From f888e173865eb9a78c2d881e8cfcd69514b8d29f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 29 Sep 2020 14:53:31 -0500
Subject: [PATCH] update designfile RNASeq
---
design_file/check_design.py | 0
design_file/check_designfile.pl | 81 ++++++++++++++++++++++++++++++++
design_file/check_inputfiles.sh | 26 ++++++++++
design_file/checkdesignfile.sh | 10 ++++
design_file/experiment_design.py | 0
5 files changed, 117 insertions(+)
mode change 100644 => 100755 design_file/check_design.py
create mode 100755 design_file/check_designfile.pl
create mode 100755 design_file/check_inputfiles.sh
create mode 100755 design_file/checkdesignfile.sh
mode change 100644 => 100755 design_file/experiment_design.py
diff --git a/design_file/check_design.py b/design_file/check_design.py
old mode 100644
new mode 100755
diff --git a/design_file/check_designfile.pl b/design_file/check_designfile.pl
new file mode 100755
index 0000000..e2ae6bc
--- /dev/null
+++ b/design_file/check_designfile.pl
@@ -0,0 +1,81 @@
+#!/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";
+}
diff --git a/design_file/check_inputfiles.sh b/design_file/check_inputfiles.sh
new file mode 100755
index 0000000..31422e7
--- /dev/null
+++ b/design_file/check_inputfiles.sh
@@ -0,0 +1,26 @@
+#!/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
diff --git a/design_file/checkdesignfile.sh b/design_file/checkdesignfile.sh
new file mode 100755
index 0000000..8be80a4
--- /dev/null
+++ b/design_file/checkdesignfile.sh
@@ -0,0 +1,10 @@
+#!/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
diff --git a/design_file/experiment_design.py b/design_file/experiment_design.py
old mode 100644
new mode 100755
--
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