veoibd_synapse.data.parsers package¶
Submodules¶
veoibd_synapse.data.parsers.GTF module¶
Provide code to build pyparsing objects that deal with GTF lines.
-
class
veoibd_synapse.data.parsers.GTF.
GTFLine
(seqname, source, feature, start, end, score, strand, frame, attributes, line_number=None)[source]¶ Bases:
object
-
attributes
¶
-
end
¶
-
feature
¶
-
frame
¶
-
line_number
¶
-
score
¶
-
seqname
¶
-
source
¶
-
start
¶
-
strand
¶
-
-
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.
-
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