update designfile RNASeq

design_file/check_designfile.pl

+#!/usr/bin/perl -w
+#check_designfile.pl
+
+use strict;
+use warnings;
+
+my $pe = shift @ARGV;
+my $dfile = shift @ARGV;
+open OUT, ">design.valid.txt" or die $!;
+open DFILE, "<$dfile" or die $!;
+my $head = <DFILE>;
+chomp($head);
+$head =~ s/FullPathTo//g;
+my @colnames = split(/\t/,$head);
+my %newcols = map {$_=> 1} @colnames;
+
+unless (grep(/FqR1/,@colnames)) {
+    die "Missing Sequence Files in Design File: FqR1\n";
+}
+unless (grep(/SampleID/,@colnames)) {
+    die "Missing SampleID in Design File\n";
+}
+
+if ($pe eq 'pe') {
+    unless (grep(/FqR2/,@colnames)) {
+	die "Missing Sequence Files in Design File: FqR2\n";
+    }
+}else {
+    delete $newcols{FqR2};
+}
+
+my @cols = sort {$a cmp $b} keys %newcols;
+print OUT join("\t",@cols),"\n";
+my @grp = ('a','b');
+my $lnct = 0;
+while (my $line = <DFILE>) {
+    chomp($line);
+    $line =~ s/FullPathTo//g;
+    my @row = split(/\t/,$line);
+    my %hash;
+    foreach my $i (0..$#row) {
+	next unless ($newcols{$colnames[$i]});
+	$row[$i] =~ s/-//g unless ($colnames[$i] =~ m/Fq/);
+	$hash{$colnames[$i]} = $row[$i];
+    }
+    if ($hash{SampleID} =~ m/^\d/) {
+	$hash{SampleID} =~ s/^/S/;
+    }
+    $hash{SampleName} = $hash{SampleID} unless ($hash{SampleName});
+    $hash{SubjectID} = $hash{SampleID} unless ($hash{SubjectID});
+    unless ($hash{SampleGroup}) {
+	my $j = $lnct %% 2;
+	$hash{SampleGroup} = $grp[$j];
+    }
+    $lnct ++;
+    $hash{SampleGroup} =~ s/_//g;
+    next unless ( -f $hash{FqR1});
+    if ($hash{FqR1} =~ m/gz/) {
+	system(qq{mv $hash{FqR1} $hash{SampleID}.R1.fastq.gz});
+    }else {
+	system(qq{mv $hash{FqR1} $hash{SampleID}.R1.fastq});
+	system(qq{pigz -f $hash{SampleID}.R1.fastq});
+    }
+    $hash{FqR1} = "$hash{SampleID}.R1.fastq.gz";
+    if ($pe eq 'pe') {
+	next unless (-f $hash{FqR2});
+	if ($hash{FqR2} =~ m/gz/) {
+	    system(qq{mv $hash{FqR2} $hash{SampleID}.R2.fastq.gz});
+	}else {
+	    system(qq{mv $hash{FqR2} $hash{SampleID}.R2.fastq});
+	    system(qq{pigz -f $hash{SampleID}.R2.fastq});
+	}
+	$hash{FqR2} = "$hash{SampleID}.R2.fastq.gz";
+    }
+    my @line;
+    foreach my $f (@cols) {
+	push @line, $hash{$f};
+    }
+    print OUT join("\t",@line),"\n";
+    print join(",",$hash{SampleID},"$hash{SampleID}.R1.fastq.gz","$hash{SampleID}.R2.fastq.gz"),"\n";
+}

design_file/check_inputfiles.sh

+#!/bin/bash
+#check_inputfiles.sh
+
+fqs=`ls *.f*`
+
+for i in $fqs;
+do
+   if [[ ${i} == *.fq ]];
+   then
+	new_name=`echo ${i} | sed -e "s/.fq\$/_good.fastq/"`;
+	mv ${i} ${new_name};
+	`pigz -f ${new_name}`;
+   elif [[ ${i} == *.fastq ]];
+   then
+	new_name=`echo ${i} | sed -e "s/.fastq\$/_good.fastq/"`;
+	mv ${i} ${new_name};
+	`pigz -f ${new_name}`;
+   elif [[ ${i} == *.fq.gz ]];
+   then
+	new_name=`echo ${i} | sed -e "s/.fq.gz\$/_good.fastq.gz/"`;
+	mv ${i} ${new_name};
+   else
+	new_name=`echo ${i} | sed -e "s/.fastq.gz\$/_good.fastq.gz/"`;
+	mv ${i} ${new_name};
+   fi;
+done

design_file/checkdesignfile.sh

+#!/bin/bash
+#check_inputfiles.sh
+
+baseDir="`dirname \"$0\"`"
+
+rpair=$1
+design=$2
+
+perl -p -e 's/\\r\\n*/\\n/g' $design > design.fix.txt
+perl $baseDir/check_designfile.pl ${rpair} design.fix.txt