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comparison lib/sRNAPipe/subgroups.pm @ 64:967512924317 draft

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planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
author brasset_jensen
date Mon, 28 Jan 2019 11:57:15 -0500
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63:11708af40030 64:967512924317
1 package sRNAPipe::subgroups;
2
3 use strict;
4 use warnings;
5 use Exporter;
6 our @ISA = qw( Exporter );
7 our @EXPORT_OK = qw( &subgroups );
8
9 use POSIX;
10 use File::Copy;
11 use FindBin;
12 use lib "$FindBin::Bin/../lib";
13 use sRNAPipe::align qw ( get_hash_alignment );
14
15 sub subgroups
16 {
17 my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_;
18 my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref );
19
20 srand();
21 print $report "----------------------------\n";
22 print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n";
23
24 mkdir $dir;
25 $dir = $dir.'/' unless $dir =~ /(.*)\/$/;
26
27 my $accept_miRNas = $dir.'miRNAs.fastq';
28 my $reject_miRNAs = $dir.'miRNAs_rejected.fastq';
29 my $sam_miRNAs = $dir.'miRNAs.sam';
30 my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report);
31 my $mi = $tmp[0]; my $sam = '';
32 $repartition{'miRNAs'} = $mi;
33
34
35 my $reject_rRNAs = $dir.'rRNAs_rejected.fastq';
36 if ( $rRNAs eq 'None')
37 {
38 move($reject_miRNAs,$reject_rRNAs);
39 }
40 else
41 {
42 $sam = new String::Random;
43 $sam = $sam->randpattern("CCcccccc");
44 @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report);
45 $repartition{'rRNAs'} = $tmp[0];
46 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
47 }
48
49 my $reject_tRNAs = $dir.'rRNAs_rejected.fastq';
50 if ( $rRNAs eq 'None')
51 {
52 move($reject_rRNAs,$reject_tRNAs);
53 }
54 else
55 {
56 $sam = new String::Random;
57 $sam = $sam->randpattern("CCcccccc");
58 @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report);
59 $repartition{'tRNAs'} = $tmp[0];
60 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
61 }
62
63
64 my $bonafide = $dir.'bonafide_reads.fastq';
65 if ( $rRNAs eq 'None')
66 {
67 move($reject_tRNAs,$bonafide);
68 }
69 else
70 {
71 $sam = new String::Random;
72 $sam = $sam->randpattern("CCcccccc");
73 @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report);
74 $repartition{'snRNAs'} = $tmp[0];
75
76 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
77 }
78 my $bo = $tmp[1];
79
80 my $sam_transcripts = $dir.'transcripts.sam';
81 my $reject_transcripts = $dir.'rejected_transcripts.fastq';
82 @tmp = get_hash_alignment($transcripts, $mis, 0, 1, 'NA', $reject_transcripts, $bonafide, $proc, 'transcripts', $sam_transcripts, $report, $dir.'transcripts.fai');
83 $repartition{'transcripts'} = $tmp[0];
84
85
86 my $sam_TEs = $dir.'TEs.sam';
87 my $reject_TEs = $dir.'rejected.fastq';
88 @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_transcripts, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' );
89 $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1];
90 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
91 unlink $reject_transcripts;
92 unlink $reject_rRNAs;
93 unlink $reject_miRNAs;
94 unlink $reject_tRNAs;
95
96 #create repartition
97 my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi );
98
99 open (my $re, '>'.$dir.'repartition.txt') || die "cannot open $dir repartition.txt $!\n";
100 print $re "type\tnumber\tpercentage\n";
101 $sum += $_ foreach values %repartition;
102 foreach my $k ( sort keys %repartition )
103 {
104 my $prct = 0;
105 $prct = $repartition{$k} / $sum * 100 if $sum != 0;
106 print $re "$k\t$repartition{$k}\t"; printf $re "%.2f\n",$prct;
107 }
108 return ( $bo, $mi, $pi);
109 }
110
111 sub fastqSubgroups
112 {
113 my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_;
114 my $fastq_siRNA = $output_directory."siRNAs.fastq";
115 my $fastq_piRNA = $output_directory."piRNAs.fastq";
116
117 open my $fic, '<', $fastq || die "cannot open input file $! \n";
118 open my $si, '>', $fastq_siRNA || die "cannot open siRNA.fastq $! \n";
119 open my $pi, '>', $fastq_piRNA || die "cannot open piRNA.fastq $! \n";
120
121 my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0);
122 my (@fastq) =(); my $seq_name;
123 my $out;
124 while(<$fic>)
125 {
126 chomp $_;
127 $cmp++;
128 if ($cmp == 1)
129 {
130 die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ );
131 $type = 0; @fastq = ();
132 if ($_ =~ /^\@(.*)\s.*/) { $seq_name = $1;}
133 elsif ($_ =~ /^\@(.*)/) {$seq_name = $1;}
134 push(@fastq,$_);
135 }
136 elsif ($cmp == 2)
137 {
138 #die "unrecognized symbol at line $cmp\n" unless $_ =~ /[atcgATCGnN]+/;
139 push(@fastq,$_);
140 $length = length($_);
141 $type = 0;
142 if ( $length >= $min_si && $length <= $max_si )
143 {
144 $type = 2;
145 $siRNA_number++;
146 }
147 if ($length >= $min_pi && $length <= $max_pi )
148 {
149 $type += 4;
150 $piRNA_number++;
151 }
152 }
153 elsif ($cmp == 3 )
154 {
155 die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/;
156 push(@fastq,$_);
157 }
158 elsif ($cmp == 4 )
159 {
160 push(@fastq,$_);
161 $cmp = 0;
162 if ($type != 0)
163 {
164 if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\n";} }
165 if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\n";} }
166 }
167 }
168 }
169 close $fic;
170 close $si; close $pi;
171 return ($piRNA_number);
172 }
173
174 1;