changeset 0:181dd378275c

Uploaded add_value tarball.
author devteam
date Tue, 04 Dec 2012 10:37:05 -0500
parents
children 4676e145a44e
files fixedValueColumn.pl fixedValueColumn.xml test-data/1.bed test-data/eq-addvalue.dat
diffstat 4 files changed, 225 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /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 = $expression;
+}
+
+while (<DATA>) {
+  chop;
+  if ($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;
--- /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 @@
+<tool id="addValue" name="Add column">
+  <description>to an existing dataset</description>
+  <command interpreter="perl">fixedValueColumn.pl $input $out_file1 "$exp" $iterate</command>
+  <inputs>
+     <param name="exp" size="20" type="text" value="1" label="Add this value"/>
+    <param format="tabular" name="input" type="data" label="to Dataset" help="Dataset missing? See TIP below" />
+    <param name="iterate" type="select" label="Iterate?">
+      <option value="no">NO</option>
+      <option value="yes">YES</option>
+    </param>    
+  </inputs>
+  <outputs>
+    <data format="input" name="out_file1" metadata_source="input"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="exp" value="1"/>
+      <param name="input" value="1.bed"/>
+      <param name="iterate" value="no"/>
+      <output name="out_file1" file="eq-addvalue.dat"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;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
+
+
+
+</help>
+</tool>
--- /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	-
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-
+chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+
+chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-
+chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+
+chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-
+chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+
+chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-
+chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-
+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	-
--- /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	-	1
+chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+	1
+chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-	1
+chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-	1
+chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+	1
+chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-	1
+chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+	1
+chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+	1
+chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-	1
+chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+	1
+chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-	1
+chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-	1
+chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+	1
+chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-	1
+chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+	1
+chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+	1
+chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-	1
+chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+	1
+chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-	1
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+	1
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-	1
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+	1
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-	1
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-	1
+chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+	1
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-	1
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+	1
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+	1
+chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-	1
+chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+	1
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-	1
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+	1
+chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-	1
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+	1
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-	1
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+	1
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-	1
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+	1
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-	1
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-	1
+chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+	1
+chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-	1
+chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+	1
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+	1
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-	1
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+	1
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-	1
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-	1
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+	1
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-	1
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+	1
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-	1
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+	1
+chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-	1
+chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+	1
+chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-	1