Mercurial > repos > dereeper > ragoo
comparison 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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12:68a9ec9ce51e | 13:b9a3aeb162ab |
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1 import argparse | |
2 | |
3 parser = argparse.ArgumentParser(description='Summary stats about contig scaffolding with RaGOO.') | |
4 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" | |
5 "the index file of the chimera broken contigs, which can be found in ragoo_output/chimera_break." | |
6 "The correct file to use is the file with the .intra.chimera.broken.fa suffix.") | |
7 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.") | |
8 | |
9 args = parser.parse_args() | |
10 contigs_index = args.index | |
11 grouping_fofn = args.groupings | |
12 | |
13 remaining_ctg = [] | |
14 all_ctg_len = dict() | |
15 with open(contigs_index) as f: | |
16 for line in f: | |
17 L1 = line.split('\t') | |
18 all_ctg_len[L1[0]] = int(L1[1]) | |
19 remaining_ctg.append(L1[0]) | |
20 | |
21 grouping_files = [] | |
22 with open(grouping_fofn) as f: | |
23 for line in f: | |
24 grouping_files.append(line.rstrip()) | |
25 | |
26 num_ctg_localized = 0 | |
27 num_bp_localized = 0 | |
28 | |
29 for group_file in grouping_files: | |
30 with open(group_file) as f: | |
31 for line in f: | |
32 L1 = line.split('\t') | |
33 header = L1[0].rstrip() | |
34 num_ctg_localized += 1 | |
35 num_bp_localized += all_ctg_len[header] | |
36 assert header in remaining_ctg | |
37 remaining_ctg.pop(remaining_ctg.index(header)) | |
38 | |
39 num_ctg_unlocalized = 0 | |
40 num_bp_unlocalized = 0 | |
41 for ctg in remaining_ctg: | |
42 num_ctg_unlocalized += 1 | |
43 num_bp_unlocalized += all_ctg_len[ctg] | |
44 | |
45 print('%r contigs were localized by RaGOO' %(num_ctg_localized)) | |
46 print('%r bp were localized by RaGOO' %(num_bp_localized)) | |
47 print('%r contigs were unlocalized by RaGOO' %(num_ctg_unlocalized)) | |
48 print('%r bp were unlocalized by RaGOO' %(num_bp_unlocalized)) | |
49 | |
50 print('%r %% of contigs were localized by RaGOO' %((num_ctg_localized/(num_ctg_localized + num_ctg_unlocalized))*100)) | |
51 print('%r %% of bp were localized by RaGOO' %((num_bp_localized/(num_bp_localized + num_bp_unlocalized))*100)) | |
52 | |
53 | |
54 | |
55 |