# HG changeset patch # User big-tiandm # Date 1406280008 14400 # Node ID 3ed8026af2d5bfedfa254d2122f5a7ff9ed16f96 # Parent c3b93bce023e9a58128a6250c3ddd81ca46a5689 Uploaded diff -r c3b93bce023e -r 3ed8026af2d5 count_rfam_express.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/count_rfam_express.pl Fri Jul 25 05:20:08 2014 -0400 @@ -0,0 +1,1800 @@ +#!/usr/bin/perl -w +#Filename: +#Author: Tian Dongmei +#Email: tiandm@big.ac.cn +#Date: 2013/7/19 +#Modified: +#Description: +my $version=1.00; + +use strict; +use Getopt::Long; +use File::Basename; + +my %opts; +GetOptions(\%opts,"i=s","o=s","tag:s","h"); +if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments +&usage; +} + +my $filein=$opts{'i'}; +my $fileout=$opts{'o'}; + +my $marks=defined $opts{'tag'} ? $opts{'tag'} : ""; + +if(!(defined $opts{'tag'})){ + my $line=`head -1 $filein`; + my @tmp=split/\t/,$line; + $tmp[0]=~/:([\d|_]+)_x(\d+)$/; + my @ss=split/_/,$1; + for (my $i=1;$i<=@ss;$i++) { + $marks .="Smp$i;"; + } +} + +my @marks=split/\;/,$marks; + +my %rfam_key; +while(){ + chomp; + if(/^(\S+)\s+(\S+)$/){ + $rfam_key{$1}=$2; + } +} + + +my %reads; +my %tags; +open IN,"<$filein"; +while (my $aline=) { + chomp $aline; + my @tmp=split/\t/,$aline; + $tmp[0]=~/:([\d|_]+)_x(\d+)$/; + + my @exp=split/_/,$1; + my @tag=split/\;/,$tmp[2]; + + if (defined $rfam_key{$tag[0]}) { + for (my $i=0;$i<@exp;$i++) { + $reads{$rfam_key{$tag[0]}}[$i]+=$exp[$i]; + $tags{$rfam_key{$tag[0]}}[$i]++ if($exp[$i]!=0); + } + }else{ + for (my $i=0;$i<@exp;$i++) { + $reads{other}[$i]+=$exp[$i]; + $tags{other}[$i]++ if($exp[$i]!=0); + } + } + +} +close IN; + +$"="\t"; ##### @array print in \t +open OUT,">$fileout"; +print OUT "####################################\n# small RNA expressed reads number #\n####################################\n"; +print OUT "#RNAname\t@marks\n"; +foreach my $key (keys %reads) { + print OUT $key; + for (my $i=0;$i<@{$reads{$key}} ;$i++) { + print OUT "\t",$reads{$key}[$i]; + } + print OUT "\n"; +} + +print OUT "\n\n####################################\n# small RNA expressed tags number #\n####################################\n"; +print OUT "#RNAname\t@marks\n"; + +foreach my $key (keys %tags) { + print OUT $key; + for (my $i=0;$i<@{$reads{$key}} ;$i++) { + if(defined $tags{$key}[$i]){print OUT "\t",$tags{$key}[$i];} + else{print OUT "\t0";} + } + print OUT "\n"; +} + +close OUT; +$"=" "; ##### @array print in \t + +sub usage{ +print <<"USAGE"; +Version $version +Usage: +$0 -i -tag -o +options: +-i input file# rfam bowtie bwt. format mapping result +-tag [string] sample marks# eg. sampleA;sampleB;sampleC +-o output file + +-h help +USAGE +exit(1); +} + +__DATA__ +RF00635 lncRNA +RF01868 lncRNA +RF01869 lncRNA +RF01870 lncRNA +RF01871 lncRNA +RF01872 lncRNA +RF01873 lncRNA +RF01874 lncRNA +RF01875 lncRNA +RF01876 lncRNA +RF01877 lncRNA +RF01878 lncRNA +RF01879 lncRNA +RF01880 lncRNA +RF01881 lncRNA +RF01882 lncRNA +RF01883 lncRNA +RF01884 lncRNA +RF01885 lncRNA +RF01886 lncRNA +RF01887 lncRNA +RF01888 lncRNA +RF01889 lncRNA +RF01890 lncRNA +RF01891 lncRNA +RF01892 lncRNA +RF01893 lncRNA +RF01894 lncRNA +RF01904 lncRNA +RF01905 lncRNA +RF01906 lncRNA +RF01907 lncRNA +RF01908 lncRNA +RF01909 lncRNA +RF01928 lncRNA +RF01929 lncRNA +RF01930 lncRNA +RF01931 lncRNA +RF01932 lncRNA +RF01933 lncRNA +RF01934 lncRNA +RF01935 lncRNA +RF01946 lncRNA +RF01947 lncRNA +RF01948 lncRNA +RF01950 lncRNA +RF01951 lncRNA +RF01952 lncRNA +RF01953 lncRNA +RF01954 lncRNA +RF01955 lncRNA +RF01956 lncRNA +RF01957 lncRNA +RF01958 lncRNA +RF01961 lncRNA +RF01962 lncRNA +RF01963 lncRNA +RF01964 lncRNA +RF01965 lncRNA +RF01966 lncRNA +RF01967 lncRNA +RF01968 lncRNA +RF01969 lncRNA +RF01970 lncRNA +RF01971 lncRNA +RF01972 lncRNA +RF01973 lncRNA +RF01974 lncRNA +RF01975 lncRNA +RF01976 lncRNA +RF01977 lncRNA +RF01978 lncRNA +RF01979 lncRNA +RF01980 lncRNA +RF01981 lncRNA +RF01983 lncRNA +RF01984 lncRNA +RF01985 lncRNA +RF01986 lncRNA +RF01987 lncRNA +RF01992 lncRNA +RF02038 lncRNA +RF02039 lncRNA +RF02040 lncRNA +RF02041 lncRNA +RF02042 lncRNA +RF02043 lncRNA +RF02044 lncRNA +RF02045 lncRNA +RF02046 lncRNA +RF02047 lncRNA +RF02085 lncRNA +RF02086 lncRNA +RF02087 lncRNA +RF02089 lncRNA +RF02090 lncRNA +RF02091 lncRNA +RF02098 lncRNA +RF02101 lncRNA +RF02102 lncRNA +RF02103 lncRNA +RF02104 lncRNA +RF02105 lncRNA +RF02106 lncRNA +RF02107 lncRNA +RF02108 lncRNA +RF02109 lncRNA +RF02110 lncRNA +RF02112 lncRNA +RF02113 lncRNA +RF02114 lncRNA +RF02115 lncRNA +RF02116 lncRNA +RF02117 lncRNA +RF02118 lncRNA +RF02119 lncRNA +RF02120 lncRNA +RF02121 lncRNA +RF02122 lncRNA +RF02123 lncRNA +RF02124 lncRNA +RF02125 lncRNA +RF02126 lncRNA +RF02127 lncRNA +RF02128 lncRNA +RF02129 lncRNA +RF02130 lncRNA +RF02131 lncRNA +RF02132 lncRNA +RF02133 lncRNA +RF02134 lncRNA +RF02135 lncRNA +RF02136 lncRNA +RF02137 lncRNA +RF02138 lncRNA +RF02139 lncRNA +RF02140 lncRNA +RF02141 lncRNA +RF02142 lncRNA +RF02143 lncRNA +RF02145 lncRNA +RF02146 lncRNA +RF02147 lncRNA +RF02148 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miRNA +RF00838 miRNA +RF00839 miRNA +RF00840 miRNA +RF00841 miRNA +RF00842 miRNA +RF00843 miRNA +RF00844 miRNA +RF00845 miRNA +RF00846 miRNA +RF00847 miRNA +RF00848 miRNA +RF00849 miRNA +RF00850 miRNA +RF00851 miRNA +RF00852 miRNA +RF00853 miRNA +RF00854 miRNA +RF00855 miRNA +RF00856 miRNA +RF00857 miRNA +RF00858 miRNA +RF00859 miRNA +RF00861 miRNA +RF00862 miRNA +RF00863 miRNA +RF00864 miRNA +RF00865 miRNA +RF00866 miRNA +RF00867 miRNA +RF00868 miRNA +RF00869 miRNA +RF00870 miRNA +RF00871 miRNA +RF00872 miRNA +RF00873 miRNA +RF00874 miRNA +RF00875 miRNA +RF00876 miRNA +RF00877 miRNA +RF00878 miRNA +RF00879 miRNA +RF00882 miRNA +RF00883 miRNA +RF00884 miRNA +RF00885 miRNA +RF00886 miRNA +RF00887 miRNA +RF00888 miRNA +RF00890 miRNA +RF00891 miRNA +RF00892 miRNA +RF00893 miRNA +RF00894 miRNA +RF00895 miRNA +RF00896 miRNA +RF00897 miRNA +RF00898 miRNA +RF00899 miRNA +RF00900 miRNA +RF00901 miRNA +RF00902 miRNA +RF00903 miRNA +RF00904 miRNA +RF00905 miRNA +RF00906 miRNA +RF00907 miRNA 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snRNA +RF01131 snRNA +RF01132 snRNA +RF01133 snRNA +RF01134 snRNA +RF01135 snRNA +RF01136 snRNA +RF01137 snRNA +RF01138 snRNA +RF01139 snRNA +RF01140 snRNA +RF01141 snRNA +RF01142 snRNA +RF01143 snRNA +RF01144 snRNA +RF01145 snRNA +RF01146 snRNA +RF01147 snRNA +RF01148 snRNA +RF01149 snRNA +RF01150 snRNA +RF01151 snRNA +RF01152 snRNA +RF01153 snRNA +RF01155 snRNA +RF01156 snRNA +RF01157 snRNA +RF01158 snRNA +RF01159 snRNA +RF01160 snRNA +RF01161 snRNA +RF01162 snRNA +RF01163 snRNA +RF01164 snRNA +RF01165 snRNA +RF01166 snRNA +RF01167 snRNA +RF01168 snRNA +RF01169 snRNA +RF01170 snRNA +RF01171 snRNA +RF01172 snRNA +RF01173 snRNA +RF01174 snRNA +RF01175 snRNA +RF01176 snRNA +RF01177 snRNA +RF01178 snRNA +RF01179 snRNA +RF01180 snRNA +RF01181 snRNA +RF01182 snRNA +RF01183 snRNA +RF01184 snRNA +RF01185 snRNA +RF01186 snRNA +RF01188 snRNA +RF01189 snRNA +RF01190 snRNA +RF01191 snRNA +RF01192 snRNA +RF01193 snRNA +RF01194 snRNA +RF01195 snRNA +RF01196 snRNA +RF01197 snRNA +RF01198 snRNA 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snRNA +RF01267 snRNA +RF01268 snRNA +RF01269 snRNA +RF01270 snRNA +RF01271 snRNA +RF01272 snRNA +RF01273 snRNA +RF01274 snRNA +RF01275 snRNA +RF01276 snRNA +RF01277 snRNA +RF01278 snRNA +RF01279 snRNA +RF01280 snRNA +RF01281 snRNA +RF01283 snRNA +RF01284 snRNA +RF01285 snRNA +RF01286 snRNA +RF01287 snRNA +RF01288 snRNA +RF01289 snRNA +RF01290 snRNA +RF01291 snRNA +RF01292 snRNA +RF01293 snRNA +RF01294 snRNA +RF01295 snRNA +RF01296 snRNA +RF01297 snRNA +RF01298 snRNA +RF01299 snRNA +RF01300 snRNA +RF01301 snRNA +RF01302 snRNA +RF01303 snRNA +RF01304 snRNA +RF01305 snRNA +RF01306 snRNA +RF01307 snRNA +RF01308 snRNA +RF01309 snRNA +RF01310 snRNA +RF01311 snRNA +RF01312 snRNA +RF01420 snRNA +RF01421 snRNA +RF01422 snRNA +RF01423 snRNA +RF01424 snRNA +RF01425 snRNA +RF01426 snRNA +RF01427 snRNA +RF01428 snRNA +RF01429 snRNA +RF01430 snRNA +RF01431 snRNA +RF01432 snRNA +RF01433 snRNA +RF01434 snRNA +RF01435 snRNA +RF01436 snRNA +RF01437 snRNA +RF01438 snRNA +RF01439 snRNA +RF01440 snRNA +RF01441 snRNA +RF01442 snRNA +RF01443 snRNA +RF01444 snRNA +RF01445 snRNA +RF01446 snRNA +RF01447 snRNA +RF01448 snRNA +RF01449 snRNA +RF01450 snRNA +RF01451 snRNA +RF01452 snRNA +RF01498 snRNA +RF01499 snRNA +RF01500 snRNA +RF01501 snRNA +RF01505 snRNA +RF01506 snRNA +RF01507 snRNA +RF01509 snRNA +RF01511 snRNA +RF01513 snRNA +RF01514 snRNA +RF01515 snRNA +RF01516 snRNA +RF01522 snRNA +RF01523 snRNA +RF01524 snRNA +RF01525 snRNA +RF01526 snRNA +RF01531 snRNA +RF01532 snRNA +RF01533 snRNA +RF01534 snRNA +RF01535 snRNA +RF01536 snRNA +RF01537 snRNA +RF01538 snRNA +RF01539 snRNA +RF01540 snRNA +RF01541 snRNA +RF01542 snRNA +RF01543 snRNA +RF01544 snRNA +RF01545 snRNA +RF01546 snRNA +RF01547 snRNA +RF01548 snRNA +RF01549 snRNA +RF01550 snRNA +RF01551 snRNA +RF01552 snRNA +RF01553 snRNA +RF01554 snRNA +RF01555 snRNA +RF01556 snRNA +RF01557 snRNA +RF01558 snRNA +RF01559 snRNA +RF01560 snRNA +RF01561 snRNA +RF01562 snRNA +RF01563 snRNA +RF01564 snRNA +RF01565 snRNA +RF01566 snRNA +RF01567 snRNA +RF01568 snRNA +RF01569 snRNA +RF01570 snRNA +RF01572 snRNA +RF01573 snRNA +RF01574 snRNA +RF01575 snRNA +RF01576 snRNA +RF01583 snRNA +RF01584 snRNA +RF01585 snRNA +RF01586 snRNA +RF01587 snRNA +RF01588 snRNA +RF01589 snRNA +RF01590 snRNA +RF01591 snRNA +RF01592 snRNA +RF01593 snRNA +RF01594 snRNA +RF01595 snRNA +RF01596 snRNA +RF01597 snRNA +RF01598 snRNA +RF01599 snRNA +RF01600 snRNA +RF01601 snRNA +RF01602 snRNA +RF01603 snRNA +RF01604 snRNA +RF01605 snRNA +RF01606 snRNA +RF01607 snRNA +RF01608 snRNA +RF01609 snRNA +RF01610 snRNA +RF01611 snRNA +RF01612 snRNA +RF01613 snRNA +RF01614 snRNA +RF01615 snRNA +RF01617 snRNA +RF01618 snRNA +RF01620 snRNA +RF01621 snRNA +RF01622 snRNA +RF01624 snRNA +RF01625 snRNA +RF01626 snRNA +RF01627 snRNA +RF01628 snRNA +RF01629 snRNA +RF01630 snRNA +RF01631 snRNA +RF01632 snRNA +RF01633 snRNA +RF01634 snRNA +RF01635 snRNA +RF01636 snRNA +RF01637 snRNA +RF01638 snRNA +RF01639 snRNA +RF01640 snRNA +RF01641 snRNA +RF01642 snRNA +RF01644 snRNA +RF01645 snRNA +RF01646 snRNA +RF01647 snRNA +RF01648 snRNA +RF01649 snRNA +RF01650 snRNA +RF01651 snRNA +RF01652 snRNA +RF01653 snRNA +RF01654 snRNA +RF01655 snRNA +RF01658 snRNA +RF01659 snRNA +RF01660 snRNA +RF01661 snRNA +RF01662 snRNA +RF01664 snRNA +RF01802 snRNA +RF01829 snRNA +RF01844 snRNA +RF01846 snRNA +RF01847 snRNA +RF01848 snRNA +RF01860 snRNA +RF01861 snRNA +RF01862 snRNA +RF01863 snRNA +RF01864 snRNA +RF01866 snRNA +RF02163 snRNA +RF00014 sRNA +RF00018 sRNA +RF00021 sRNA +RF00034 sRNA +RF00035 sRNA +RF00057 sRNA +RF00077 sRNA +RF00078 sRNA +RF00079 sRNA +RF00081 sRNA +RF00082 sRNA +RF00083 sRNA +RF00084 sRNA +RF00101 sRNA +RF00110 sRNA +RF00111 sRNA +RF00112 sRNA +RF00113 sRNA +RF00115 sRNA +RF00116 sRNA +RF00117 sRNA +RF00118 sRNA +RF00119 sRNA +RF00121 sRNA +RF00122 sRNA +RF00124 sRNA +RF00125 sRNA +RF00126 sRNA +RF00128 sRNA +RF00166 sRNA +RF00195 sRNA +RF00368 sRNA +RF00369 sRNA +RF00370 sRNA +RF00371 sRNA +RF00372 sRNA +RF00378 sRNA +RF00444 sRNA +RF00505 sRNA +RF00519 sRNA +RF00615 sRNA +RF00616 sRNA +RF01116 sRNA +RF01385 sRNA +RF01386 sRNA +RF01387 sRNA +RF01388 sRNA +RF01389 sRNA +RF01390 sRNA +RF01391 sRNA +RF01392 sRNA +RF01393 sRNA +RF01394 sRNA +RF01395 sRNA +RF01396 sRNA +RF01397 sRNA +RF01398 sRNA +RF01399 sRNA +RF01400 sRNA +RF01401 sRNA +RF01402 sRNA +RF01403 sRNA +RF01404 sRNA +RF01405 sRNA +RF01406 sRNA +RF01407 sRNA +RF01408 sRNA +RF01409 sRNA +RF01410 sRNA +RF01411 sRNA +RF01412 sRNA +RF01457 sRNA +RF01459 sRNA +RF01460 sRNA +RF01461 sRNA +RF01462 sRNA +RF01463 sRNA +RF01464 sRNA +RF01465 sRNA +RF01466 sRNA +RF01467 sRNA +RF01468 sRNA +RF01469 sRNA +RF01470 sRNA +RF01471 sRNA +RF01472 sRNA +RF01473 sRNA +RF01474 sRNA +RF01476 sRNA +RF01477 sRNA +RF01478 sRNA +RF01479 sRNA +RF01487 sRNA +RF01488 sRNA +RF01489 sRNA +RF01492 sRNA +RF01493 sRNA +RF01494 sRNA +RF01496 sRNA +RF01503 sRNA +RF01504 sRNA +RF01512 sRNA +RF01519 sRNA +RF01520 sRNA +RF01521 sRNA +RF01527 sRNA +RF01528 sRNA +RF01529 sRNA +RF01530 sRNA +RF01571 sRNA +RF01578 sRNA +RF01579 sRNA +RF01580 sRNA +RF01581 sRNA +RF01582 sRNA +RF01619 sRNA +RF01623 sRNA +RF01643 sRNA +RF01656 sRNA +RF01663 sRNA +RF01665 sRNA +RF01668 sRNA +RF01669 sRNA +RF01670 sRNA +RF01671 sRNA +RF01672 sRNA +RF01673 sRNA +RF01674 sRNA +RF01675 sRNA +RF01676 sRNA +RF01677 sRNA +RF01678 sRNA +RF01679 sRNA +RF01680 sRNA +RF01681 sRNA +RF01682 sRNA +RF01683 sRNA +RF01684 sRNA +RF01685 sRNA +RF01686 sRNA +RF01687 sRNA +RF01690 sRNA +RF01691 sRNA +RF01693 sRNA +RF01694 sRNA +RF01696 sRNA +RF01698 sRNA +RF01699 sRNA +RF01700 sRNA +RF01701 sRNA +RF01702 sRNA +RF01703 sRNA +RF01705 sRNA +RF01706 sRNA +RF01710 sRNA +RF01712 sRNA +RF01714 sRNA +RF01718 sRNA +RF01719 sRNA +RF01722 sRNA +RF01723 sRNA +RF01728 sRNA +RF01732 sRNA +RF01742 sRNA +RF01757 sRNA +RF01762 sRNA +RF01775 sRNA +RF01781 sRNA +RF01782 sRNA +RF01783 sRNA +RF01784 sRNA +RF01789 sRNA +RF01791 sRNA +RF01793 sRNA +RF01796 sRNA +RF01808 sRNA +RF01810 sRNA +RF01812 sRNA +RF01814 sRNA +RF01815 sRNA +RF01816 sRNA +RF01817 sRNA +RF01818 sRNA +RF01819 sRNA +RF01820 sRNA +RF01821 sRNA +RF01822 sRNA +RF01823 sRNA +RF01827 sRNA +RF01828 sRNA +RF01858 sRNA +RF01867 sRNA +RF02029 sRNA +RF02030 sRNA +RF02031 sRNA +RF02049 sRNA +RF02050 sRNA +RF02051 sRNA +RF02052 sRNA +RF02053 sRNA +RF02054 sRNA +RF02055 sRNA +RF02056 sRNA +RF02057 sRNA +RF02059 sRNA +RF02060 sRNA +RF02062 sRNA +RF02063 sRNA +RF02064 sRNA +RF02065 sRNA +RF02066 sRNA +RF02067 sRNA +RF02070 sRNA +RF02071 sRNA +RF02072 sRNA +RF02073 sRNA +RF02074 sRNA +RF02075 sRNA +RF02077 sRNA +RF02078 sRNA +RF02079 sRNA +RF02080 sRNA +RF02081 sRNA +RF02082 sRNA +RF02099 sRNA +RF02100 sRNA +RF02151 sRNA +RF02221 sRNA +RF02222 sRNA +RF02223 sRNA +RF02224 sRNA +RF02225 sRNA +RF02226 sRNA +RF02227 sRNA +RF02228 sRNA +RF02230 sRNA +RF02231 sRNA +RF02232 sRNA +RF02233 sRNA +RF02234 sRNA +RF02235 sRNA +RF02236 sRNA +RF02237 sRNA +RF02238 sRNA +RF02239 sRNA +RF02240 sRNA +RF02241 sRNA +RF02242 sRNA +RF02243 sRNA +RF02268 sRNA +RF02269 sRNA +RF00127 sRNA +RF01852 tRNA +RF00005 tRNA