wub.wrappers package

Submodules

wub.wrappers.dnadiff module

Wrapper for mummer’s dnadiff

class wub.wrappers.dnadiff.Property(ref, query)

Bases: tuple

Create new instance of Property(ref, query)

query

Alias for field number 1

ref

Alias for field number 0

class wub.wrappers.dnadiff.PropertyWithPerc(ref, ref_perc, query, query_perc)

Bases: tuple

Create new instance of PropertyWithPerc(ref, ref_perc, query, query_perc)

query

Alias for field number 2

query_perc

Alias for field number 3

ref

Alias for field number 0

ref_perc

Alias for field number 1

wub.wrappers.dnadiff.cleanup_dnadiff_report(directory, prefix='out')[source]

Cleanup dnadiff output files in the specified directory.

Parameters:
  • directory – Output directory.
  • prefix – Output prefix.
Returns:

None
Return type:

object
wub.wrappers.dnadiff.dnadiff(reference, query, working_directory=None, cleanup=True)[source]

Run dnadiff on reference and query fasta and parse results.

Parameters:
  • reference – Reference fasta.
  • query – Query fasta.
  • working_directory – Write output in this directory if specified.
  • cleanup – Delete dnadiff output after parsing if True.
Returns:

Parsed results, raw report and log.
Return type:

3-tuple
wub.wrappers.dnadiff.parse_dnadiff_report(report_file)[source]

Parse dnadiff report file.

Parameters:report_file – dnadiff report output.
Returns:Data structure with parsed results.
Return type:dict

Module contents