Mercurial > repos > dereeper > ragoo
view RaGOO/ragoo_utilities/get_ragoo_stats.py @ 13:b9a3aeb162ab draft default tip
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author | dereeper |
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date | Mon, 26 Jul 2021 18:22:37 +0000 |
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import argparse parser = argparse.ArgumentParser(description='Summary stats about contig scaffolding with RaGOO.') parser.add_argument("index", metavar="<contigs.fasta.fai>", type=str, help="Samtools fasta index file for input contigs. If chimera breaking mode was used, this must be" "the index file of the chimera broken contigs, which can be found in ragoo_output/chimera_break." "The correct file to use is the file with the .intra.chimera.broken.fa suffix.") parser.add_argument("groupings", metavar="<groupings.fofn>", type=str, help="file of file names for all *_groupings.txt produced by RaGOO. Single column with full path to each grouping file.") args = parser.parse_args() contigs_index = args.index grouping_fofn = args.groupings remaining_ctg = [] all_ctg_len = dict() with open(contigs_index) as f: for line in f: L1 = line.split('\t') all_ctg_len[L1[0]] = int(L1[1]) remaining_ctg.append(L1[0]) grouping_files = [] with open(grouping_fofn) as f: for line in f: grouping_files.append(line.rstrip()) num_ctg_localized = 0 num_bp_localized = 0 for group_file in grouping_files: with open(group_file) as f: for line in f: L1 = line.split('\t') header = L1[0].rstrip() num_ctg_localized += 1 num_bp_localized += all_ctg_len[header] assert header in remaining_ctg remaining_ctg.pop(remaining_ctg.index(header)) num_ctg_unlocalized = 0 num_bp_unlocalized = 0 for ctg in remaining_ctg: num_ctg_unlocalized += 1 num_bp_unlocalized += all_ctg_len[ctg] print('%r contigs were localized by RaGOO' %(num_ctg_localized)) print('%r bp were localized by RaGOO' %(num_bp_localized)) print('%r contigs were unlocalized by RaGOO' %(num_ctg_unlocalized)) print('%r bp were unlocalized by RaGOO' %(num_bp_unlocalized)) print('%r %% of contigs were localized by RaGOO' %((num_ctg_localized/(num_ctg_localized + num_ctg_unlocalized))*100)) print('%r %% of bp were localized by RaGOO' %((num_bp_localized/(num_bp_localized + num_bp_unlocalized))*100))