques: Dict[str, pd.DataFrame], stat: str) -> pl
)

ax.set_xticks(
range(df["size"].min(), df["size"].max() + 1), labels=range(df["size"].min(), df["size"].max() + 1)
range(df["size"].min(), df["size"].max() + 1),
labels=range(df["size"].min(), df["size"].max() + 1),
)

return fig
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3 changes: 2 additions & 1 deletion bin/plot_maximal_clique_sizes.py
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Expand Up @@ -130,7 +130,8 @@ def plot_maximal_clique_sizes(cliques: Dict[str, pd.DataFrame], stat: str) -> pl
)

ax.set_xticks(
range(df["size"].min(), df["size"].max() + 1), labels=range(df["size"].min(), df["size"].max() + 1)
range(df["size"].min(), df["size"].max() + 1),
labels=range(df["size"].min(), df["size"].max() + 1),
)

return fig
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