kb_python.gtf¶
Module Contents¶
Classes¶
Utility class to easily read and parse GTF files. |
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kb_python.gtf.logger¶
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class
kb_python.gtf.GTF(gtf_path)¶ Utility class to easily read and parse GTF files.
- Parameters
gtf_path (str) – path to GTF file
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PARSER¶
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GROUP_PARSER¶
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static
parse_entry(line)¶ Parse a single GTF entry.
- Parameters
line (str) – a line in the GTF file
- Returns
parsed GTF information
- Return type
dict
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entries(self)¶ Generator that yields one GTF entry at a time.
- Returns
a generator that yields a dict of the GTF entry
- Return type
generator
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sort(self, out_path)¶ Sort the GTF file by chromosome, start position, line number.
- Parameters
out_path (str) – path to generate the sorted GTF
- Returns
path to sorted GTF file, set of chromosomes in GTF file
- Return type
tuple