update style in script for SmartSeq-3 (4ce22e6d) · Commits · github_fork / Universc

sub/FilterSmartSeqReadUMI.pl

+14 −18

Original line number	Diff line number	Diff line
		@@ -18,7 +18,8 @@ use Getopt::Long;


		#####Options#####
		my $ss3i = "ATTGCGCAATG";
		#SmartSeq3 tag
		my $ss3t = "ATTGCGCAATG";

		#setting the default values.
		my $i1 = "";
		@@ -57,21 +58,22 @@ elsif (!$out_dir) {
		die "USAGE: option --out_dir <OUTPUT_DIRECTORY> is required.\n";
		}

		$i1_out = $out_dir."/"."SmartSeq3_parsed_I1.fastq";
		#set output file names
		$i1_out = $out_dir."/".$i1_out;
		$i1_out =~ s/\/\//\//;
		$i2_out = $out_dir."/"."SmartSeq3_parsed_I2.fastq";
		$i2_out = $out_dir."/".$i2_out;
		$i2_out =~ s/\/\//\//;
		$r1_out = $out_dir."/"."SmartSeq3_parsed_R1.fastq";
		$r1_out = $out_dir."/".$r1_out;
		$r1_out =~ s/\/\//\//;
		$r2_out = $out_dir."/"."SmartSeq3_parsed_R2.fastq";
		$r2_out = $out_dir."/".$r2_out;
		$r2_out =~ s/\/\//\//;
		##########



		#####MAIN#####
		#get order of reads to keep
		my @keepreads = map { ($_ + 2) / 4 } split(/\n/, `grep $ss3i $r1 -n \| cut -f1 -d\:`);
		#get list of reads to keep
		my @keepreads = map { ($_ + 2) / 4 } split(/\n/, `grep $ss3t $r1 -n \| cut -f1 -d\:`);
		my %keepreads = map { $_ => 1 } @keepreads;

		#parse reads to keep
		@@ -86,6 +88,8 @@ open (R1OUT, ">", $r1_out) or die "cannot open $r1_out.\n";
		open (R2OUT, ">", $r2_out) or die "cannot open $r2_out.\n";
		while (my $line = <R1>) {
		$readcount++;

		#read in data
		my $i1_head = <I1>;
		my $i1_seq = <I1>;
		my $i1_plus = <I1>;
		@@ -108,9 +112,9 @@ while (my $line = <R1>) {
		}
		else {
		#trim r1 data
		my @trim = split (/$ss3i/, $r1_seq);
		my @trim = split (/$ss3t/, $r1_seq);
		shift @trim;
		my $new_r1_seq = join ("$ss3i", @trim);
		my $new_r1_seq = join ("$ss3t", @trim);
		my $new_r1_q = $r1_q;
		chomp $new_r1_q;
		$new_r1_q = reverse $new_r1_q;
		@@ -118,6 +122,7 @@ while (my $line = <R1>) {
		$new_r1_q = reverse $new_r1_q;
		$new_r1_q = $new_r1_q."\n";

		#print out data
		print I1OUT "$i1_head";
		print I1OUT "$i1_seq";
		print I1OUT "$i1_plus";
		@@ -144,13 +149,4 @@ close (I1OUT);
		close (I2OUT);
		close (R1OUT);
		close (R2OUT);









		##########
		No newline at end of file

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