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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,198 @@ | ||
| #!/usr/bin/env perl | ||
|
|
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| use strict; | ||
| use warnings; | ||
| use File::Basename; | ||
| use Getopt::Long; | ||
|
|
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| my $outputDir=''; | ||
|
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| my @unpairedList= (); | ||
| my @pairedList= (); | ||
|
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| GetOptions( | ||
| 'u:s{1,}' => \@unpairedList, | ||
| 'p:s{1,}' => \@pairedList, | ||
| 'd=s' => \$outputDir, | ||
| ); | ||
|
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||
|
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| my $all_R1_fastq = "$outputDir/all.1.fastq"; | ||
| my $all_R2_fastq = "$outputDir/all.2.fastq"; | ||
| my $all_SE_fastq = "$outputDir/all.se.fastq"; | ||
| my $count_file_list= "$outputDir/fastqCount.txt"; | ||
| my $avg_read_len= 0 ; | ||
| my $PE_count = 0 ; | ||
| my $PE_total_len = 0; | ||
| my $SE_count= 0 ; | ||
| my $SE_total_len = 0 ; | ||
|
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|
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|
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| open (my $fh, ">$count_file_list") or die "Cannot write $count_file_list\n"; | ||
| while(my ($R1,$R2) = splice (@pairedList,0,2)) | ||
| { | ||
| ($PE_count, $PE_total_len) = &countPE_exe($R1,$R2,$all_R1_fastq,$all_R2_fastq,$all_SE_fastq,$fh); | ||
| } | ||
| foreach my $file (@unpairedList) | ||
| { | ||
| ($SE_count,$SE_total_len)=&countFastq_exe($file,$all_SE_fastq); | ||
| printf $fh ("%s\t%d\t%d\t%.2f\n",basename($file),$SE_count,$SE_total_len,$SE_total_len/$SE_count); | ||
| printf ("%s\t%d\t%d\t%.2f\n",basename($file),$SE_count,$SE_total_len,$SE_total_len/$SE_count); | ||
| } | ||
| close $fh; | ||
| $avg_read_len = ($PE_count + $SE_count) > 0 ? ($PE_total_len + $SE_total_len) / ($PE_count + $SE_count) : 0 ; | ||
|
|
||
| sub countPE_exe{ | ||
| my $r1=shift; | ||
| my $r2=shift; | ||
| my $out_r1=shift; | ||
| my $out_r2=shift; | ||
| my $out_se=shift; | ||
| my $count_fh=shift; | ||
| my %seq_hash; | ||
| my $pair_char; | ||
| my $unpaired_count=0; | ||
| my $read1_count=0; | ||
| my $read2_count=0; | ||
| my $se2_count=0; | ||
| my $se1_count=0; | ||
| my $paired_count=0; | ||
| my $read1_total_len=0; | ||
| my $read2_total_len=0; | ||
| my $existed_id1=0; | ||
| my $existed_id2=0; | ||
| my ($fh1,$pid) = open_file($r1); | ||
| open (my $ofh1, ">>$out_r1") or die "Cannot write $out_r1\n"; | ||
| open (my $ofh2, ">>$out_r2") or die "Cannot write $out_r2\n"; | ||
| open (my $ofhse, ">>$out_se") or die "Cannot write $out_se\n"; | ||
| while(<$fh1>){ | ||
| chomp; | ||
| next unless $_ =~ /\S/; | ||
| next if ($_ =~ /length=0/); | ||
| my $id_line=$_; | ||
| my ($id) = $id_line =~ /^\@(\S+).?\/?1?\s*/; | ||
| my $seq = <$fh1>; | ||
| chomp $seq; | ||
| if ($seq_hash{$id}){ | ||
| $existed_id1++; | ||
| } | ||
| my $len = length $seq; | ||
| $read1_total_len += $len; | ||
| my $qual_id = <$fh1>; | ||
| my $qual = <$fh1>; | ||
| $seq = $seq."\n".$qual_id.$qual; | ||
| $seq_hash{$id}++; | ||
| $read1_count++; | ||
| } | ||
| close $fh1; | ||
| my %seq_hash2; | ||
| my ($fh2,$pid2) = open_file($r2); | ||
| while(<$fh2>){ | ||
| chomp; | ||
| next unless $_ =~ /\S/; | ||
| next if ($_ =~ /length=0/); | ||
| my $id_line=$_; | ||
| my ($id2) = $id_line =~ /^\@(\S+)\.?\/?2?\s*/; | ||
| $read2_count++; | ||
| my $seq2 = <$fh2>; | ||
| chomp $seq2; | ||
| if ($seq_hash2{$id2}){ | ||
| $existed_id2++; | ||
| } | ||
| my $len = length $seq2; | ||
| $read2_total_len += $len; | ||
| my $qual_id = <$fh2>; | ||
| my $qual = <$fh2>; | ||
| $seq2 = $seq2."\n".$qual_id.$qual; | ||
| $seq_hash2{$id2}++; | ||
| if ($seq_hash{$id2}){ | ||
| $seq_hash{$id2}++; | ||
| $paired_count++; | ||
| print $ofh2 $id_line,"\n",$seq2; | ||
| }else{ | ||
| print $ofhse $id_line,"\n",$seq2; | ||
| $se2_count++; | ||
| } | ||
| } | ||
| close $fh2; | ||
| ($fh1,$pid) = open_file($r1); | ||
| while(<$fh1>){ | ||
| chomp; | ||
| next unless $_ =~ /\S/; | ||
| next if ($_ =~ /length=0/); | ||
| my $id_line=$_; | ||
| my ($id) = $id_line =~ /^\@(\S+)\.?\/?1?\s*/; | ||
| my $seq = <$fh1>; | ||
| chomp $seq; | ||
| my $qual_id = <$fh1>; | ||
| my $qual = <$fh1>; | ||
| $seq = $seq."\n".$qual_id.$qual; | ||
| if ($seq_hash{$id} == 2){ | ||
| print $ofh1 $id_line,"\n",$seq; | ||
| } | ||
| if ($seq_hash{$id} == 1){ | ||
| print $ofhse $id_line,"\n",$seq; | ||
| $se1_count++; | ||
| } | ||
| } | ||
| close $fh1; | ||
| close $ofh1; | ||
| close $ofh2; | ||
| close $ofhse; | ||
| printf ("%s\t%d\t%d\t%.2f\n",basename($r1),$read1_count,$read1_total_len,$read1_total_len/$read1_count); | ||
| printf ("%s\t%d\t%d\t%.2f\n",basename($r2),$read2_count,$read2_total_len,$read2_total_len/$read2_count); | ||
| printf $count_fh ("%s\t%d\t%d\t%.2f\n",basename($r1),$read1_count,$read1_total_len,$read1_total_len/$read1_count); | ||
| printf $count_fh ("%s\t%d\t%d\t%.2f\n",basename($r2),$read2_count,$read2_total_len,$read2_total_len/$read2_count); | ||
| printf ("%d duplicate id from %s\n", $existed_id1, basename($r1)) if ($existed_id1 > 0); | ||
| printf ("%d duplicate id from %s\n", $existed_id2, basename($r2)) if ($existed_id2 > 0); | ||
| printf ("There are %d reads from %s don't have corresponding paired read.\n", $se1_count, basename($r1)) if ($se1_count >0); | ||
| printf ("There are %d reads from %s don't have corresponding paired read.\n", $se2_count, basename($r2)) if ($se2_count >0); | ||
|
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||
| unlink $out_se if (-z $out_se); | ||
| return ($read1_count + $read2_count, $read1_total_len + $read2_total_len); | ||
| } | ||
|
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||
| sub countFastq_exe | ||
| { | ||
| my $file=shift; | ||
| my $output=shift; | ||
| my $seq_count=0; | ||
| my $total_length; | ||
| my ($fh,$pid)= open_file($file); | ||
| open (my $ofh, ">>$output") or die "Cannot write $output\n"; | ||
| while (<$fh>) | ||
| { | ||
| next unless $_ =~ /\S/; | ||
| next if ($_ =~ /length=0/); | ||
| my $id=$_; | ||
| $id = '@'."seq_$seq_count\n" if ($id =~ /No name/); | ||
| my $seq=<$fh>; | ||
| chomp $seq; | ||
| my $q_id=<$fh>; | ||
| my $q_seq=<$fh>; | ||
| my $len = length $seq; | ||
| $seq_count++; | ||
| $total_length +=$len; | ||
| print $ofh "$id$seq\n$q_id$q_seq"; | ||
| } | ||
| close $fh; | ||
| return ($seq_count,$total_length); | ||
| } | ||
|
|
||
| sub touchFile{ | ||
| my $file=shift; | ||
| open (my $fh,">",$file) or die "$!"; | ||
| close $fh; | ||
| } | ||
|
|
||
| sub open_file | ||
| { | ||
| my ($file) = @_; | ||
| print "$file\n"; | ||
| my $fh; | ||
| my $pid; | ||
| if ( $file=~/\.gz\.?\d?$/i ) { $pid=open($fh, "gunzip -c $file |") or die ("gunzip -c $file: $!"); } | ||
| else { $pid=open($fh,'<',$file) or die("$file: $!"); } | ||
| return ($fh,$pid); | ||
| } |
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