Changed behavior for --ambiguity-usage ploid parameter

quast_libs/ca_utils/analyze_contigs.py

@@ -10,6 +10,7 @@
 from quast_libs.ca_utils.analyze_misassemblies import process_misassembled_contig, IndelsInfo, find_all_sv, Misassembly
 from quast_libs.ca_utils.best_set_selection import get_best_aligns_sets, get_used_indexes, score_single_align
 from quast_libs.ca_utils.misc import ref_labels_by_chromosomes
+from quast_libs.diputils import DipQuastAnalyzer
 
 
 def add_potential_misassembly(ref, misassemblies_by_ref, refs_with_translocations):
@@ -202,17 +203,31 @@ def analyze_contigs(ca_output, contigs_fpath, unaligned_fpath, unaligned_info_fp
  top_aligns = top_aligns[1:]
  for align in top_aligns:
  ca_output.stdout_f.write('\t\t\tSkipping alignment ' + str(align) + '\n')
- # This is a template for future "ploid" ambiguity-usage flag, need to change it later:
  elif qconfig.ambiguity_usage == "ploid":
- ca_output.stdout_f.write('\t\tUsing only first of these alignment (option --ambiguity-usage is set to "one"):\n')
- ca_output.stdout_f.write('\t\t\tAlignment: %s\n' % str(top_aligns[0]))
- ca_output.icarus_out_f.write(top_aligns[0].icarus_report_str() + '\n')
- ref_aligns.setdefault(top_aligns[0].ref, []).append(top_aligns[0])
- aligned_lengths.append(top_aligns[0].len2)
- contigs_aligned_lengths[-1] = top_aligns[0].len2
- ca_output.coords_filtered_f.write(top_aligns[0].coords_str() + '\n')
- top_aligns = top_aligns[1:]
- for align in top_aligns:
+ dip_dict_haplotypes = DipQuastAnalyzer().fill_dip_dict_by_chromosomes(qconfig.reference) # MOVE HIGHER!
+ ploidy = len(dip_dict_haplotypes)
+ ca_output.stdout_f.write(f'\t\tThere are {ploidy} haplotypes. Using no more than one alignment for each haplotype\n')
+ used_haplotypes = []
+ skipped_aligns = []
+ while len(top_aligns):
+ if len(used_haplotypes) == ploidy:
+ break
+ for key, value in dip_dict_haplotypes.items(): # Create method for this later!
+ if top_aligns[0].ref in value:
+ haplotype = key
+ if haplotype not in used_haplotypes:
+ ca_output.stdout_f.write('\t\t\tAlignment: %s\n' % str(top_aligns[0]))
+ ca_output.icarus_out_f.write(top_aligns[0].icarus_report_str() + '\n')
+ ref_aligns.setdefault(top_aligns[0].ref, []).append(top_aligns[0])
+ aligned_lengths.append(top_aligns[0].len2)
+ contigs_aligned_lengths[-1] = top_aligns[0].len2
+ ca_output.coords_filtered_f.write(top_aligns[0].coords_str() + '\n')
+ used_haplotypes.append(haplotype)
+ top_aligns = top_aligns[1:]
+ else:
+ skipped_aligns.append(top_aligns[0])
+ top_aligns = top_aligns[1:]
+ for align in skipped_aligns:
  ca_output.stdout_f.write('\t\t\tSkipping alignment ' + str(align) + '\n')
  elif qconfig.ambiguity_usage == "all":
  ca_output.stdout_f.write('\t\tUsing all these alignments (option --ambiguity-usage is set to "all"):\n')