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
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
|
#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\nusage: $0 nameSorted.sam iworm_fasta_file\n\n";
my $name_sorted_sam_file = $ARGV[0] or die $usage;
my $iworm_fasta = $ARGV[1] or die $usage;
my $SAM_OFH;
main: {
open ($SAM_OFH, ">scaffolding_entries.sam") or die $!;
my %iworm_acc_to_fasta_index;
{
my $counter = 0;
open (my $fh, $iworm_fasta) or die "Error, cannot open file $iworm_fasta";
while (<$fh>) {
if (/^>(\S+)/) {
my $acc = $1;
$iworm_acc_to_fasta_index{$acc} = $counter; # starts at zero
$counter++;
}
}
close $fh;
}
my %paired_iworm_contigs;
my $prev_core_acc = "";
my %end_to_iworm;
my $num_warnings = 0;
my $num_unrecognized_iworm_contig_names = 0;
if ($name_sorted_sam_file =~ /\.bam$/) {
$name_sorted_sam_file = "samtools view $name_sorted_sam_file | ";
}
open (my $fh, $name_sorted_sam_file) or die "Error, cannot open file $name_sorted_sam_file";
while (<$fh>) {
my $line = $_;
chomp;
my @x = split(/\t/);
my $read_acc = $x[0];
my $iworm_acc = $x[2];
unless (defined $iworm_acc) { next; }
if ($iworm_acc eq '*') {
# unmapped read
next;
}
unless ($iworm_acc =~ /^a\d+;\d+/) {
$num_unrecognized_iworm_contig_names++;
if ($num_unrecognized_iworm_contig_names <= 10) {
print STDERR "warning, inchworm contig ($iworm_acc) isn't recognized. Ignoring entry: [[$line]]\n";
}
if ($num_unrecognized_iworm_contig_names == 11) {
print STDERR "warning, too many unrecognized inchworm contig names. Will report summary of counts later.\n";
}
next;
}
my $core_acc;
my $frag_end;
if ($read_acc =~ /^(\S+)\/([12])$/) {
$core_acc = $1;
$frag_end = $2;
}
else {
# must have mixed in a single read with the pairs...
if ($num_warnings <= 10) {
print STDERR "warning, ignoring read: $read_acc since cannot decipher if /1 or /2 of a pair.\n";
}
elsif ($num_warnings == 11) {
print STDERR "number of read warnings exceeded 10. Turning off warning messages from here out.\n";
}
$num_warnings++;
next;
}
if ($core_acc ne $prev_core_acc) {
&examine_frags(\%end_to_iworm, \%paired_iworm_contigs);
%end_to_iworm = ();
}
$end_to_iworm{$frag_end}->{$iworm_acc} = $line;
$prev_core_acc = $core_acc;
}
close $fh;
## get last one
&examine_frags(\%end_to_iworm, \%paired_iworm_contigs);
if ($num_warnings) {
print STDERR "WARNING: note there were $num_warnings reads that could not be deciphered as being /1 or /2 of a PE fragment. Hopefully, these were SE reads that should have been ignored. Otherwise, please research this further.\n\n";
}
if ($num_unrecognized_iworm_contig_names) {
print STDERR "WARNING: note, there were $num_unrecognized_iworm_contig_names inchworm contig names in the SAM file that were ignored due to the inchworm contig accession not being recognized.\n";
}
foreach my $pairing (reverse sort {$paired_iworm_contigs{$a}<=>$paired_iworm_contigs{$b}} keys %paired_iworm_contigs) {
my ($iworm_acc_A, $iworm_acc_B) = split(/\t/, $pairing);
my $index_A = $iworm_acc_to_fasta_index{$iworm_acc_A};
unless (defined $index_A) {
print STDERR "WARNING, no index for iworm acc: $iworm_acc_A\n";
next;
}
my $index_B = $iworm_acc_to_fasta_index{$iworm_acc_B};
unless (defined $index_B) {
print STDERR "WARNING, no index for iworm acc: $iworm_acc_B\n";
next;
}
print join("\t", $iworm_acc_A, $index_A, $iworm_acc_B, $index_B, $paired_iworm_contigs{$pairing}) . "\n";
}
close $SAM_OFH;
exit(0);
}
####
sub examine_frags {
my ($end_to_iworm_href, $paired_iworm_contigs_href) = @_;
my @ends = keys %$end_to_iworm_href;
unless (scalar @ends == 2) {
## no pairs
return;
}
my @iworm_left = keys %{$end_to_iworm_href->{1}};
my @iworm_right = keys %{$end_to_iworm_href->{2}};
if (scalar(@iworm_left) == 1 && scalar(@iworm_right) == 1
&&
$iworm_left[0] ne $iworm_right[0]) {
my $pair = join("\t", sort (@iworm_left, @iworm_right));
#print STDERR "Got pairing: $pair\n";
$paired_iworm_contigs_href->{$pair}++;
foreach my $sam_line (values %{$end_to_iworm_href->{1}}, values %{$end_to_iworm_href->{2}}) {
print $SAM_OFH $sam_line;
}
}
return;
}
|
