p.bustard = b
p.gerald = g
runs.append(p)
- except IOError, e:
+ except IOError as e:
LOGGER.error("Ignoring " + str(e))
return len(runs) - start
if aligned:
p.gerald = gerald.gerald(aligned)
runs.append(p)
- except IOError, e:
+ except IOError as e:
LOGGER.error("Ignoring " + str(e))
return len(runs) - start
summarized_reads = {}
genome_reads = 0
genome = 'unknown'
- for k, v in mapped_reads.items():
+ for k, v in list(mapped_reads.items()):
path, k = os.path.split(k)
if len(path) > 0 and path not in genome_map:
genome = path
report.append("Mapped Reads")
mapped_reads = summarize_mapped_reads(eland_result.genome_map,
eland_result.mapped_reads)
- for name, counts in mapped_reads.items():
+ for name, counts in list(mapped_reads.items()):
report.append(" %s: %d" % (name, counts))
report.append('')