veoibd_synapse.data.parsers package¶
Submodules¶
veoibd_synapse.data.parsers.GTF module¶
Provide code to build pyparsing objects that deal with GTF lines.
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class
veoibd_synapse.data.parsers.GTF.GTFLine(seqname, source, feature, start, end, score, strand, frame, attributes, line_number=None)[source]¶ Bases:
object-
attributes¶
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end¶
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feature¶
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frame¶
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line_number¶
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score¶
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seqname¶
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source¶
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start¶
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strand¶
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veoibd_synapse.data.parsers.GTF.parse_gtf_file(path)[source]¶ Parse full GTF file by yielding parsed GTF lines.
Commented text is ignored.
Parameters: path (Path) – Path obj pointing to GTF file. Yields: GTFLine – representing a parsed GTP line.
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veoibd_synapse.data.parsers.GTF.parse_gtf_line(line, line_number=None)[source]¶ Parse a single line of GTF file into it’s columns, converting the attributes into a dict.
Parameters: - line (str) – One line of GTF formatted information.
- line_number (int|None) – Optional: number of the line this comes from in the file (starting from 1).
Returns: dict-like