Mercurial > repos > big-tiandm > mirplant2
comparison miRPlant.pl @ 44:0c4e11018934 draft
Uploaded
author | big-tiandm |
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date | Thu, 30 Oct 2014 21:29:19 -0400 |
parents | 554fbaf5f451 |
children | ca05d68aca13 |
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43:4c0b1a94b882 | 44:0c4e11018934 |
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11 use Getopt::Long; | 11 use Getopt::Long; |
12 use threads; | 12 use threads; |
13 use threads::shared; | 13 use threads::shared; |
14 use File::Path; | 14 use File::Path; |
15 use File::Basename; | 15 use File::Basename; |
16 #use RNA; | 16 use RNA; |
17 use Term::ANSIColor; | 17 use Term::ANSIColor; |
18 | 18 |
19 my %opts; | 19 my %opts; |
20 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"); | 20 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"); |
21 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 | 21 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 |
233 # 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"; | 233 # 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"; |
234 | 234 |
235 system("bowtie-build -f excised_precursor.fa excised_precursor"); | 235 system("bowtie-build -f excised_precursor.fa excised_precursor"); |
236 # print "\nbowtie-build -f excised_precursor.fa excised_precursor\n"; | 236 # print "\nbowtie-build -f excised_precursor.fa excised_precursor\n"; |
237 | 237 |
238 system("bowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt"); | 238 system("bowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt 2> run.log"); |
239 # print "\nbowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt\n"; | 239 # print "\nbowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt\n"; |
240 | 240 |
241 system("perl $scipt_path/convert_bowtie_to_blast.pl precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst"); | 241 system("perl $scipt_path/convert_bowtie_to_blast.pl precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst"); |
242 # print "\nconvert_bowtie_to_blast.pl precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst\n"; | 242 # print "\nconvert_bowtie_to_blast.pl precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst\n"; |
243 | 243 |
244 system("sort +3 -25 precursor_mapped.bst > signatures.bst"); | 244 system("sort -k 4 precursor_mapped.bst > signatures.bst"); |
245 # print "\nsort +3 -25 precursor_mapped.bst > ../signatures.bst\n"; | 245 # print "\nsort +3 -25 precursor_mapped.bst > ../signatures.bst\n"; |
246 | 246 |
247 chdir $dir; | 247 chdir $dir; |
248 system("perl $scipt_path/miRDeep_plant.pl $predict/signatures.bst $predict/excised_precursor_struc.txt novel_tmp_dir -y > microRNA_prediction.mrd"); | 248 system("perl $scipt_path/miRDeep_plant.pl $predict/signatures.bst $predict/excised_precursor_struc.txt novel_tmp_dir -y > microRNA_prediction.mrd"); |
249 # print "\nmiRDeep_plant.pl $dir/signatures.bst $predict/excised_precursor_struc.txt tmp_dir -y > microRNA_prediction.txt\n"; | 249 # print "\nmiRDeep_plant.pl $dir/signatures.bst $predict/excised_precursor_struc.txt tmp_dir -y > microRNA_prediction.txt\n"; |
250 system("rm novel_tmp_dir -rf"); | 250 #system("rm novel_tmp_dir -rf"); |
251 my $tag=join "," ,@mark; | 251 my $tag=join "," ,@mark; |
252 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"); | 252 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"); |
253 } | 253 } |
254 | 254 |
255 sub genome{ | 255 sub genome{ |
277 # 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"; | 277 # 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"; |
278 } | 278 } |
279 sub filterbylength{ | 279 sub filterbylength{ |
280 my $tmpmark=join ",", @mark; | 280 my $tmpmark=join ",", @mark; |
281 system("perl $scipt_path/filterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark"); | 281 system("perl $scipt_path/filterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark"); |
282 system("perl $scipt_path/Length_Distibution.pl -i $preprocess/reads_length_distribution.txt -o $preprocess/length.html"); | |
282 # print "\nfilterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark\n"; | 283 # print "\nfilterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark\n"; |
283 | 284 |
284 } | 285 } |
285 sub collapse{ | 286 sub collapse{ |
286 my ($ins,$data)=@_; | 287 my ($ins,$data)=@_; |