def fetch_pairwise(mapping):
pairwise_alignments = []
enst = mapping.transcript.enst_id
uniprot_id = mapping.uniprot.uniprot_acc
for alignment in mapping.alignments.all():
if alignment.alignment_run.score1_type == 'identity':
cigarplus = alignment.pairwise.cigarplus
mdz = alignment.pairwise.mdz
if mdz.startswith('MD:Z:'):
mdz = mdz[len('MD:Z:'):]
ens_release = alignment.alignment_run.ensembl_release
ensp = ensembl_protein(enst, ens_release)
seq = ensembl_sequence(ensp, ens_release)
uniprot_seq, match_str, ensembl_seq = pairwise_alignment(
seq, cigarplus, mdz)
pairwise_alignments.append({
'uniprot_alignment': uniprot_seq,
'ensembl_alignment': ensembl_seq,
'match_str': match_str,
'alignment_id': alignment.alignment_id,
'ensembl_release': ens_release,
'ensembl_id': ensp,
'uniprot_id': uniprot_id,
'alignment_type': 'identity'
})
# Break out of the loop, we're done
break
elif alignment.alignment_run.score1_type == 'perfect_match' and alignment.score1 == 1:
ens_release = alignment.alignment_run.ensembl_release
ensp = ensembl_protein(enst, ens_release)
seq = ensembl_sequence(ensp, ens_release)
pairwise_alignments.append({
'uniprot_alignment': seq,
'ensembl_alignment': seq,
'match_str': '|' * len(seq),
'alignment_id': alignment.alignment_id,
'ensembl_release': ens_release,
'ensembl_id': ensp,
'uniprot_id': uniprot_id,
'alignment_type': 'perfect_match'
})
return {
'mapping_id': mapping.mapping_id,
'alignments': pairwise_alignments
}
def _fetch_alignment(alignment, enst, uniprot_id):
"""
Parameters
----------
alignment
enst : str
uniprot_id : str
Returns
-------
pw_alignment : dict
Alignment object
"""
ens_release = alignment.alignment_run.ensembl_release
ensp = ensembl_protein(enst, ens_release)
seq = ensembl_sequence(ensp, ens_release)
ensembl_seq = seq
uniprot_seq = seq
match_str = '|' * len(seq)
alignment_type = 'perfect_match'
if alignment.alignment_run.score1_type == 'identity':
cigarplus = alignment.pairwise.cigarplus
mdz = alignment.pairwise.mdz
if mdz.startswith('MD:Z:'):
mdz = mdz[len('MD:Z:'):]
uniprot_seq, match_str, ensembl_seq = pairwise_alignment(seq, cigarplus, mdz)
alignment_type = 'identity'
pw_alignment = {
'uniprot_alignment': ensembl_seq,
'ensembl_alignment': uniprot_seq,
'match_str': match_str,
'alignment_id': alignment.alignment_id,
'ensembl_release': ens_release,
'ensembl_id': ensp,
'uniprot_id': uniprot_id,
'alignment_type': alignment_type
}
return pw_alignment
def build_mapping(cls, mapping, fetch_sequence=False, authenticated=False):
mapping_history = mapping.mapping_history.select_related(
'release_mapping_history').select_related(
'release_mapping_history__ensembl_species_history').latest(
'mapping_history_id')
release_mapping_history = mapping_history.release_mapping_history
ensembl_history = mapping_history.release_mapping_history.ensembl_species_history
status = mapping.status.id
sequence = None
if fetch_sequence:
try:
sequence = ensembl_sequence(mapping.transcript.enst_id,
ensembl_history.ensembl_release)
except Exception as e:
print(e) # TODO: log
sequence = None
mapping_obj = {
'mappingId': mapping.mapping_id,
'timeMapped': release_mapping_history.time_mapped,
'ensemblRelease': ensembl_history.ensembl_release,
'uniprotRelease': release_mapping_history.uniprot_release,
'uniprotEntry': {
'uniprotAccession': mapping.uniprot.uniprot_acc,
'entryType': Mapping.entry_type(mapping_history.entry_type_id),
'sequenceVersion': mapping.uniprot.sequence_version,
'upi': mapping.uniprot.upi,
'md5': mapping.uniprot.md5,
'isCanonical':
True if mapping.uniprot.canonical_uniprot_id else False,
'alias': mapping.uniprot.alias,
'ensemblDerived': mapping.uniprot.ensembl_derived,
'gene_symbol': mapping.uniprot.gene_symbol,
'gene_accession': mapping.uniprot.gene_accession,
'length': mapping.uniprot.length
},
'ensemblTranscript': {
'enstId': mapping.transcript.enst_id,
'enstVersion': mapping.transcript.enst_version,
'upi': mapping.transcript.uniparc_accession,
'biotype': mapping.transcript.biotype,
'deleted': mapping.transcript.deleted,
'chromosome': mapping.transcript.gene.chromosome,
'seqRegionStart': mapping.transcript.seq_region_start,
'seqRegionEnd': mapping.transcript.seq_region_end,
'seqRegionStrand': mapping.transcript.gene.seq_region_strand,
'ensgId': mapping.transcript.gene.ensg_id,
'ensgName': mapping.transcript.gene.gene_name,
'ensgSymbol': mapping.transcript.gene.gene_symbol,
'ensgAccession': mapping.transcript.gene.gene_accession,
'sequence': sequence,
'enspId': mapping.transcript.ensp_id,
'enspLen': mapping.transcript.ensp_len,
'select': mapping.transcript.select
},
'alignment_difference': mapping.alignment_difference,
'status': Mapping.status_type(status),
'status_history': mapping.statuses(usernames=authenticated)
}
return mapping_obj
def test_ensembl_sequence(self):
seq = external.ensembl_sequence('ENST00000382038', 95)
self.assertEqual(seq[0:7], 'GCTTGCC')
def build_mapping(cls,
mapping_view,
fetch_sequence=False,
authenticated=False):
status = mapping_view.status
sequence = None
if fetch_sequence:
try:
sequence = ensembl_sequence(mapping_view.enst_id,
mapping_view.ensembl_release)
except Exception as e:
print(e)
sequence = None
mapping_obj = {
'id': mapping_view.id,
'mappingId': mapping_view.mapping_id,
'groupingId': mapping_view.grouping_id,
'timeMapped': mapping_view.time_mapped,
'ensemblRelease': mapping_view.ensembl_release,
'uniprotRelease': mapping_view.uniprot_release,
'uniprotEntry': {
'uniprot_id': mapping_view.uniprot_id,
'uniprotAccession': mapping_view.uniprot_acc,
'entryType':
MappingView.entry_description(mapping_view.entry_type),
'sequenceVersion': mapping_view.sequence_version,
'upi': mapping_view.upi,
'md5': mapping_view.md5,
'isCanonical': not mapping_view.canonical_uniprot_id,
'alias': mapping_view.alias,
'ensemblDerived': mapping_view.ensembl_derived,
'gene_symbol': mapping_view.gene_symbol_up,
'gene_accession': mapping_view.chromosome_line,
'length': mapping_view.length,
'protein_existence_id': mapping_view.protein_existence_id
},
'ensemblTranscript': {
'transcript_id': mapping_view.transcript_id,
'enstId': mapping_view.enst_id,
'enstVersion': mapping_view.enst_version,
'upi': mapping_view.uniparc_accession,
'biotype': mapping_view.biotype,
'deleted': mapping_view.deleted,
'chromosome': mapping_view.chromosome,
'regionAccession': mapping_view.region_accession,
'seqRegionStart': mapping_view.seq_region_start,
'seqRegionEnd': mapping_view.seq_region_end,
'seqRegionStrand': mapping_view.seq_region_strand,
'ensgId': mapping_view.ensg_id,
'ensgName': mapping_view.gene_name,
'ensgSymbol': mapping_view.gene_symbol_eg,
'ensgAccession': mapping_view.gene_accession,
'ensgRegionAccession': mapping_view.region_accession,
'sequence': sequence,
'enspId': mapping_view.ensp_id,
'enspLen': mapping_view.ensp_len,
'source': mapping_view.source,
'select': mapping_view.select
},
'alignment_difference': mapping_view.alignment_difference,
'status': MappingView.status_description(status),
'status_history': mapping_view.statuses(usernames=authenticated)
}
return mapping_obj