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changeset 3:dc24da0a3bd5 draft default tip

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Deleted selected files
author julius
date Wed, 01 Aug 2012 07:41:31 -0400
parents 1dfc6d345abd
children
files convert_characters.pl convert_characters.py convert_characters.xml
diffstat 3 files changed, 0 insertions(+), 200 deletions(-) [+]
line wrap: on
line diff
--- a/convert_characters.pl	Wed Aug 01 07:36:48 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,101 +0,0 @@
-#! /usr/bin/perl -w
-
-use strict;
-use warnings;
-
-# converts all characters of one type into another 
-# convert_characters.pl [input] [convert_from] [convert_to] [output]
-
-die "Check argument\n" unless @ARGV == 4;
-
-my $inputfile = $ARGV[0];
-my $convert_from = $ARGV[1];
-my $convert_to = $ARGV[2];
-my $outputfile = $ARGV[3];
-
-if ($convert_from eq "s")
-{
-    $convert_from = '\s';
-}
-elsif ($convert_from eq "T")
-{
-    $convert_from = '\t';
-}
-elsif ($convert_from eq "Sp")
-{
-    $convert_from = '\s';
-}
-elsif ($convert_from eq "Dt")
-{
-    $convert_from = '\.';
-}
-elsif ($convert_from eq "C")
-{
-    $convert_from = ",";
-}
-elsif ($convert_from eq "D")
-{
-    $convert_from = "-";
-}
-elsif ($convert_from eq "U")
-{
-    $convert_from = "_";
-}
-elsif ($convert_from eq "P")
-{
-    $convert_from = '\|';
-}
-else
-{
-    die "Invalid value specified for convert from\n";
-}
-
-
-if ($convert_to eq "T")
-{
-    $convert_to = "\t";
-}
-elsif ($convert_to eq "Sp")
-{
-    $convert_to = '\s';
-}
-elsif ($convert_to eq "Dt")
-{
-    $convert_to = "\.";
-}
-elsif ($convert_to eq "C")
-{
-    $convert_to = ",";
-}
-elsif ($convert_to eq "D")
-{
-    $convert_to = "-";
-}
-elsif ($convert_to eq "U")
-{
-    $convert_to = "_";
-}
-elsif ($convert_to eq "P")
-{
-    $convert_to = "|";
-}
-else
-{
-    die "Invalid value specified for convert to\n";
-}
-
-my $fhIn;
-open ($fhIn, "< $inputfile") or die "Cannot open source file";
-
-my $fhOut;
-open ($fhOut, "> $outputfile");
-
-while (<$fhIn>)
-{
-    my $thisLine = $_;
-    chomp $thisLine;
-    $thisLine =~ s/$convert_from{1,}/$convert_to/g;
-    print $fhOut $thisLine,"\n";    
-}
-close ($fhIn) or die "Cannot close source file\n";
-close ($fhOut) or die "Cannot close output fil\n";
--- a/convert_characters.py	Wed Aug 01 07:36:48 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-#By, Guruprasad Ananda.
-
-from galaxy import eggs
-import sys, re
-
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit()
-    
-def main():
-    if len(sys.argv) != 4:
-        stop_err("usage: convert_characters infile from_char outfile")
-
-    try:
-        fin = open(sys.argv[1],'r')
-    except:
-        stop_err("Input file cannot be opened for reading.")
-    
-    from_char = sys.argv[2]
-    
-    try:
-        fout = open(sys.argv[3],'w')
-    except:
-        stop_err("Output file cannot be opened for writing.")
-    
-    char_dict = {'T':'\t','s':'\s','Dt':'\.','C':',','D':'-','U':'_','P':'\|'}
-    from_ch = char_dict[from_char] + '+'    #making an RE to match 1 or more occurences.
-    skipped = 0
-    
-    for line in fin:
-        line = line.strip()
-        try:
-            fout.write("%s\n" %(re.sub(from_ch,'\t',line)))     
-        except:
-            skipped += 1
-            
-    if skipped:
-        print "Skipped %d lines as invalid." %skipped
-    
-if __name__ == "__main__": 
-    main()
\ No newline at end of file
--- a/convert_characters.xml	Wed Aug 01 07:36:48 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<tool id="Convert characters1" name="Convert" version="1.1.0">
-  <description>delimiters to TAB</description>
-  <command interpreter="python">convert_characters.py $input $convert_from $out_file1</command>
-  <inputs>
-    <param name="convert_from" type="select" label="Convert all">
-      <option value="s">Whitespaces</option>
-      <option value="T">Tabs</option>
-      <!--<option value="Sp">Spaces</option>-->
-      <option value="Dt">Dots</option>
-      <option value="C">Commas</option>
-      <option value="D">Dashes</option>
-      <option value="U">Underscores</option>
-      <option value="P">Pipes</option>
-    </param>
-    <param format="txt" name="input" type="data" label="in Query"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="convert_from" value="s"/>
-      <param name="input" value="1.bed"/>
-      <output name="out_file1" file="eq-convert.dat"/>
-    </test>
-    <test>
-      <param name="convert_from" value="s"/>
-      <param name="input" value="a.txt"/>
-      <output name="out_file1" file="a.tab"/>
-    </test>
-  </tests>
-  <help>
-
-**What it does**
-
-Converts all delimiters of a specified type into TABs.  Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab.
-
------
-
-**Example**
-
-- Input file::
-
-    chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
-    chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
-    chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
-    chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
-
-- Converting all pipe delimiters of the above file to TABs will get::
-
-    chrX  151283558  151283724  NM_000808_exon_8_0_chrX_151283559_r  0  -
-    chrX  151370273  151370486  NM_000808_exon_9_0_chrX_151370274_r  0  -
-    chrX  151559494  151559583  NM_018558_exon_1_0_chrX_151559495_f  0  +
-    chrX  151564643  151564711  NM_018558_exon_2_0_chrX_151564644_f  0  +
-
-</help>
-</tool>