rotifer.genome.utils.seqrecords_to_dataframe#

rotifer.genome.utils.seqrecords_to_dataframe(seqrecs=None, exclude_type=[], autopid=False, assembly=None, codontable='Bacterial', parsers={})[source]#

Extract BioPython’s SeqRecord features data to a Pandas dataframe Arguments:

seqrecsrotifer.genome.io.parse generator, Bio.SeqIO generator

or (list of) Bio.SeqRecord object(s)

exclude_typelist of strings

Exclude features by type

autopidstring

Auto-generate missing PIDs from locus_tag

You can set autopid to: - ‘auto’, for transforming the locus_tag into unique PIDs, or - ‘copy’, copy the locus_tag if there is no alternative splicing

codontableinteger or string (see Bio.Seq)

Genetic code name for translating CDSs

parsers: dict of functions

Data extractor routines for non-standard columns.

This dictionary’s keys will be used as column names.

The corresponding values should be function names or references and should support three arguments:

  1. the column name

  2. the current feature being processed

  3. the current sequence object