2bRAD_trim_launch.pl

#!/usr/bin/perl

my $usage= "

Prints out list of commands for launcher_creator.py 
to trim 2bRAD reads

Arguments:
arg1, required: glob to fastq files
site=[pattern] perl-style pattern of the restriction site to recognise, in single quotes.
		default is BcgI: \'.{12}CGA.{6}TGC.{12}|.{12}GCA.{6}TCG.{12}\'
		if you need AlfI, here is how to define it: \'.{12}GCA.{6}TGC.{12}\'
adaptor=[dna sequence] adaptor sequence to look for on the far end of the read. 
		Default AGATCGGAA
sampleID=[integer] the position of name-deriving string in the file name
					if separated by underscores, such as: 
					for input file Sample_RNA_2DVH_L002_R1.cat.fastq
					specifying arg2 as \'3\' would create output 
					file with a name \'2DVH.trim'	
barcode2=[integer] length of the in-line barcode immediately following 
			   the restriction fragment. Default 0. 	
";

my $glob=shift or die $usage;
my $site=".{12}CGA.{6}TGC.{12}|.{12}GCA.{6}TCG.{12}";
if("@ARGV"=~/site=(\S+)/){ $site=$1;}
my $sampleid=100;
if("@ARGV"=~/sampleID=(\d)/){ $sampleid=$1;}
my $adaptor="AGATC?";
if("@ARGV"=~/adaptor=(\S+)/){ $adaptor=$1;}
my $q33="-Q33";
if("@ARGV"=~/q33=0/){ $q33="";}
my $bar2=0;
if("@ARGV"=~/barcode2=(\d)/){ $bar2=$1;}


opendir THIS, ".";
my @fqs=grep /$glob/,readdir THIS;
my $outname="";
my @outnames;

foreach $fqf (@fqs) {
	if ($sampleid<100) {
		my @parts=split('_',$fqf);
		$outname=$parts[$sampleid-1].".tr0";
	}
	else { $outname=$fqf.".tr0";}
	if ($bar2==0){
		print "trim2bRAD.pl $fqf \"$site\" \"$adaptor\" >$outname\n";
	}
	else {
		print "trim2bRAD_2barcodes.pl fastq=$fqf site=\"$site\" barcode2=\"[ATGC]{$bar2}\" adaptor=\"$adaptor\" sampleID=$sampleid\n";
	}
}