Subprocesses path for bigwig and bigbed outputs #125
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gfudenberg
reviewed
Oct 10, 2022
bioframe/io/fileops.py
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| @@ -488,7 +491,7 @@ def read_bigbed(path, chrom, start=None, end=None, engine="auto"): | |||
| return df | |||
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| def to_bigwig(df, chromsizes, outpath, value_field=None): | |||
| def to_bigwig(df, chromsizes, outpath, value_field=None, path=None): | |||
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path_to_binary would be more explicit
gfudenberg
reviewed
Oct 10, 2022
bioframe/io/fileops.py
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| cmd = os.path.join(path, "bedGraphToBigWig") | ||
| if not os.path.isfile(cmd) and os.access(cmd, os.X_OK): | ||
| raise ValueError( | ||
| f"bedGraphToBigWig is absent in the provided path: {path}. " |
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absent or cannot be exectuted
gfudenberg
reviewed
Oct 10, 2022
bioframe/io/fileops.py
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| with tempfile.NamedTemporaryFile(suffix=".bg") as f, tempfile.NamedTemporaryFile( | ||
| "wt", suffix=".chrom.sizes" | ||
| ) as cs: | ||
| with open(outpath+'.bg', 'w') as f, open(outpath+'.cs', 'w') as cs: #tempfile.NamedTemporaryFile(suffix=".bg") as f, tempfile.NamedTemporaryFile( |
gfudenberg
reviewed
Oct 10, 2022
bioframe/io/fileops.py
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| stdout=subprocess.PIPE, | ||
| stderr=subprocess.PIPE, | ||
| ) | ||
| return p | ||
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| def to_bigbed(df, chromsizes, outpath, schema="bed6"): | ||
| def to_bigbed(df, chromsizes, outpath, schema="bed6", path=None): |
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same comment about argument name
gfudenberg
approved these changes
Oct 10, 2022
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Option to change bedgraphToBigwig path #124