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GenomeDiff (*.gd) file reader

Project description

genomediff-python parses files in the GenomeDiff format generated by the breseq variant caller for haploid microbial organisms.


pip3 install genomediff==0.1a

Only Python 3.x is tested.


GenomeDiff files are read using The GenomeDiff object contains a metadata dict with the meta data, as well as mutations, evidence and validation lists—each containing records of that type. Records can be accessed through this list or by id. GenomeDiff is iterable and iterating will return all records of all types.

>>> from genomediff import *
>>> document ='', 'r', encoding='utf-8'))
>>> document.metadata
{'GENOME_DIFF': '1.0', 'AUTHOR': ''}
>>> document.mutations[0]
Record('SNP', 1, [191], new_seq='A', seq_id='NC_000913', snp_type='intergenic',  position=12346)
>>> document.mutations[0].parent_ids
>>> document[191]
Record('RA', 191, None, tot_cov='46/42', new_base='A', insert_position=0, ref_base='G', seq_id='NC_000913', quality=252.9, position=12345)


Contribution to this project is welcomed. Wishlist:

  • Writing GD files
  • Automatically resolving parent_ids into parents
  • Python 2.x support

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