def calc_reconstruction(self, exons, blocks, size=None): """Calcuates reconstruction given list of alignment blocks and exons""" bases_reconstructed = intspan.intersect(exons, blocks) if size is None: size = intspan.cardinality_multi(exons) fraction_reconstructed = float(bases_reconstructed)/float(size) return bases_reconstructed, fraction_reconstructed
def combine_results(self, records, add_reads=False):
"""Combines match results to calculate coverage"""
pool_headers = ['num_reads', 'depth', 'contigs', 'num_contigs', 'best_contig', 'best_contig_reconstruction']
grouped_records = self.group_results(records)
pooled = {}
for model in grouped_records.keys():
pooled[model] = []
genes = grouped_records[model]['genes'].keys()
for gene in genes:
records = grouped_records[model]['genes'][gene]
pooled_gene = {'contigs_list': [],
'best_contig': None,
'best_contig_reconstruction': None,
'num_reads': None,
'depth': None,
'align_blocks': None,
'exons': None
}
for field in self.report_fields:
if field not in pool_headers:
pooled_gene[field] = records[0][field]
pooled_transcripts = []
exons_gene = self.string_as_blocks(records[0]['exons'])
blocks_gene = []
transcripts = grouped_records[model]['transcripts'][gene].keys()
for transcript in transcripts:
records = grouped_records[model]['transcripts'][gene][transcript]
pooled_transcript = {'contigs_list': [],
'best_contig': None,
'best_contig_reconstruction': None,
'num_reads': None,
'depth': None,
'align_blocks': None,
'exons': None
}
for field in self.report_fields:
if field not in pool_headers:
pooled_transcript[field] = records[0][field]
exons_transcript = self.string_as_blocks(records[0]['exons'])
blocks_transcript = []
for record in records:
# contigs
contigs = record['contigs'].split(',')
pooled_transcript['contigs_list'].extend(contigs)
pooled_gene['contigs_list'].extend(contigs)
# best contig
if pooled_transcript['best_contig'] is None or float(record['best_contig_reconstruction']) > float(pooled_transcript['best_contig_reconstruction']):
pooled_transcript['best_contig'] = record['best_contig']
pooled_transcript['best_contig_reconstruction'] = record['best_contig_reconstruction']
# num_reads
if pooled_transcript['num_reads'] is None:
pooled_transcript['num_reads'] = record['num_reads']
pooled_transcript['depth'] = record['depth']
elif record['num_reads'] != '-' and record['num_reads'] != 'na':
pooled_transcript['num_reads'] = int(pooled_transcript['num_reads'])
if add_reads:
pooled_transcript['num_reads'] += int(record['num_reads'])
elif pooled_transcript['num_reads'] < int(record['num_reads']):
pooled_transcript['num_reads'] = int(record['num_reads'])
# reconstruction
blocks = self.string_as_blocks(record['align_blocks'])
blocks_transcript.append(blocks)
blocks_gene.append(blocks)
# reconstruction transcript
union_blocks = intspan.union(blocks_transcript)
bases_reconstructed = intspan.intersect(exons_transcript, union_blocks)
fraction_reconstructed = float(bases_reconstructed)/float(pooled_transcript['feature_size'])
# update transcript
pooled_transcript['contigs'] = ','.join(pooled_transcript['contigs_list'])
pooled_transcript['num_contigs'] = len(pooled_transcript['contigs_list'])
if pooled_transcript['num_reads'] != '-' and pooled_transcript['num_reads'] != 'na':
pooled_transcript['depth'] = "%.3f" % (float(pooled_transcript['num_reads']) / float(pooled_transcript['feature_size']))
pooled_transcripts.append(pooled_transcript)
pooled_transcript['bases_reconstructed'] = bases_reconstructed
pooled_transcript['reconstruction'] = "%.3f" % (fraction_reconstructed)
pooled_transcript['align_blocks'] = self.blocks_as_string(union_blocks)
# update gene
for pt in pooled_transcripts:
if pooled_gene['best_contig'] is None or float(pt['best_contig_reconstruction']) > float(pooled_gene['best_contig_reconstruction']):
pooled_gene['best_contig'] = pt['best_contig']
pooled_gene['best_contig_reconstruction'] = pt['best_contig_reconstruction']
if pooled_gene['num_reads'] is None:
pooled_gene['num_reads'] = pt['num_reads']
pooled_gene['depth'] = pt['depth']
elif pt['num_reads'] != '-' and pt['num_reads'] != 'na':
pooled_gene['num_reads'] = int(pt['num_reads'])
if add_reads:
pooled_gene['num_reads'] += int(pt['num_reads'])
elif pooled_gene['num_reads'] < int(pt['num_reads']):
pooled_gene['num_reads'] = int(pt['num_reads'])
# coverage gene
union_blocks = intspan.union(blocks_gene)
bases_reconstructed = intspan.intersect(exons_gene, union_blocks)
fraction_reconstructed = float(bases_reconstructed)/float(pooled_gene['feature_size'])
pooled_gene['contigs'] = ','.join(pooled_gene['contigs_list'])
pooled_gene['num_contigs'] = len(pooled_gene['contigs_list'])
if pooled_gene['num_reads'] != '-' and pooled_gene['num_reads'] != 'na':
pooled_gene['depth'] = "%.3f" % (float(pooled_gene['num_reads']) / float(pooled_gene['feature_size']))
pooled_gene['bases_reconstructed'] = bases_reconstructed
pooled_gene['reconstruction'] = "%.3f" % (fraction_reconstructed)
pooled_gene['align_blocks'] = self.blocks_as_string(union_blocks)
pooled[model].append(pooled_gene)
for pt in pooled_transcripts:
pooled[model].append(pt)
self.results = []
for model in self.models:
if not pooled.has_key(model):
continue
self.results.extend(pooled[model])
