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comparison RaGOO/ragoo_utilities/get_ragoo_stats.py @ 13:b9a3aeb162ab draft default tip

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author dereeper
date Mon, 26 Jul 2021 18:22:37 +0000
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12:68a9ec9ce51e 13:b9a3aeb162ab
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))
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