mclumi.align package

Submodules

mclumi.align.Read module

class mclumi.align.Read.read(bam_fpn, verbose=False)

Bases: object

bycol(col='sname')

Parameters: col

todf(tags=[])

Notes

11 columns from alignments deciphered by Pysam: # read.query_name # read.flag # read.reference_id # read.reference_start # read.mapping_quality # read.cigar # read.query_sequence # read.next_reference_id # read.next_reference_start # read.template_length # read.query_qualities

See also

https: //pysam.readthedocs.io/en/latest/usage.html#creating-bam-cram-sam-files-from-scratch
https: //pysam.readthedocs.io/_/downloads/en/v0.12.0/pdf/

Parameters: tags

todf11()

Notes

11 columns from alignments deciphered by Pysam: # read.query_name # read.flag # read.reference_id # read.reference_start # read.mapping_quality # read.cigar # read.query_sequence # read.next_reference_id # read.next_reference_start # read.template_length # read.query_qualities

See also

https: //pysam.readthedocs.io/en/latest/usage.html#creating-bam-cram-sam-files-from-scratch
https: //pysam.readthedocs.io/_/downloads/en/v0.12.0/pdf/

todf11_depr()

Note

Deprecated.

Returns
Return type: Dataframe of a bam file

mclumi.align.Read_umitools module

mclumi.align.Write module

class mclumi.align.Write.write(df, is_sv=False, verbose=False)

Bases: object

property is_sv

tobam(tobam_fpn, tmpl_bam_fpn, whitelist=[])

Module contents