1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
|
--- a/centrifuge_simulate_reads.py 2023-04-14 21:27:38.630430207 +0530
+++ b/centrifuge_simulate_reads.py 2023-04-14 22:03:27.790914404 +0530
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#
# Copyright 2015, Daehwan Kim <infphilo@gmail.com>
@@ -156,7 +156,7 @@
transcripts[transcript_id][2].append([left, right])
# Sort exons and merge where separating introns are <=5 bps
- for tran, [chr, strand, exons] in transcripts.items():
+ for tran, [chr, strand, exons] in list(transcripts.items()):
exons.sort()
tmp_exons = [exons[0]]
for i in range(1, len(exons)):
@@ -167,7 +167,7 @@
transcripts[tran] = [chr, strand, tmp_exons]
tmp_transcripts = {}
- for tran, [chr, strand, exons] in transcripts.items():
+ for tran, [chr, strand, exons] in list(transcripts.items()):
exon_lens = [e[1] - e[0] + 1 for e in exons]
transcript_len = sum(exon_lens)
if transcript_len >= frag_len:
@@ -444,8 +444,8 @@
MD += ("{}".format(MD_match_len))
if len(read_seq) != read_len:
- print >> sys.stderr, "read length differs:", len(read_seq), "vs.", read_len
- print >> sys.stderr, pos, "".join(cigars), cigar_descs, MD, XM, NM, Zs
+ print("read length differs:", len(read_seq), "vs.", read_len, file=sys.stderr)
+ print(pos, "".join(cigars), cigar_descs, MD, XM, NM, Zs, file=sys.stderr)
assert False
return pos, cigars, cigar_descs, MD, XM, NM, Zs, read_seq
@@ -575,8 +575,8 @@
tMD += ("{}".format(match_len))
if tMD != MD or tXM != XM or tNM != NM or XM > max_mismatch or XM != NM:
- print >> sys.stderr, chr, pos, cigar, MD, XM, NM, Zs
- print >> sys.stderr, tMD, tXM, tNM
+ print(chr, pos, cigar, MD, XM, NM, Zs, file=sys.stderr)
+ print(tMD, tXM, tNM, file=sys.stderr)
assert False
@@ -631,7 +631,7 @@
# Read genome sequences into memory
genomes_fname = index_fname + ".fa"
if not os.path.exists(genomes_fname):
- print >> sys.stderr, "Extracting genomes from Centrifuge index to %s, which may take a few hours ..." % (genomes_fname)
+ print("Extracting genomes from Centrifuge index to %s, which may take a few hours ..." % (genomes_fname), file=sys.stderr)
extract_cmd = [centrifuge_inspect,
index_fname]
extract_proc = subprocess.Popen(extract_cmd, stdout=open(genomes_fname, 'w'))
@@ -660,15 +660,15 @@
assert num_frag == sum(expr_profile)
if dna:
- genome_ids = genome_seqs.keys()
+ genome_ids = list(genome_seqs.keys())
else:
- transcript_ids = transcripts.keys()
+ transcript_ids = list(transcripts.keys())
random.shuffle(transcript_ids)
assert len(transcript_ids) >= len(expr_profile)
# Truth table
truth_file = open(base_fname + ".truth", "w")
- print >> truth_file, "taxID\tgenomeLen\tnumReads\tabundance\tname"
+ print("taxID\tgenomeLen\tnumReads\tabundance\tname", file=truth_file)
truth_list = []
normalized_sum = 0.0
debug_num_frag = 0
@@ -695,19 +695,19 @@
if can_tax_id in names:
name = names[can_tax_id]
abundance = raw_abundance / genome_len / normalized_sum
- print >> truth_file, "{}\t{}\t{}\t{:.6}\t{}".format(tax_id, genome_len, t_num_frags, abundance, name)
+ print("{}\t{}\t{}\t{:.6}\t{}".format(tax_id, genome_len, t_num_frags, abundance, name), file=truth_file)
truth_file.close()
# Sequence Classification Map (SCM) - something I made up ;-)
scm_file = open(base_fname + ".scm", "w")
# Write SCM header
- print >> scm_file, "@HD\tVN:1.0\tSO:unsorted"
- for tax_id in genome_seqs.keys():
+ print("@HD\tVN:1.0\tSO:unsorted", file=scm_file)
+ for tax_id in list(genome_seqs.keys()):
name = ""
if tax_id in names:
name = names[tax_id]
- print >> scm_file, "@SQ\tTID:%s\tSN:%s\tLN:%d" % (tax_id, name, len(genome_seqs[tax_id]))
+ print("@SQ\tTID:%s\tSN:%s\tLN:%d" % (tax_id, name, len(genome_seqs[tax_id])), file=scm_file)
read_file = open(base_fname + "_1.fa", "w")
if paired_end:
@@ -718,11 +718,11 @@
t_num_frags = expr_profile[t]
if dna:
tax_id = genome_ids[t]
- print >> sys.stderr, "TaxID: %s, num fragments: %d" % (tax_id, t_num_frags)
+ print("TaxID: %s, num fragments: %d" % (tax_id, t_num_frags), file=sys.stderr)
else:
transcript_id = transcript_ids[t]
chr, strand, transcript_len, exons = transcripts[transcript_id]
- print >> sys.stderr, transcript_id, t_num_frags
+ print(transcript_id, t_num_frags, file=sys.stderr)
genome_seq = genome_seqs[tax_id]
genome_len = len(genome_seq)
@@ -763,14 +763,14 @@
XS = "\tXS:A:{}".format(strand)
TI = "\tTI:Z:{}".format(transcript_id)
- print >> read_file, ">{}".format(cur_read_id)
- print >> read_file, read_seq
+ print(">{}".format(cur_read_id), file=read_file)
+ print(read_seq, file=read_file)
output = "{}\t{}\t{}\t{}\tNM:i:{}\tMD:Z:{}".format(cur_read_id, tax_id, pos + 1, cigar_str, NM, MD)
if paired_end:
- print >> read2_file, ">{}".format(cur_read_id)
- print >> read2_file, reverse_complement(read2_seq)
+ print(">{}".format(cur_read_id), file=read2_file)
+ print(reverse_complement(read2_seq), file=read2_file)
output += "\t{}\t{}\tNM2:i:{}\tMD2:Z:{}".format(pos2 + 1, cigar2_str, NM2, MD2)
- print >> scm_file, output
+ print(output, file=scm_file)
cur_read_id += 1
@@ -865,7 +865,7 @@
parser.print_help()
exit(1)
if not args.dna:
- print >> sys.stderr, "Error: --rna is not implemented."
+ print("Error: --rna is not implemented.", file=sys.stderr)
exit(1)
# if args.dna:
# args.expr_profile = "constant"
|