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changeset 0:e6f966602870 draft

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Uploaded change_case tarball.
author devteam
date Tue, 04 Dec 2012 10:49:46 -0500
parents
children 3970d288ee1f
files changeCase.pl changeCase.xml test-data/1.bed test-data/1.txt test-data/changeCase_out1.tabular test-data/changeCase_out2.tabular
diffstat 6 files changed, 285 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/changeCase.pl	Tue Dec 04 10:49:46 2012 -0500
@@ -0,0 +1,58 @@
+#! /usr/bin/perl -w
+
+use strict;
+use warnings;
+
+my $columns = {};
+my $del = "";
+my @in = ();
+my @out = ();
+my $command = "";
+my $field = 0;
+
+# a wrapper for changing the case of columns from within galaxy
+# isaChangeCase.pl [filename] [columns] [delim] [casing] [output]
+
+die "Check arguments: $0 [filename] [columns] [delim] [casing] [output]\n" unless @ARGV == 5;
+
+# process column input
+$ARGV[1] =~ s/\s+//g;
+foreach ( split /,/, $ARGV[1] ) {
+  if (m/^c\d{1,}$/i) {
+    s/c//ig;
+    $columns->{$_} = --$_;
+  }
+}
+
+die "No columns specified, columns are not preceeded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if keys %$columns == 0;
+
+my $column_delimiters_href = {
+	'TAB' => q{\t},
+	'COMMA' => ",",
+	'DASH' => "-",
+	'UNDERSCORE' => "_",
+	'PIPE' => q{\|},
+	'DOT' => q{\.},
+	'SPACE' => q{\s+}
+};
+	
+$del = $column_delimiters_href->{$ARGV[2]};
+
+open (OUT, ">$ARGV[4]") or die "Cannot create $ARGV[4]:$!\n";
+open (IN,  "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
+while (<IN>) {
+  chop;
+  @in = split /$del/; 
+  for ( my $i = 0; $i <= $#in; ++$i) {
+	if (exists $columns->{$i}) {
+		push(@out, $ARGV[3] eq 'up' ? uc($in[$i]) : lc($in[$i]));
+	} else {
+		push(@out, $in[$i]);
+	}
+  }
+  print OUT join("\t",@out), "\n";
+  @out = ();
+}
+close IN;
+
+close OUT;
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/changeCase.xml	Tue Dec 04 10:49:46 2012 -0500
@@ -0,0 +1,77 @@
+<tool id="ChangeCase" name="Change Case">
+  <description> of selected columns</description>
+  <stdio>
+    <exit_code range="1:" err_level="fatal" />
+  </stdio>
+  <command interpreter="perl">changeCase.pl $input "$cols" $delimiter $casing $out_file1</command>
+  <inputs>
+    <param name="input" format="txt" type="data" label="From"/>
+    <param name="cols" size="10" type="text" value="c1,c2" label="Change case of columns"/>
+    <param name="delimiter" type="select" label="Delimited by">
+      <option value="TAB">Tab</option>
+      <option value="SPACE">Whitespace</option>
+      <option value="DOT">Dot</option>
+      <option value="COMMA">Comma</option>
+      <option value="DASH">Dash</option>
+      <option value="UNDERSCORE">Underscore</option>
+      <option value="PIPE">Pipe</option>
+    </param>
+    <param name="casing" type="select" label="To">
+      <option value="up">Upper case</option>
+      <option value="lo">Lower case</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="1.txt" ftype="txt"/>
+      <param name="cols" value="c1"/>
+      <param name="delimiter" value="SPACE"/>
+      <param name="casing" value="up"/>
+      <output name="out_file1" file="changeCase_out1.tabular"/>
+    </test>
+    <test>
+      <param name="input" value="1.bed" ftype="bed"/>
+      <param name="cols" value="c1"/>
+      <param name="delimiter" value="TAB"/>
+      <param name="casing" value="up"/>
+      <output name="out_file1" file="changeCase_out2.tabular"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: warningmark
+
+**This tool breaks column assignments.** To re-establish column assignments run the tool and click on the pencil icon in the resulting history item.
+
+.. class:: warningmark
+
+The format of the resulting dataset from this tool is always tabular.
+
+-----
+
+**What it does**
+
+This tool selects specified columns from a dataset and converts the values of those columns to upper or lower case.
+
+- Columns are specified as **c1**, **c2**, and so on.
+- Columns can be specified in any order (e.g., **c2,c1,c6**)
+
+-----
+
+**Example**
+
+Changing columns 1 and 3 ( delimited by Comma ) to upper case in::
+
+  apple,is,good
+  windows,is,bad
+
+will result in::
+
+  APPLE is GOOD
+  WINDOWS is BAD
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.bed	Tue Dec 04 10:49:46 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/1.txt	Tue Dec 04 10:49:46 2012 -0500
@@ -0,0 +1,10 @@
+chr1    4225    19670
+chr10   6       8
+chr1    24417   24420
+chr6_hla_hap2   0       150
+chr2    1       5
+chr10   2       10
+chr1    30      55
+chrY    1       20
+chr1    1225979 42287290
+chr10   7       8
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/changeCase_out1.tabular	Tue Dec 04 10:49:46 2012 -0500
@@ -0,0 +1,10 @@
+CHR1	4225	19670
+CHR10	6	8
+CHR1	24417	24420
+CHR6_HLA_HAP2	0	150
+CHR2	1	5
+CHR10	2	10
+CHR1	30	55
+CHRY	1	20
+CHR1	1225979	42287290
+CHR10	7	8
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/changeCase_out2.tabular	Tue Dec 04 10:49:46 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	-