pygfe package

pygfe

Created on Feb 8, 2017

@author: mhalagan

exception pygfe.pygfe.SeqAnnException(inputtype=None, reason=None)[source]

Bases: Exception

pygfe.pygfe.flatten(l)
pygfe.pygfe.is_classI(x)
pygfe.pygfe.is_gfe(x)
pygfe.pygfe.lc(x)
class pygfe.pygfe.pyGFE(url='http://feature.nmdp-bioinformatics.org', loci=['HLA-A', 'HLA-B', 'HLA-C', 'HLA-DRB1', 'HLA-DQB1', 'HLA-DRB4', 'HLA-DRB5', 'HLA-DPB1', 'HLA-DPA1', 'HLA-DQA1', 'HLA-DRB3'], graph: py2neo.database.Graph = None, seqann: Any = {}, features: Dict[KT, VT] = None, verbose: bool = False, kir: bool = False, pid: str = 'NA', gfe2hla: Dict[KT, VT] = None, gfe_feats: pandas.core.frame.DataFrame = None, seq2hla: pandas.core.frame.DataFrame = None, load_gfe2hla: bool = False, load_seq2hla: bool = False, load_gfe2feat: bool = False, verbosity=1)[source]

Bases: object

classdocs

breakup_gfe(gfe)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
calcDiff(gfe1, gfe2)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
calcSim(gfe1, gfe2)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
create_typing(similar_data, gfe, features)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
diff_seq(ref_allele, annotation, imgtdb_version)[source]
find_gfe_kir(gfe, features)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
find_similar(gfe, features, imgtdb_version)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
gfe_create(locus, sequence, imgtdb_version)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

Dict.
list_all_db_releases()[source]
map_structures(gfe_structs)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
matching_features(gfe1, gfe2, structures)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
rename_feat(f)[source]
sequence_lookup(locus, sequence, imgtdb_version)[source]

Looks up sequence from

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
type_from_seq(locus: str = None, sequence: str = None, imgtdb_version: str = '3.31.0', nseqs: int = 20, alignseqs: int = 10, skip: List[T] = [])[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.
unique_features(features, locus, imgtdb_version)[source]

creates GFE from HLA sequence and locus

Parameters:
  • locus – string containing HLA locus.
  • sequence – string containing sequence data.
Returns:

GFEobject.