Mercurial > repos > big-tiandm > mirplant2
diff miRPlant.pl @ 44:0c4e11018934 draft
Uploaded
author | big-tiandm |
---|---|
date | Thu, 30 Oct 2014 21:29:19 -0400 |
parents | 554fbaf5f451 |
children | ca05d68aca13 |
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--- a/miRPlant.pl Tue Oct 28 01:35:32 2014 -0400 +++ b/miRPlant.pl Thu Oct 30 21:29:19 2014 -0400 @@ -13,7 +13,7 @@ use threads::shared; use File::Path; use File::Basename; -#use RNA; +use RNA; use Term::ANSIColor; my %opts; @@ -235,19 +235,19 @@ 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"); + 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 +3 -25 precursor_mapped.bst > signatures.bst"); + 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"); + #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"); } @@ -279,6 +279,7 @@ 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"; }