details: http://www.bx.psu.edu/hg/galaxy/rev/67dce52402fd
changeset: 2942:67dce52402fd
user: Nate Coraor <nate(a)bx.psu.edu>
date: Mon Nov 02 16:21:28 2009 -0500
description:
Remove old encode import tools
diffstat:
tools/data_source/encode_import.py | 82 ----------
tools/data_source/encode_import_all_latest_datasets.xml | 65 --------
tools/data_source/encode_import_chromatin_and_chromosomes.xml | 64 --------
tools/data_source/encode_import_code.py | 54 ------
tools/data_source/encode_import_gencode.xml | 67 --------
tools/data_source/encode_import_genes_and_transcripts.xml | 64 --------
tools/data_source/encode_import_multi-species_sequence_analysis.xml | 66 --------
tools/data_source/encode_import_transcription_regulation.xml | 65 --------
8 files changed, 0 insertions(+), 527 deletions(-)
diffs (565 lines):
diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import.py
--- a/tools/data_source/encode_import.py Mon Nov 02 16:12:31 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Script that imports locally stored data as a new dataset for the user
-Usage: import id outputfile
-"""
-import sys, os
-from shutil import copyfile
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-BUFFER = 1048576
-
-def stop_err( msg ):
- sys.stderr.write( msg )
- sys.exit()
-
-def main():
- uids = sys.argv[1].split(",")
- out_file1 = sys.argv[2]
- file_name = "%s/encode_datasets.loc" % sys.argv[3]
-
- #remove NONE from uids
- have_none = True
- while have_none:
- try:
- uids.remove('None')
- except:
- have_none = False
-
- #create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files
- available_files = {}
- try:
- for i, line in enumerate( file ( file_name ) ):
- line = line.rstrip( '\r\n' )
- if line and not line.startswith( '#' ):
- fields = line.split( '\t' )
- try:
- encode_group = fields[0].strip()
- build = fields[1].strip()
- description = fields[2].strip()
- uid = fields[3].strip()
- path = fields[4].strip()
- try:
- file_type = fields[5].strip()
- except:
- file_type = "bed"
- except:
- continue
- available_files[uid] = ( description, path, build, file_type )
- except:
- stop_err( "It appears that the configuration file for this tool is missing." )
-
- #create list of tuples of ( displayName, FileName, build ) for desired files
- desired_files = []
- for uid in uids:
- try:
- desired_files.append( available_files[uid] )
- except:
- continue
-
- #copy first file to contents of given output file
- file1_copied = False
- while not file1_copied:
- try:
- first_file = desired_files.pop(0)
- except:
- stop_err( "There were no valid files requested." )
- file1_desc, file1_path, file1_build, file1_type = first_file
- try:
- copyfile( file1_path, out_file1 )
- print "#File1\t" + file1_desc + "\t" + file1_build + "\t" + file1_type
- file1_copied = True
- except:
- stop_err( "The file '%s' is missing." %str( file1_path ) )
-
- #Tell post-process filter where remaining files reside
- for extra_output in desired_files:
- file_desc, file_path, file_build, file_type = extra_output
- print "#NewFile\t" + file_desc + "\t" + file_build + "\t" + file_path + "\t" + file_type
-
-if __name__ == "__main__": main()
diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_all_latest_datasets.xml
--- a/tools/data_source/encode_import_all_latest_datasets.xml Mon Nov 02 16:12:31 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-<tool id="encode_import_all_latest_datasets1" name="Combined Datasets">
- <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
- <inputs>
- <display>
- <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>
- <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
- </display>
- <param name="hg17" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="ALD" column="0"/>
- <filter type="static_value" name="dbkey" value="hg17" column="1"/>
- </options>
- </param>
- <param name="hg16" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="ALD" column="0"/>
- <filter type="static_value" name="dbkey" value="hg16" column="1"/>
- </options>
- </param>
- </inputs>
- <outputs>
- <data format="bed" name="output"/>
- </outputs>
- <code file="encode_import_code.py"/>
- <help>
-
-.. class:: warningmark
-
-The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data.
-
-.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
-
-For detailed information about data deposition and partitioning, click here_.
-
-.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A…
-
-*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below:
-
-A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories:
- 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
- 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other)
- 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other)
- 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
- 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
- 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
- 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.
-
------
-
-.. class:: infomark
-
-**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
-
-
- </help>
-</tool>
diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_chromatin_and_chromosomes.xml
--- a/tools/data_source/encode_import_chromatin_and_chromosomes.xml Mon Nov 02 16:12:31 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-<tool id="encode_import_chromatin_and_chromosomes1" name="Chromatin and Chromosomes">
- <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
- <inputs>
- <display>
- <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>
- <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
- </display>
- <param name="hg17" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="CC" column="0"/>
- <filter type="static_value" name="dbkey" value="hg17" column="1"/>
- </options>
- </param>
- <param name="hg16" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="CC" column="0"/>
- <filter type="static_value" name="dbkey" value="hg16" column="1"/>
- </options>
- </param>
- </inputs>
- <outputs>
- <data format="bed" name="output"/>
- </outputs>
- <code file="encode_import_code.py"/>
- <help>
-
-.. class:: warningmark
-
-The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data.
-
-.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
-
-For detailed information about data deposition and partitioning, click here_.
-
-.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A…
-
-*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below:
-
-A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories:
- 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
- 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other)
- 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other)
- 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
- 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
- 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
- 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.
-
------
-
-.. class:: infomark
-
-**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
-
- </help>
-</tool>
diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_code.py
--- a/tools/data_source/encode_import_code.py Mon Nov 02 16:12:31 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-import os, sys
-
-from galaxy import datatypes, config, jobs
-from shutil import copyfile
-
-#post processing, set build for data and add additional data to history
-def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
- base_dataset = out_data.items()[0][1]
- history = base_dataset.history
- if history == None:
- print "unknown history!"
- return
- new_stdout = ""
- split_stdout = stdout.split("\n")
- basic_name = ""
- for line in split_stdout:
- fields = line.split("\t")
- if fields[0] == "#File1":
- description = fields[1]
- dbkey = fields[2]
- file_type = fields[3]
- name, data = out_data.items()[0]
- data.set_size()
- basic_name = data.name
- data.name = data.name + " (" + description + ")"
- data.dbkey = dbkey
- data.info = data.name
- data = app.datatypes_registry.change_datatype( data, file_type )
- data.init_meta()
- data.set_peek()
- app.model.flush()
- elif fields[0] == "#NewFile":
- description = fields[1]
- dbkey = fields[2]
- filepath = fields[3]
- file_type = fields[4]
- newdata = app.model.HistoryDatasetAssociation( create_dataset = True ) #This import should become a library
- newdata.set_size()
- newdata.extension = file_type
- newdata.name = basic_name + " (" + description + ")"
- history.add_dataset( newdata )
- app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset )
- app.model.flush()
- try:
- copyfile(filepath,newdata.file_name)
- newdata.info = newdata.name
- newdata.state = jobs.JOB_OK
- except:
- newdata.info = "The requested file is missing from the system."
- newdata.state = jobs.JOB_ERROR
- newdata.dbkey = dbkey
- newdata.set_meta()
- newdata.set_peek()
- app.model.flush()
diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_gencode.xml
--- a/tools/data_source/encode_import_gencode.xml Mon Nov 02 16:12:31 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-<tool id="encode_import_gencode1" name="Gencode Datasets">
- <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
- <inputs>
- <display>
- <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>
- <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
- </display>
- <param name="hg17" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="GENCODE" column="0"/>
- <filter type="static_value" name="dbkey" value="hg17" column="1"/>
- </options>
- </param>
- <param name="hg16" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="GENCODE" column="0"/>
- <filter type="static_value" name="dbkey" value="hg16" column="1"/>
- </options>
- </param>
- </inputs>
- <outputs>
- <data format="bed" name="output"/>
- </outputs>
- <code file="encode_import_code.py"/>
- <help>
-
-.. class:: warningmark
-
-The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data.
-
-.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
-
-These are the datasets used for partitioning files.
-
-For detailed information about data deposition and partitioning, click here_.
-
-.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A…
-
-*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below:
-
-A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories:
- 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
- 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other)
- 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other)
- 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
- 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
- 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
- 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.
-
------
-
-.. class:: infomark
-
-**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
-
- </help>
-
-</tool>
diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_genes_and_transcripts.xml
--- a/tools/data_source/encode_import_genes_and_transcripts.xml Mon Nov 02 16:12:31 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-<tool id="encode_import_genes_and_transcripts1" name="Genes and Transcripts">
- <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
- <inputs>
- <display>
- <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>
- <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
- </display>
- <param name="hg17" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="GT" column="0"/>
- <filter type="static_value" name="dbkey" value="hg17" column="1"/>
- </options>
- </param>
- <param name="hg16" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="GT" column="0"/>
- <filter type="static_value" name="dbkey" value="hg16" column="1"/>
- </options>
- </param>
- </inputs>
- <outputs>
- <data format="bed" name="output"/>
- </outputs>
- <code file="encode_import_code.py"/>
- <help>
-
-.. class:: warningmark
-
-The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data.
-
-.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
-
-For detailed information about data deposition and partitioning, click here_.
-
-.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A…
-
-*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below:
-
-A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories:
- 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
- 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other)
- 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other)
- 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
- 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
- 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
- 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.
-
------
-
-.. class:: infomark
-
-**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
-
- </help>
-</tool>
diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_multi-species_sequence_analysis.xml
--- a/tools/data_source/encode_import_multi-species_sequence_analysis.xml Mon Nov 02 16:12:31 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-<tool id="encode_import_multi-species_sequence_analysis1" name="Multi-species Sequence Analysis">
- <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
- <inputs>
- <display>
- <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>
- <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
- </display>
- <param name="hg17" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="MSA" column="0"/>
- <filter type="static_value" name="dbkey" value="hg17" column="1"/>
- </options>
- </param>
- <param name="hg16" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="MSA" column="0"/>
- <filter type="static_value" name="dbkey" value="hg16" column="1"/>
- </options>
- </param>
- </inputs>
- <outputs>
- <data format="bed" name="output"/>
- </outputs>
- <code file="encode_import_code.py"/>
- <help>
-
-.. class:: warningmark
-
-The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data.
-
-.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
-
-For detailed information about data deposition and partitioning, click here_.
-
-.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A…
-
-*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below:
-
-A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories:
- 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
- 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other)
- 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other)
- 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
- 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
- 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
- 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.
-
------
-
-.. class:: infomark
-
-**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
-
-
-
- </help>
-</tool>
diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_transcription_regulation.xml
--- a/tools/data_source/encode_import_transcription_regulation.xml Mon Nov 02 16:12:31 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-<tool id="encode_import_transcription_regulation1" name="Transcription Regulation">
- <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
- <inputs>
- <display>
- <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>
- <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
- </display>
- <param name="hg17" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="TR" column="0"/>
- <filter type="static_value" name="dbkey" value="hg17" column="1"/>
- </options>
- </param>
- <param name="hg16" type="select" display="checkboxes" multiple="true">
- <options from_file="encode_datasets.loc">
- <column name="name" index="2"/>
- <column name="value" index="3"/>
- <column name="dbkey" index="1"/>
- <column name="encode_group" index="0"/>
- <column name="uid" index="3"/>
- <filter type="static_value" name="encode_group" value="TR" column="0"/>
- <filter type="static_value" name="dbkey" value="hg16" column="1"/>
- </options>
- </param>
- </inputs>
- <outputs>
- <data format="bed" name="output"/>
- </outputs>
- <code file="encode_import_code.py"/>
- <help>
-
-.. class:: warningmark
-
-The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data.
-
-.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
-
-For detailed information about data deposition and partitioning, click here_.
-
-.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A…
-
-*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below:
-
-A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories:
- 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
- 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other)
- 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other)
- 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
- 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
- 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
- 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.
-
------
-
-.. class:: infomark
-
-**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
-
- </help>
-
-</tool>
details: http://www.bx.psu.edu/hg/galaxy/rev/6e657b4aa837
changeset: 2943:6e657b4aa837
user: Nate Coraor <nate(a)bx.psu.edu>
date: Mon Nov 02 16:52:32 2009 -0500
description:
Update rg test data sample outputs to match the new versions Ross uploaded
diffstat:
test-data/rgenetics.bed | 2 +-
test-data/rgenetics.bim | 35 ++++++++---
test-data/rgenetics.fam | 130 +++++++++++++------------------------------
test-data/rgenetics.map | 35 ++++++++---
test-data/rgenetics.ped | 130 +++++++++++++------------------------------
5 files changed, 131 insertions(+), 201 deletions(-)
diffs (354 lines):
diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.bed
--- a/test-data/rgenetics.bed Mon Nov 02 16:21:28 2009 -0500
+++ b/test-data/rgenetics.bed Mon Nov 02 16:52:32 2009 -0500
@@ -1,1 +1,1 @@
-lÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿï¾î¸ÿÿüþ¿ÿ¿ûú¿¿ï/ÿÿþÿï¯ê¸ëê°®¾î®ãê¸;ì/âïú¯ï¯Îê¼ïâ°¯þϪã¯ø+ì?âÿú¯ïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïÿÿÿÿÿºÿÿþ¯þï¿ÿ»ÿÿþÿÿÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿÿÿÿÿþïÿÿÿþÿÿÿÿûÿûÿÿÿ»ÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïëÿê¾ÿºúïþ¯îë¿þ;¯>âïþ»
\ No newline at end of file
+lÿëþ¿¾+êóª¿ü £ïªîþ¨êÿïªûÿÿÿÿÿÿþﮨª"ëú £ïªîþ¨ÿÿ»ÿÿïïþÿèÿþ"ÿ«ïªîþ¨:*ÿïêüº.«ë:*ÿïêüº.«ëÿÿÿÿ¯ÿ¿ïþ¿ÿþªÿ¯û¿ïþ¿:*»ïêìª,«À:*»ïêìª,«Àÿëþ¿¾+êóª¿ÿÿÿÿûÿúÿÿÿÿÿÿÿÿÿ¿þ¿ÿëþ¿¾+ê󪿺ûÿÿ¿»ÿÿþ¿êÿÿªûÿÿÿÿÿºûÿÿ¿»ÿÿþ¿mÿÿÿýÿÿÿÿÿ ú¢ª±«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(
\ No newline at end of file
diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.bim
--- a/test-data/rgenetics.bim Mon Nov 02 16:21:28 2009 -0500
+++ b/test-data/rgenetics.bim Mon Nov 02 16:52:32 2009 -0500
@@ -1,10 +1,25 @@
-22 rs5992809 16.5965 16596539 0 C
-22 rs12168131 16.6573 16657262 G A
-22 rs390041 16.6629 16662916 T C
-22 rs437633 16.6697 16669684 A G
-22 rs450960 16.6909 16690858 T C
-22 rs450975 16.6909 16690887 T C
-22 rs451740 16.6912 16691174 T C
-22 rs8139723 16.6917 16691696 T C
-22 rs405490 16.6922 16692175 G A
-22 rs415170 16.6935 16693517 G C
+22 rs2283802 0 21784722 4 2
+22 rs2267000 0 21785366 4 2
+22 rs16997606 0 21794754 1 3
+22 rs4820537 0 21794810 1 3
+22 rs3788347 0 21797804 3 1
+22 rs756632 0 21799918 4 2
+22 rs4820539 0 21807970 1 3
+22 rs2283804 0 21820335 1 2
+22 rs2267006 0 21820990 3 1
+22 rs4822363 0 21821000 4 2
+22 rs5751592 0 21827674 4 2
+22 rs5759608 0 21832708 2 4
+22 rs5759612 0 21833170 3 1
+22 rs2267009 0 21860168 3 4
+22 rs2267010 0 21864366 3 1
+22 rs5759636 0 21868698 4 2
+22 rs2071436 0 21871488 4 2
+22 rs2267013 0 21875879 3 1
+22 rs6003566 0 21889806 3 1
+22 rs2256725 0 21892891 2 1
+22 rs12160770 0 21892925 1 3
+22 rs5751611 0 21896019 2 4
+22 rs762601 0 21898858 1 3
+22 rs2156921 0 21899063 3 1
+22 rs4822375 0 21905642 1 3
diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.fam
--- a/test-data/rgenetics.fam Mon Nov 02 16:21:28 2009 -0500
+++ b/test-data/rgenetics.fam Mon Nov 02 16:52:32 2009 -0500
@@ -1,90 +1,40 @@
-CH18526 NA18526 0 0 2 1
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+1340 1 9 10 1 2
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+1340 9 0 0 1 1
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+1341 11 0 0 1 1
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diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.map
--- a/test-data/rgenetics.map Mon Nov 02 16:21:28 2009 -0500
+++ b/test-data/rgenetics.map Mon Nov 02 16:52:32 2009 -0500
@@ -1,10 +1,25 @@
-22 rs5992809 16.5965 16596539
-22 rs12168131 16.6573 16657262
-22 rs390041 16.6629 16662916
-22 rs437633 16.6697 16669684
-22 rs450960 16.6909 16690858
-22 rs450975 16.6909 16690887
-22 rs451740 16.6912 16691174
-22 rs8139723 16.6917 16691696
-22 rs405490 16.6922 16692175
-22 rs415170 16.6935 16693517
+22 rs2283802 0 21784722
+22 rs2267000 0 21785366
+22 rs16997606 0 21794754
+22 rs4820537 0 21794810
+22 rs3788347 0 21797804
+22 rs756632 0 21799918
+22 rs4820539 0 21807970
+22 rs2283804 0 21820335
+22 rs2267006 0 21820990
+22 rs4822363 0 21821000
+22 rs5751592 0 21827674
+22 rs5759608 0 21832708
+22 rs5759612 0 21833170
+22 rs2267009 0 21860168
+22 rs2267010 0 21864366
+22 rs5759636 0 21868698
+22 rs2071436 0 21871488
+22 rs2267013 0 21875879
+22 rs6003566 0 21889806
+22 rs2256725 0 21892891
+22 rs12160770 0 21892925
+22 rs5751611 0 21896019
+22 rs762601 0 21898858
+22 rs2156921 0 21899063
+22 rs4822375 0 21905642
diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.ped
--- a/test-data/rgenetics.ped Mon Nov 02 16:21:28 2009 -0500
+++ b/test-data/rgenetics.ped Mon Nov 02 16:52:32 2009 -0500
@@ -1,90 +1,40 @@
-CH18526 NA18526 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
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