Repository 'mirplant2'
hg clone https://toolshed.g2.bx.psu.edu/repos/big-tiandm/mirplant2

Changeset 28:5e05c9bb919c (2014-07-31)
Previous changeset 27:eaf9715e5143 (2014-07-31) Next changeset 29:253b51f72993 (2014-07-31)
Commit message:
Uploaded
added:
count_rfam_express.pl
b
diff -r eaf9715e5143 -r 5e05c9bb919c count_rfam_express.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/count_rfam_express.pl Thu Jul 31 03:06:29 2014 -0400
[
b'@@ -0,0 +1,1800 @@\n+#!/usr/bin/perl -w\n+#Filename:\n+#Author: Tian Dongmei\n+#Email: tiandm@big.ac.cn\n+#Date: 2013/7/19\n+#Modified:\n+#Description: \n+my $version=1.00;\n+\n+use strict;\n+use Getopt::Long;\n+use File::Basename;\n+\n+my %opts;\n+GetOptions(\\%opts,"i=s","o=s","tag:s","h");\n+if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments\n+&usage;\n+}\n+\n+my $filein=$opts{\'i\'};\n+my $fileout=$opts{\'o\'};\n+\n+my $marks=defined $opts{\'tag\'} ? $opts{\'tag\'} : "";\n+\n+if(!(defined $opts{\'tag\'})){\n+\tmy $line=`head -1 $filein`;\n+\tmy @tmp=split/\\t/,$line;\n+\t$tmp[0]=~/:([\\d|_]+)_x(\\d+)$/;\n+\tmy @ss=split/_/,$1;\n+\tfor (my $i=1;$i<=@ss;$i++) {\n+\t\t$marks .="Smp$i;";\n+\t}\n+}\n+\n+my @marks=split/\\;/,$marks;\n+\n+my %rfam_key;\n+while(<DATA>){\n+    chomp;\n+    if(/^(\\S+)\\s+(\\S+)$/){\n+\t\t$rfam_key{$1}=$2;\n+    }\n+}\n+\n+\n+my %reads;\n+my %tags;\n+open IN,"<$filein";\n+while (my $aline=<IN>) {\n+\tchomp $aline;\n+\tmy @tmp=split/\\t/,$aline;\n+\t$tmp[0]=~/:([\\d|_]+)_x(\\d+)$/;\n+\n+\tmy @exp=split/_/,$1;\n+\tmy @tag=split/\\;/,$tmp[2];\n+\n+\tif (defined $rfam_key{$tag[0]}) {\n+\t\tfor (my $i=0;$i<@exp;$i++) {\n+\t\t\t$reads{$rfam_key{$tag[0]}}[$i]+=$exp[$i];\n+\t\t\t$tags{$rfam_key{$tag[0]}}[$i]++ if($exp[$i]!=0);\n+\t\t}\n+\t}else{\n+\t\tfor (my $i=0;$i<@exp;$i++) {\n+\t\t\t$reads{other}[$i]+=$exp[$i];\n+\t\t\t$tags{other}[$i]++ if($exp[$i]!=0);\n+\t\t}\n+\t}\n+\n+}\n+close IN;\n+\n+$"="\\t"; ##### @array print in \\t\n+open OUT,">$fileout";\n+print OUT "####################################\\n# small RNA expressed reads number #\\n####################################\\n";\n+print OUT "#RNAname\\t@marks\\n";\n+foreach my $key (keys %reads) {\n+\tprint OUT $key;\n+\tfor (my $i=0;$i<@{$reads{$key}} ;$i++) {\n+\t\tprint OUT "\\t",$reads{$key}[$i];\n+\t}\n+\tprint OUT "\\n";\n+}\n+\n+print OUT "\\n\\n####################################\\n# small RNA expressed tags number #\\n####################################\\n";\n+print OUT "#RNAname\\t@marks\\n";\n+\n+foreach my $key (keys %tags) {\n+\tprint OUT  $key;\n+\tfor (my $i=0;$i<@{$reads{$key}} ;$i++) {\n+\t\tif(defined $tags{$key}[$i]){print OUT "\\t",$tags{$key}[$i];}\n+\t\telse{print OUT "\\t0";}\n+\t}\n+\tprint OUT  "\\n";\n+}\n+\n+close OUT;\n+$"=" "; ##### @array print in \\t\n+\n+sub usage{\n+print <<"USAGE";\n+Version $version\n+Usage:\n+$0 -i -tag -o\n+options:\n+-i input file# rfam bowtie bwt. format mapping result\n+-tag [string] sample marks# eg. sampleA;sampleB;sampleC\n+-o output file\n+\n+-h help\n+USAGE\n+exit(1);\n+}\n+\n+__DATA__\n+RF00635\tlncRNA\n+RF01868\tlncRNA\n+RF01869\tlncRNA\n+RF01870\tlncRNA\n+RF01871\tlncRNA\n+RF01872\tlncRNA\n+RF01873\tlncRNA\n+RF01874\tlncRNA\n+RF01875\tlncRNA\n+RF01876\tlncRNA\n+RF01877\tlncRNA\n+RF01878\tlncRNA\n+RF01879\tlncRNA\n+RF01880\tlncRNA\n+RF01881\tlncRNA\n+RF01882\tlncRNA\n+RF01883\tlncRNA\n+RF01884\tlncRNA\n+RF01885\tlncRNA\n+RF01886\tlncRNA\n+RF01887\tlncRNA\n+RF01888\tlncRNA\n+RF01889\tlncRNA\n+RF01890\tlncRNA\n+RF01891\tlncRNA\n+RF01892\tlncRNA\n+RF01893\tlncRNA\n+RF01894\tlncRNA\n+RF01904\tlncRNA\n+RF01905\tlncRNA\n+RF01906\tlncRNA\n+RF01907\tlncRNA\n+RF01908\tlncRNA\n+RF01909\tlncRNA\n+RF01928\tlncRNA\n+RF01929\tlncRNA\n+RF01930\tlncRNA\n+RF01931\tlncRNA\n+RF01932\tlncRNA\n+RF01933\tlncRNA\n+RF01934\tlncRNA\n+RF01935\tlncRNA\n+RF01946\tlncRNA\n+RF01947\tlncRNA\n+RF01948\tlncRNA\n+RF01950\tlncRNA\n+RF01951\tlncRNA\n+RF01952\tlncRNA\n+RF01953\tlncRNA\n+RF01954\tlncRNA\n+RF01955\tlncRNA\n+RF01956\tlncRNA\n+RF01957\tlncRNA\n+RF01958\tlncRNA\n+RF01961\tlncRNA\n+RF01962\tlncRNA\n+RF01963\tlncRNA\n+RF01964\tlncRNA\n+RF01965\tlncRNA\n+RF01966\tlncRNA\n+RF01967\tlncRNA\n+RF01968\tlncRNA\n+RF01969\tlncRNA\n+RF01970\tlncRNA\n+RF01971\tlncRNA\n+RF01972\tlncRNA\n+RF01973\tlncRNA\n+RF01974\tlncRNA\n+RF01975\tlncRNA\n+RF01976\tlncRNA\n+RF01977\tlncRNA\n+RF01978\tlncRNA\n+RF01979\tlncRNA\n+RF01980\tlncRNA\n+RF01981\tlncRNA\n+RF01983\tlncRNA\n+RF01984\tlncRNA\n+RF01985\tlncRNA\n+RF01986\tlncRNA\n+RF01987\tlncRNA\n+RF01992\tlncRNA\n+RF02038\tlncRNA\n+RF02039\tlncRNA\n+RF02040\tlncRNA\n+RF02041\tlncRNA\n+RF02042\tlncRNA\n+RF02043\tlncRNA\n+RF02044\tlncRNA\n+RF02045\tlncRNA\n+RF02046\tlncRNA\n+RF02047\tlncRNA\n+RF02085\tlncRNA\n+RF02086\tlncRNA\n+RF02087\tlncRNA\n+RF02089\tlncRNA\n+RF02090\tlncRNA\n+RF02091\tlncRNA\n+RF02098\tlncRNA\n+RF02101\tlncRNA\n+RF02102\tlncR'..b'5\tsnRNA\n+RF01646\tsnRNA\n+RF01647\tsnRNA\n+RF01648\tsnRNA\n+RF01649\tsnRNA\n+RF01650\tsnRNA\n+RF01651\tsnRNA\n+RF01652\tsnRNA\n+RF01653\tsnRNA\n+RF01654\tsnRNA\n+RF01655\tsnRNA\n+RF01658\tsnRNA\n+RF01659\tsnRNA\n+RF01660\tsnRNA\n+RF01661\tsnRNA\n+RF01662\tsnRNA\n+RF01664\tsnRNA\n+RF01802\tsnRNA\n+RF01829\tsnRNA\n+RF01844\tsnRNA\n+RF01846\tsnRNA\n+RF01847\tsnRNA\n+RF01848\tsnRNA\n+RF01860\tsnRNA\n+RF01861\tsnRNA\n+RF01862\tsnRNA\n+RF01863\tsnRNA\n+RF01864\tsnRNA\n+RF01866\tsnRNA\n+RF02163\tsnRNA\n+RF00014\tsRNA\n+RF00018\tsRNA\n+RF00021\tsRNA\n+RF00034\tsRNA\n+RF00035\tsRNA\n+RF00057\tsRNA\n+RF00077\tsRNA\n+RF00078\tsRNA\n+RF00079\tsRNA\n+RF00081\tsRNA\n+RF00082\tsRNA\n+RF00083\tsRNA\n+RF00084\tsRNA\n+RF00101\tsRNA\n+RF00110\tsRNA\n+RF00111\tsRNA\n+RF00112\tsRNA\n+RF00113\tsRNA\n+RF00115\tsRNA\n+RF00116\tsRNA\n+RF00117\tsRNA\n+RF00118\tsRNA\n+RF00119\tsRNA\n+RF00121\tsRNA\n+RF00122\tsRNA\n+RF00124\tsRNA\n+RF00125\tsRNA\n+RF00126\tsRNA\n+RF00128\tsRNA\n+RF00166\tsRNA\n+RF00195\tsRNA\n+RF00368\tsRNA\n+RF00369\tsRNA\n+RF00370\tsRNA\n+RF00371\tsRNA\n+RF00372\tsRNA\n+RF00378\tsRNA\n+RF00444\tsRNA\n+RF00505\tsRNA\n+RF00519\tsRNA\n+RF00615\tsRNA\n+RF00616\tsRNA\n+RF01116\tsRNA\n+RF01385\tsRNA\n+RF01386\tsRNA\n+RF01387\tsRNA\n+RF01388\tsRNA\n+RF01389\tsRNA\n+RF01390\tsRNA\n+RF01391\tsRNA\n+RF01392\tsRNA\n+RF01393\tsRNA\n+RF01394\tsRNA\n+RF01395\tsRNA\n+RF01396\tsRNA\n+RF01397\tsRNA\n+RF01398\tsRNA\n+RF01399\tsRNA\n+RF01400\tsRNA\n+RF01401\tsRNA\n+RF01402\tsRNA\n+RF01403\tsRNA\n+RF01404\tsRNA\n+RF01405\tsRNA\n+RF01406\tsRNA\n+RF01407\tsRNA\n+RF01408\tsRNA\n+RF01409\tsRNA\n+RF01410\tsRNA\n+RF01411\tsRNA\n+RF01412\tsRNA\n+RF01457\tsRNA\n+RF01459\tsRNA\n+RF01460\tsRNA\n+RF01461\tsRNA\n+RF01462\tsRNA\n+RF01463\tsRNA\n+RF01464\tsRNA\n+RF01465\tsRNA\n+RF01466\tsRNA\n+RF01467\tsRNA\n+RF01468\tsRNA\n+RF01469\tsRNA\n+RF01470\tsRNA\n+RF01471\tsRNA\n+RF01472\tsRNA\n+RF01473\tsRNA\n+RF01474\tsRNA\n+RF01476\tsRNA\n+RF01477\tsRNA\n+RF01478\tsRNA\n+RF01479\tsRNA\n+RF01487\tsRNA\n+RF01488\tsRNA\n+RF01489\tsRNA\n+RF01492\tsRNA\n+RF01493\tsRNA\n+RF01494\tsRNA\n+RF01496\tsRNA\n+RF01503\tsRNA\n+RF01504\tsRNA\n+RF01512\tsRNA\n+RF01519\tsRNA\n+RF01520\tsRNA\n+RF01521\tsRNA\n+RF01527\tsRNA\n+RF01528\tsRNA\n+RF01529\tsRNA\n+RF01530\tsRNA\n+RF01571\tsRNA\n+RF01578\tsRNA\n+RF01579\tsRNA\n+RF01580\tsRNA\n+RF01581\tsRNA\n+RF01582\tsRNA\n+RF01619\tsRNA\n+RF01623\tsRNA\n+RF01643\tsRNA\n+RF01656\tsRNA\n+RF01663\tsRNA\n+RF01665\tsRNA\n+RF01668\tsRNA\n+RF01669\tsRNA\n+RF01670\tsRNA\n+RF01671\tsRNA\n+RF01672\tsRNA\n+RF01673\tsRNA\n+RF01674\tsRNA\n+RF01675\tsRNA\n+RF01676\tsRNA\n+RF01677\tsRNA\n+RF01678\tsRNA\n+RF01679\tsRNA\n+RF01680\tsRNA\n+RF01681\tsRNA\n+RF01682\tsRNA\n+RF01683\tsRNA\n+RF01684\tsRNA\n+RF01685\tsRNA\n+RF01686\tsRNA\n+RF01687\tsRNA\n+RF01690\tsRNA\n+RF01691\tsRNA\n+RF01693\tsRNA\n+RF01694\tsRNA\n+RF01696\tsRNA\n+RF01698\tsRNA\n+RF01699\tsRNA\n+RF01700\tsRNA\n+RF01701\tsRNA\n+RF01702\tsRNA\n+RF01703\tsRNA\n+RF01705\tsRNA\n+RF01706\tsRNA\n+RF01710\tsRNA\n+RF01712\tsRNA\n+RF01714\tsRNA\n+RF01718\tsRNA\n+RF01719\tsRNA\n+RF01722\tsRNA\n+RF01723\tsRNA\n+RF01728\tsRNA\n+RF01732\tsRNA\n+RF01742\tsRNA\n+RF01757\tsRNA\n+RF01762\tsRNA\n+RF01775\tsRNA\n+RF01781\tsRNA\n+RF01782\tsRNA\n+RF01783\tsRNA\n+RF01784\tsRNA\n+RF01789\tsRNA\n+RF01791\tsRNA\n+RF01793\tsRNA\n+RF01796\tsRNA\n+RF01808\tsRNA\n+RF01810\tsRNA\n+RF01812\tsRNA\n+RF01814\tsRNA\n+RF01815\tsRNA\n+RF01816\tsRNA\n+RF01817\tsRNA\n+RF01818\tsRNA\n+RF01819\tsRNA\n+RF01820\tsRNA\n+RF01821\tsRNA\n+RF01822\tsRNA\n+RF01823\tsRNA\n+RF01827\tsRNA\n+RF01828\tsRNA\n+RF01858\tsRNA\n+RF01867\tsRNA\n+RF02029\tsRNA\n+RF02030\tsRNA\n+RF02031\tsRNA\n+RF02049\tsRNA\n+RF02050\tsRNA\n+RF02051\tsRNA\n+RF02052\tsRNA\n+RF02053\tsRNA\n+RF02054\tsRNA\n+RF02055\tsRNA\n+RF02056\tsRNA\n+RF02057\tsRNA\n+RF02059\tsRNA\n+RF02060\tsRNA\n+RF02062\tsRNA\n+RF02063\tsRNA\n+RF02064\tsRNA\n+RF02065\tsRNA\n+RF02066\tsRNA\n+RF02067\tsRNA\n+RF02070\tsRNA\n+RF02071\tsRNA\n+RF02072\tsRNA\n+RF02073\tsRNA\n+RF02074\tsRNA\n+RF02075\tsRNA\n+RF02077\tsRNA\n+RF02078\tsRNA\n+RF02079\tsRNA\n+RF02080\tsRNA\n+RF02081\tsRNA\n+RF02082\tsRNA\n+RF02099\tsRNA\n+RF02100\tsRNA\n+RF02151\tsRNA\n+RF02221\tsRNA\n+RF02222\tsRNA\n+RF02223\tsRNA\n+RF02224\tsRNA\n+RF02225\tsRNA\n+RF02226\tsRNA\n+RF02227\tsRNA\n+RF02228\tsRNA\n+RF02230\tsRNA\n+RF02231\tsRNA\n+RF02232\tsRNA\n+RF02233\tsRNA\n+RF02234\tsRNA\n+RF02235\tsRNA\n+RF02236\tsRNA\n+RF02237\tsRNA\n+RF02238\tsRNA\n+RF02239\tsRNA\n+RF02240\tsRNA\n+RF02241\tsRNA\n+RF02242\tsRNA\n+RF02243\tsRNA\n+RF02268\tsRNA\n+RF02269\tsRNA\n+RF00127\tsRNA\n+RF01852\ttRNA\n+RF00005\ttRNA\n'