Merge pull request #96 from cfe-lab/report-merges

Report contig merges and name changes at the end.

iva/assembly.py

@@ -93,14 +93,22 @@ def write_contigs_to_file(self, filename, min_length=None, do_not_write=None, on
  if len(self.contigs[name]) >= min_length and name not in do_not_write and (name in only_write or len(only_write)==0):
  if order_by_orfs and contig_revcomp[i]:
  self.contigs[name].fa.revcomp()
+ suffix = ' (reversed)'
+ else:
+ suffix = ''
 
  if prefix is None:
  print(self.contigs[name].fa, file=f)
  else:
  printed += 1
- self.contigs[name].fa.id = prefix + '.' + str(printed).zfill(5)
+ new_name = prefix + '.' + str(printed).zfill(5)
+ self.contigs[name].fa.id = new_name
  print(self.contigs[name].fa, file=f)
  self.contigs[name].fa.id = name
+ if self.verbose >= 2:
+ print('Reported {} as {}{}.'.format(name,
+ new_name,
+ suffix))
 
  if order_by_orfs and contig_revcomp[i]:
  self.contigs[name].fa.revcomp()
@@ -483,19 +491,30 @@ def _remove_contained_contigs(self, contigs):
  hits = self._remove_contig_from_nucmer_hits(hits, contig)
  self._remove_contig(contig)
  contigs.remove(contig)
+ if self.verbose >= 2:
+ print('Removing contained contig:', contig)
 
 
  def _coords_to_new_contig(self, coords_list):
  new_contig = pyfastaq.sequences.Fasta(coords_list[0][0], '')
+ descriptions = []
  for name, coords, reverse in coords_list:
  assert name in self.contigs
  if reverse:
  seq = pyfastaq.sequences.Fasta('ni', self.contigs[name].fa.seq[coords.start:coords.end+1])
  seq.revcomp()
  new_contig.seq += seq.seq
+ descriptions.append('{}[{}<-{}]'.format(name, coords.end, coords.start))
  else:
  new_contig.seq += self.contigs[name].fa.seq[coords.start:coords.end+1]
-
+ descriptions.append('{}[{}->{}]'.format(name, coords.start, coords.end))
+ if self.verbose >= 2:
+ final_description = '{}[0->{}]'.format(new_contig.id,
+ len(new_contig.seq))
+ print('Merging contigs:',
+ ' + '.join(descriptions),
+ '==>',
+ final_description)
  return new_contig