comparison miRPlant.pl @ 44:0c4e11018934 draft

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43:4c0b1a94b882

use Getopt::Long;
use threads;
use threads::shared;
use File::Path;
use File::Basename;
#use RNA;
use Term::ANSIColor;

my %opts;
GetOptions(\%opts,"i:s@","tag:s@","format=s","gfa=s","pre=s","mat=s","rfam:s","dis:i","flank:i","mfe:f","idx:s","idx2:s","mis:i","r:i","v:i","e:i","f:i","a:s","M:i","t:i","min:i","max:i","o:s","path:s","D","h");
if (!(defined $opts{i} and defined $opts{format} and defined $opts{gfa} and defined $opts{pre} and defined $opts{mat}) || defined $opts{h}) { #necessary arguments

#	print "\nprecursors.pl -map $mapfile -g $opts{gfa} -d $maxd -f $flank -o $predict/excised_precursor.fa -s $predict/excised_precursor_struc.txt -e $mfe\n";
	
	system("bowtie-build -f excised_precursor.fa excised_precursor");
#	print "\nbowtie-build -f excised_precursor.fa excised_precursor\n";
	
	system("bowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt");
#	print "\nbowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt\n";
	
	system("perl $scipt_path/convert_bowtie_to_blast.pl  precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst");
#	print "\nconvert_bowtie_to_blast.pl  precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst\n";

	system("sort +3 -25  precursor_mapped.bst  > signatures.bst");
#	print "\nsort +3 -25  precursor_mapped.bst  > ../signatures.bst\n";

	chdir $dir;
	system("perl $scipt_path/miRDeep_plant.pl $predict/signatures.bst $predict/excised_precursor_struc.txt novel_tmp_dir -y > microRNA_prediction.mrd");
#	print "\nmiRDeep_plant.pl $dir/signatures.bst $predict/excised_precursor_struc.txt tmp_dir -y > microRNA_prediction.txt\n";
	system("rm novel_tmp_dir -rf");
	my $tag=join "," ,@mark;
	system("perl $scipt_path/miRNA_Express_and_sequence.pl -i microRNA_prediction.mrd -list novel_microRNA_express.txt -fa novel_microRNA_mature.fa -pre novel_microRNA_precursor.fa -tag $tag");
}

sub genome{

#	print "\nquantify.pl -p $opts{pre} -m $opts{mat} -r $data -o $dir -time $time -mis $mis -t $t -e $upstream -f $downstream -tag $tag\n";
}
sub filterbylength{
	my $tmpmark=join ",", @mark;
	system("perl $scipt_path/filterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark");
#	print "\nfilterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark\n";

}
sub collapse{
	my ($ins,$data)=@_;

44:0c4e11018934

use Getopt::Long;
use threads;
use threads::shared;
use File::Path;
use File::Basename;
use RNA;
use Term::ANSIColor;

my %opts;
GetOptions(\%opts,"i:s@","tag:s@","format=s","gfa=s","pre=s","mat=s","rfam:s","dis:i","flank:i","mfe:f","idx:s","idx2:s","mis:i","r:i","v:i","e:i","f:i","a:s","M:i","t:i","min:i","max:i","o:s","path:s","D","h");
if (!(defined $opts{i} and defined $opts{format} and defined $opts{gfa} and defined $opts{pre} and defined $opts{mat}) || defined $opts{h}) { #necessary arguments

#	print "\nprecursors.pl -map $mapfile -g $opts{gfa} -d $maxd -f $flank -o $predict/excised_precursor.fa -s $predict/excised_precursor_struc.txt -e $mfe\n";
	
	system("bowtie-build -f excised_precursor.fa excised_precursor");
#	print "\nbowtie-build -f excised_precursor.fa excised_precursor\n";
	
	system("bowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt 2> run.log");
#	print "\nbowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt\n";
	
	system("perl $scipt_path/convert_bowtie_to_blast.pl  precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst");
#	print "\nconvert_bowtie_to_blast.pl  precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst\n";

	system("sort -k 4  precursor_mapped.bst  > signatures.bst");
#	print "\nsort +3 -25  precursor_mapped.bst  > ../signatures.bst\n";

	chdir $dir;
	system("perl $scipt_path/miRDeep_plant.pl $predict/signatures.bst $predict/excised_precursor_struc.txt novel_tmp_dir -y > microRNA_prediction.mrd");
#	print "\nmiRDeep_plant.pl $dir/signatures.bst $predict/excised_precursor_struc.txt tmp_dir -y > microRNA_prediction.txt\n";
	#system("rm novel_tmp_dir -rf");
	my $tag=join "," ,@mark;
	system("perl $scipt_path/miRNA_Express_and_sequence.pl -i microRNA_prediction.mrd -list novel_microRNA_express.txt -fa novel_microRNA_mature.fa -pre novel_microRNA_precursor.fa -tag $tag");
}

sub genome{

#	print "\nquantify.pl -p $opts{pre} -m $opts{mat} -r $data -o $dir -time $time -mis $mis -t $t -e $upstream -f $downstream -tag $tag\n";
}
sub filterbylength{
	my $tmpmark=join ",", @mark;
	system("perl $scipt_path/filterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark");
	system("perl $scipt_path/Length_Distibution.pl -i $preprocess/reads_length_distribution.txt  -o $preprocess/length.html");
#	print "\nfilterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark\n";

}
sub collapse{
	my ($ins,$data)=@_;