Changeset 955:be728f043856

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Timestamp:
02/06/08 14:17:02 (1 year ago)
Author:
Guruprasad Anada <gua110@bx.psu.edu>
branch:
default
convert_revision:
svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@2311
Message:

Modified Lift-Over tool. The "TO" build-list will now be dynamically generated based on the input dataset's build.

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  • lib/galaxy/tools/dynamic_options.py

    r890 r955  
    509509                        except:  
    510510                            d[ fields[ name_col ] ] = [ fields[ value_col ] ] 
    511                 elif self.data_file == 'regions.loc' or self.data_file == 'phastOdds.loc' or self.data_file == 'binned_scores.loc': 
     511                elif self.data_file == 'regions.loc' or self.data_file == 'phastOdds.loc' or self.data_file == 'binned_scores.loc' or self.data_file == 'liftOver.loc': 
    512512                    if not fields[ build_col ] in d:  
    513513                        d[ fields[ build_col ] ] = [] 
    …… 
    541541                for val in d[ build ]: 
    542542                    options.append( ( val, val, False ) ) 
    543         elif self.data_file == 'regions.loc' or self.data_file == 'phastOdds.loc' or self.data_file == 'binned_scores.loc': 
     543        elif self.data_file == 'regions.loc' or self.data_file == 'phastOdds.loc' or self.data_file == 'binned_scores.loc' or self.data_file == 'liftOver.loc': 
    544544            if build in d: 
    545545                for (key, val) in d[ build ]: 

  • tool_conf.xml.main

    r948 r955  
    2121    <tool file="encode/random_intervals.xml" /> 
    2222  </section> 
    23   <!-- 
    24   TODO: uncomment when ready for main 
    25   <section name="LiftOver" id="liftOver"> 
     23  <section name="Lift-Over" id="liftOver"> 
    2624    <tool file="extract/liftOver_wrapper.xml" /> 
    2725  </section> 
    28   --> 
    2926  <section name="Text Manipulation" id="textutil"> 
    3027    <tool file="filters/fixedValueColumn.xml" /> 

  • tool_conf.xml.sample

    r944 r955  
    2525    <tool file="encode/random_intervals.xml" /> 
    2626  </section> 
    27   <section name="LiftOver" id="liftOver"> 
     27  <section name="Lift-Over" id="liftOver"> 
    2828    <tool file="extract/liftOver_wrapper.xml" /> 
    2929  </section> 

  • tools/extract/liftOver_wrapper.py

    r879 r955  
    11#!/usr/bin/env python2.4 
    2 #Guru 
     2#Guruprasad Ananda 
    33""" 
    44Converts coordinates from one build/assembly to another using liftOver binary and mapping files downloaded from UCSC. 
    …… 
    2626    stop_err("Please specify a build for the output dataset using the 'To' dropdown menu.") 
    2727 
    28 #Check if the apping file exists     
     28#Check if the Mapping file exists     
    2929#example file path: hg18ToHg17.over.chain 
    30 mapfilename = in_dbkey + "To" + out_dbkey[0].capitalize() + out_dbkey[1:] + ".over.chain" 
     30mapfilename = in_dbkey + "To" + out_dbkey[0].upper() + out_dbkey[1:] + ".over.chain" 
    3131mapfilepath = "/depot/data2/galaxy/" + in_dbkey + "/liftOver/" + mapfilename 
    3232try: 

  • tools/extract/liftOver_wrapper.xml

    r879 r955  
    33  <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey</command> 
    44  <inputs> 
    5     <param format="bed" name="input" type="data" label="Convert coordinates of"/> 
    6     <param name="to_dbkey" type="genomebuild" label="To" /> 
     5    <param format="bed" name="input" type="data" label="Convert co-ordinates of" /> 
     6    <param name="to_dbkey" type="select" label="To"> 
     7      <options from_file="/depot/data2/galaxy/liftOver.loc"> 
     8        <filter type="data_meta" data_ref="input" key="build" /> 
     9        <filter type="column" name="build_col" value="0" /> 
     10        <filter type="column" name="name_col" value="1" /> 
     11        <filter type="column" name="value_col" value="1" /> 
     12      </options> 
     13    </param> 
    714  </inputs> 
    815  <outputs> 
    …… 
    2633Make sure that the genome build is specified for the input dataset (click the pencil icon if it is not specified). 
    2734 
     35.. class:: warningmark 
     36 
     37The tool will fail to run when the value in the **To** box is **unspecified**. This means that either we don't carry any liftover mappings corresponding to the genome build of the chosen input dataset or the genome build for the input dataset is not specified (click the pencil icon if it is not specified).  
     38 
    2839----- 
     40 
     41.. class:: infomark 
    2942 
    3043**What it does** 
    3144 
    32 This tool converts genome coordinates and annotation files between assemblies and genomes. It outputs 2 files, one containing all the mapped coordinates and one containing the unmapped coordinates (if any).  
     45This tool converts genome coordinates and annotation files between assemblies and genomes. It outputs 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates (if any).  
    3346 
    3447-----