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comparison bin/subgroups.pm @ 1:1df6aaac800e draft

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author brasset_jensen
date Wed, 13 Dec 2017 10:40:50 -0500
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children 4155dba0d57a
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0:e4e71401c577 1:1df6aaac800e
1 package 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 FindBin;
11 use lib $FindBin::Bin;
12 use align qw ( get_hash_alignment );
13
14 sub subgroups
15 {
16 my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_;
17 my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref );
18
19 srand();
20 print $report "----------------------------\n";
21 print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n";
22
23 mkdir $dir;
24 $dir = $dir.'/' unless $dir =~ /(.*)\/$/;
25
26 my $accept_miRNas = $dir.'miRNAs.fastq';
27 my $reject_miRNAs = $dir.'miRNAs_rejected.fastq';
28 my $sam_miRNAs = $dir.'miRNAs.sam';
29 my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report);
30 my $mi = $tmp[0];
31 $repartition{'miRNAs'} = $mi;
32
33 my $sam = new String::Random;
34 $sam = $sam->randpattern("CCcccccc");
35 my $reject_rRNAs = $dir.'rRNAs_rejected.fastq';
36 @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report);
37 $repartition{'rRNAs'} = $tmp[0];
38 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
39
40 $sam = new String::Random;
41 $sam = $sam->randpattern("CCcccccc");
42 my $reject_tRNAs = $dir.'tRNAs_rejected.fastq';
43 @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report);
44 $repartition{'tRNAs'} = $tmp[0];
45 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
46
47 $sam = new String::Random;
48 $sam = $sam->randpattern("CCcccccc");
49 my $bonafide = $dir.'bonafide_reads.fastq';
50 @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report);
51 $repartition{'snRNAs'} = $tmp[0];
52 my $bo = $tmp[1];
53 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
54
55 my $sam_transcripts = $dir.'transcripts.sam';
56 my $reject_transcripts = $dir.'rejected_transcripts.fastq';
57 @tmp = get_hash_alignment($transcripts, $mis, 0, 1, 'NA', $reject_transcripts, $bonafide, $proc, 'transcripts', $sam_transcripts, $report, $dir.'transcripts.fai');
58 $repartition{'transcripts'} = $tmp[0];
59
60
61 my $sam_TEs = $dir.'TEs.sam';
62 my $reject_TEs = $dir.'rejected.fastq';
63 @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_transcripts, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' );
64 $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1];
65 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
66 unlink $reject_transcripts;
67 unlink $reject_rRNAs;
68 unlink $reject_miRNAs;
69 unlink $reject_tRNAs;
70
71 #create repartition
72 my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi );
73
74 open (my $re, '>'.$dir.'repartition.txt') || die "cannot open $dir repartition.txt $!\n";
75 print $re "type\tnumber\tpercentage\n";
76 $sum += $_ foreach values %repartition;
77 foreach my $k ( sort keys %repartition )
78 {
79 my $prct = 0;
80 $prct = $repartition{$k} / $sum * 100 if $sum != 0;
81 print $re "$k\t$repartition{$k}\t"; printf $re "%.2f\n",$prct;
82 }
83 return ( $bo, $mi, $pi);
84 }
85
86 sub fastqSubgroups
87 {
88 my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_;
89 my $fastq_siRNA = $output_directory."siRNAs.fastq";
90 my $fastq_piRNA = $output_directory."piRNAs.fastq";
91
92 open my $fic, '<', $fastq || die "cannot open input file $! \n";
93 open my $si, '>', $fastq_siRNA || die "cannot open siRNA.fastq $! \n";
94 open my $pi, '>', $fastq_piRNA || die "cannot open piRNA.fastq $! \n";
95
96 my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0);
97 my (@fastq) =(); my $seq_name;
98 my $out;
99 while(<$fic>)
100 {
101 chomp $_;
102 $cmp++;
103 if ($cmp == 1)
104 {
105 die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ );
106 $type = 0; @fastq = ();
107 if ($_ =~ /^\@(.*)\s.*/) { $seq_name = $1;}
108 elsif ($_ =~ /^\@(.*)/) {$seq_name = $1;}
109 push(@fastq,$_);
110 }
111 elsif ($cmp == 2)
112 {
113 #die "unrecognized symbol at line $cmp\n" unless $_ =~ /[atcgATCGnN]+/;
114 push(@fastq,$_);
115 $length = length($_);
116 $type = 0;
117 if ( $length >= $min_si && $length <= $max_si )
118 {
119 $type = 2;
120 $siRNA_number++;
121 }
122 if ($length >= $min_pi && $length <= $max_pi )
123 {
124 $type += 4;
125 $piRNA_number++;
126 }
127 }
128 elsif ($cmp == 3 )
129 {
130 die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/;
131 push(@fastq,$_);
132 }
133 elsif ($cmp == 4 )
134 {
135 push(@fastq,$_);
136 $cmp = 0;
137 if ($type != 0)
138 {
139 if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\n";} }
140 if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\n";} }
141 }
142 }
143 }
144 close $fic;
145 close $si; close $pi;
146 return ($piRNA_number);
147 }
148
149 1;