# HG changeset patch # User devteam # Date 1354635425 18000 # Node ID 181dd378275c2f9c5dfb22821f1d7a2a3ccbff18 Uploaded add_value tarball. diff -r 000000000000 -r 181dd378275c fixedValueColumn.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fixedValueColumn.pl Tue Dec 04 10:37:05 2012 -0500 @@ -0,0 +1,34 @@ +#! /usr/bin/perl -w + +use strict; +use warnings; + +# fixedValueColumn.pl $input $out_file1 "expression" "iterate [yes|no]" + +my ($input, $out_file1, $expression, $iterate) = @ARGV; +my $i = 0; +my $numeric = 0; + +die "Check arguments\n" unless @ARGV == 4; + +open (DATA, "<$input") or die "Cannot open $input:$!\n"; +open (OUT, ">$out_file1") or die "Cannot create $out_file1:$!\n"; + +if ($expression =~ m/^\d+$/) { + $numeric = 1; + $i = $expression; +} + +while () { + chop; + if ($iterate eq "no") { + print OUT "$_\t$expression\n"; + } else { + print OUT "$_\t$i\n" if $numeric == 1; + print OUT "$_\t$expression-$i\n" if $numeric == 0; + ++$i; + } +} + +close DATA; +close OUT; diff -r 000000000000 -r 181dd378275c fixedValueColumn.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fixedValueColumn.xml Tue Dec 04 10:37:05 2012 -0500 @@ -0,0 +1,61 @@ + + to an existing dataset + fixedValueColumn.pl $input $out_file1 "$exp" $iterate + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + +----- + +**What it does** + +You can enter any value and it will be added as a new column to your dataset + +----- + +**Example** + +If you original data looks like this:: + + chr1 10 100 geneA + chr2 200 300 geneB + chr2 400 500 geneC + +Typing **+** in the text box will generate:: + + chr1 10 100 geneA + + chr2 200 300 geneB + + chr2 400 500 geneC + + + +You can also add line numbers by selecting **Iterate: YES**. In this case if you enter **1** in the text box you will get:: + + chr1 10 100 geneA 1 + chr2 200 300 geneB 2 + chr2 400 500 geneC 3 + + + + + diff -r 000000000000 -r 181dd378275c test-data/1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Tue Dec 04 10:37:05 2012 -0500 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - 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+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 000000000000 -r 181dd378275c test-data/eq-addvalue.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eq-addvalue.dat Tue Dec 04 10:37:05 2012 -0500 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 1 +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + 1 +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - 1 +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + 1 +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - 1 +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - 1 +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + 1 +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - 1 +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + 1 +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - 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