| Previous changeset 21:b963c4a161d2 (2014-07-25) Next changeset 23:45de5e1ff487 (2014-07-25) |
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Commit message:
Deleted selected files |
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removed:
miRPlant.pl |
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| diff -r b963c4a161d2 -r c0aecae5eb03 miRPlant.pl --- a/miRPlant.pl Fri Jul 25 05:57:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,503 +0,0 @@\n-#!/usr/bin/perl -w\n-#Filename:\n-#Author: Tian Dongmei\n-#Email: tiandm@big.ac.cn\n-#Date: 2014-4-22\n-#Modified:\n-#Description: plant microRNA prediction\n-my $version=1.00;\n-\n-use strict;\n-use Getopt::Long;\n-use threads;\n-use threads::shared;\n-use File::Path;\n-use File::Basename;\n-#use RNA;\n-use Term::ANSIColor;\n-\n-my %opts;\n-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");\n-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\n-&usage;\n-}\n-\n-my $time=&Time();\n-print "miPlant program start:\\n The time is $time!\\n";\n-print "Command line:\\n $0 @ARGV\\n";\n-\n-my $format=$opts{\'format\'};\n-if ($format ne "fastq" && $format ne "fq" && $format ne "fasta" && $format ne "fa") { \n-\t&printErr();\n-\tdie "Parameter \\"-format\\" is error! Parameter is fastq, fq, fasta or fa\\n";\n-}\n-\n-my $phred_qv=64;\n-\n-\n-my @inputfiles=@{$opts{\'i\'}};\n-my @inputtags=@{$opts{\'tag\'}};\n-\n-my $mypath=`pwd`;\n-chomp $mypath;\n-\n-my $dir=defined $opts{\'o\'} ? $opts{\'o\'} : "$mypath/miRPlant_out/";\n-\n-\n-unless ($dir=~/\\/$/) {$dir.="/";}\n-if (not -d $dir) {\n-\tmkdir $dir;\n-}\n-my $config=$dir."/input_config";\n-open CONFIG,">$config";\n-\tfor (my $i=0;$i<@inputfiles;$i++) {\n-\t\tprint CONFIG $inputfiles[$i],"\\t",$inputtags[$i],"\\n";\n-\t}\n-close CONFIG;\n-\n-my $scipt_path=defined $opts{\'path\'} ? $opts{\'path\'} : "/Users/big/galaxy-dist/tools/myTools/";\n-\n-my $a="ATCTCGTATG"; #adapter\n-if (defined $opts{\'a\'}) {$a=$opts{\'a\'};}\n-\n-my $m=6; #adapter minimum mapped nt\n-if (defined $opts{\'M\'}) {$m=$opts{\'M\'};}\n-\n-my $t=1; #threads number\n-if (defined $opts{\'t\'}) {$t=$opts{\'t\'};}\n-\n-my $min_nt=19; # minimum reads length\n-if (defined $opts{\'min\'}) {$min_nt=$opts{\'min\'};}\n-\n-my $max_nt=28; #maximum reads length\n-if (defined $opts{\'max\'}) {$max_nt=$opts{\'max\'};}\n-\n-my $mis=0; #mismatch number for microRNA\n-if (defined $opts{\'mis\'}) {$mis=$opts{\'mis\'};}\n-\n-my $mis_rfam=0;# mismatch number for rfam\n-if (defined $opts{\'v\'}) {$mis_rfam=$opts{\'v\'};}\n-\n-my $hit=25; # maximum reads mapping hits in genome\n-if (defined $opts{\'r\'}) {$hit=$opts{\'r\'};}\n-\n-my $upstream = 2; # microRNA 5\' extension\n-$upstream = $opts{\'e\'} if(defined $opts{\'e\'});\n-\n-my $downstream = 5;# microRNA 3\' extension\n-$downstream = $opts{\'f\'} if(defined $opts{\'f\'});\n-\n-my $maxd=defined $opts{\'dis\'} ? $opts{\'dis\'} : 200;\n-my $flank=defined $opts{\'flank\'} ? $opts{\'flank\'} :10;\n-my $mfe=defined $opts{\'mfe\'} ? $opts{\'mfe\'} : -20;\n-\n-$time=&Time();\n-print "$time, Checking input file!\\n";\n-\n-my (@filein,@mark,@clean);\n-#&read_config();\n-@filein=@inputfiles;\n-@mark=@inputtags;\n-\n-&checkfa($opts{pre});\n-&checkfa($opts{mat});\n-&checkfa($opts{gfa});\n-\n-\n-##### clip adpter --> clean data start\n-$time=&Time();\n-print "$time, Preprocess:\\n trim adapter, reads collapse and filter reads by length.\\n";\n-\n-$time=~s/:/-/g;\n-$time=~s/ /-/g;\n-my $preprocess=$dir."preProcess_${time}/";\n-mkdir $preprocess;\n-my $can_use_threads = eval \'use threads; 1\';\n-if ($can_use_threads) {\n-# Do processing using threads\n-\tprint "Do processing using threads\\n";\n-\tmy @filein1=@filein; my @mark1=@mark;\n-\twhile (@filein1>0) {\n-\t\tmy @thrs; my @res;\n-\t\tfor (my $i=0;$i<$t ;$i++) {\n-\t\t\tlast if(@filein1==0);\n-\t\t\tmy $in=shift @filein1;\n-\t\t\tmy $out=shift @mark1;\n-\t\t\tpush @clean,$preprocess.$out."_clips_adapter.fq";\n-\t\t\t$thrs[$i]=threads->create(\\&clips,$in,$out);\n-\t\t}\n-\t\tfor (my $i=0;$i<@thrs;$i++) {\n-\t\t\t$res[$i]=$thrs[$i]->join();\n-\t\t}\n-\t}\n-} else {\n-# Do not processing using threads\n-\tprint "Do not processing using threads\\n";\n-\tfor (my $i=0;$i<@filein ;$i++) {\n-\t\tmy $in=$filein[$i];\n-\t\tmy $out=$mark[$i];\n-\t\tpush @clean,$preprocess.$out."_clips_adapter.fq";\n-\t\t&clips($in,$out);\n-\t}\n-}\n-\n-##### clip adpter --> clean data end\n-\n-my $collapsed=$preprocess."collapse_reads.fa";\n-my $data='..b'-\tclose N;\n-}\n-\n-sub search{\n-\tmy ($dir,$str)=@_;\n-\topendir I,$dir;\n-\tmy @ret;\n-\twhile (my $file=readdir I) {\n-\t\tif ($file=~/$str/) {\n-\t\t\tpush @ret, $file;\n-\t\t}\n-\t}\n-\tclosedir I;\n-\tif (@ret != 1) {\n-\t\t&printErr();\n-\n-\t\tdie "Can not find directory or file which name has string: $str !!!\\n";\n-\t}\n-\treturn $ret[0];\n-}\n-\n-sub printErr{\n- print STDERR color \'bold red\';\n- print STDERR "Error: ";\n- print STDERR color \'reset\';\n-}\n-=cut\n-sub Time{\n- my $time=time();\n- my ($sec,$min,$hour,$day,$month,$year) = (localtime($time))[0,1,2,3,4,5,6];\n- $month++;\n- $year+=1900;\n- if (length($sec) == 1) {$sec = "0"."$sec";}\n- if (length($min) == 1) {$min = "0"."$min";}\n- if (length($hour) == 1) {$hour = "0"."$hour";}\n- if (length($day) == 1) {$day = "0"."$day";}\n- if (length($month) == 1) {$month = "0"."$month";}\n- #print "$year-$month-$day $hour:$min:$sec\\n";\n- return("$year-$month-$day-$hour-$min-$sec");\n-}\n-=cut\n-sub Time{\n- my $time=time();\n- my ($sec,$min,$hour,$day,$month,$year) = (localtime($time))[0,1,2,3,4,5,6];\n- $month++;\n- $year+=1900;\n- if (length($sec) == 1) {$sec = "0"."$sec";}\n- if (length($min) == 1) {$min = "0"."$min";}\n- if (length($hour) == 1) {$hour = "0"."$hour";}\n- if (length($day) == 1) {$day = "0"."$day";}\n- if (length($month) == 1) {$month = "0"."$month";}\n- #print "$year-$month-$day $hour:$min:$sec\\n";\n- return("$year-$month-$day $hour:$min:$sec");\n-}\n-\n-\n-sub usage{\n-print <<"USAGE";\n-Version $version\n-Usage:\n-$0 -i -format -gfa -index -pre -mat -rfam -D -a -M -min -max -mis -e -f -v -t -o -path\n-options:\n--i string, input file#input files information file\n-\t\t/path/filename\tmark\n-\t\t/path/filename\tmark\n-\t\t...\n-\n--format string,#specific input rawdata file format : fastq|fq|fasta|fa\n-\n--gfa string, input file # genome fasta. sequence file\n--idx string, genome file index, file-prefix #(must be indexed by bowtie-build) The parameter\n- string must be the prefix of the bowtie index. For instance, if\n- the first indexed file is called \'h_sapiens_37_asm.1.ebwt\' then\n- the prefix is \'h_sapiens_37_asm\'.##can be null\n-\n--pre string, input file #species specific microRNA precursor sequences\n--mat string, input file #species specific microRNA mature sequences\n-\n--rfam string, input file# rfam database file, microRNAs must not be contained in this file## if not define, rfam small RNA will not be count.\n--idx2 string, rfam file index, file-prefix #(must be indexed by bowtie-build) The parameter\n- string must be the prefix of the bowtie index. For instance, if\n- the first indexed file is called \'h_sapiens_37_asm.1.ebwt\' then\n- the prefix is \'h_sapiens_37_asm\'.##can be null\n-\n--D If [-D] is specified,will discard rfam mapped reads(nead -rfam).\n-\n--a string, ADAPTER string. default is ATCTCGTATG.\n--M int, require minimum adapter alignment length of N. If less than N nucleotides aligned with the adapter - don\'t clip it. \n--min int, reads min length,default is 19.\n--max int, reads max length,default is 28.\n-\n--mis [int] number of allowed mismatches when mapping reads to precursors, default 0\n--e [int] number of nucleotides upstream of the mature sequence to consider, default 2\n--f [int] number of nucleotides downstream of the mature sequence to consider, default 5\n--v <int> report end-to-end hits w/ <=v mismatches; ignore qualities,default 0; used in rfam alignment\n--r int a read is allowed to map up to this number of positions in the genome,default is 25 \n-\n--dis <int> Maximal space between miRNA and miRNA* (200)\n--flank <int> Flank sequence length of miRNA precursor (10)\n--mfe <folat> Maximal free energy allowed for a miRNA precursor (-20)\n-\n--t int, number of threads [1]\n-\n--o output directory# absolute path\n--h help\n-USAGE\n-exit(1);\n-}\n-\n' |