changeset 0:d5677eecbad4

Imported from capsule None
author devteam
date Tue, 01 Apr 2014 10:51:55 -0400
parents
children 9fcc3a1c3d26
files cluster.xml gops_cluster.py operation_filter.py test-data/5.bed test-data/gops-cluster-1.bed test-data/gops-cluster-2.bed test-data/gops-cluster-3.bed test-data/gops_cluster_bigint.bed tool_dependencies.xml
diffstat 9 files changed, 716 insertions(+), 0 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.xml	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,100 @@
+<tool id="gops_cluster_1" name="Cluster" version="0.0.1">
+  <description>the intervals of a dataset</description>
+  <requirements>
+    <requirement type="package" version="0.7.1">bx-python</requirement>
+    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
+  </requirements>
+  <trackster_conf/>
+  <command interpreter="python">gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype</command>
+  <inputs>
+    <param format="interval" name="input1" type="data">
+      <label>Cluster intervals of</label>
+    </param>
+    <param name="distance" size="5" type="integer" value="1" help="(bp)">
+      <label>max distance between intervals</label>
+    </param>
+    <param name="minregions" size="5" type="integer" value="2">
+      <label>min number of intervals per cluster</label>
+    </param>
+	<param name="returntype" type="select" label="Return type">
+		<option value="1">Merge clusters into single intervals</option>
+		<option value="2">Find cluster intervals; preserve comments and order</option>
+		<option value="3">Find cluster intervals; output grouped by clusters</option>
+		<option value="4">Find the smallest interval in each cluster</option>
+		<option value="5">Find the largest interval in each cluster</option>
+	</param>
+   </inputs>
+  <outputs>
+    <data format="input" name="output" metadata_source="input1" />
+  </outputs>
+  <code file="operation_filter.py">
+    <hook exec_after_process="exec_after_cluster" />
+  </code>
+  <tests>
+    <test>
+      <param name="input1" value="5.bed" />
+      <param name="distance" value="1" />
+      <param name="minregions" value="2" />
+      <param name="returntype" value="1" />
+      <output name="output" file="gops-cluster-1.bed" />     
+    </test>
+    <test>
+      <param name="input1" value="gops_cluster_bigint.bed" />
+      <param name="distance" value="1" />
+      <param name="minregions" value="2" />
+      <param name="returntype" value="1" />
+      <output name="output" file="gops-cluster-1.bed" />     
+    </test>
+    <test>
+      <param name="input1" value="5.bed" />
+      <param name="distance" value="1" />
+      <param name="minregions" value="2" />
+      <param name="returntype" value="2" />
+      <output name="output" file="gops-cluster-2.bed" />     
+    </test>    
+    <test>
+      <param name="input1" value="5.bed" />
+      <param name="distance" value="1" />
+      <param name="minregions" value="2" />
+      <param name="returntype" value="3" />
+      <output name="output" file="gops-cluster-3.bed" />     
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
+
+-----
+
+**Screencasts!**
+
+See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
+
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
+
+-----
+
+**Syntax**
+
+- **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered &quot;clustered&quot;.  **Negative** values for distance are allowed, and are useful for clustering intervals that overlap.
+- **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster.  Any area with less than this minimum will not be included in the output.
+- **Merge clusters into single intervals** outputs intervals that span the entire cluster.
+- **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file.
+- **Find cluster intervals; output grouped by clusters** filters out non-cluster intervals, but outputs the cluster intervals so that they are grouped together. Comments and original ordering in the file are lost.
+
+-----
+
+**Examples**
+
+Find Clusters:
+
+.. image:: ${static_path}/operation_icons/gops_clusterFind.gif
+
+Merge Clusters:
+
+.. image:: ${static_path}/operation_icons/gops_clusterMerge.gif
+
+</help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gops_cluster.py	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,129 @@
+#!/usr/bin/env python
+"""
+Cluster regions of intervals.
+
+usage: %prog in_file out_file
+    -1, --cols1=N,N,N,N: Columns for start, end, strand in file
+    -d, --distance=N: Maximum distance between clustered intervals
+    -v, --overlap=N: Minimum overlap require (negative distance)
+    -m, --minregions=N: Minimum regions per cluster
+    -o, --output=N: 1)merged 2)filtered 3)clustered 4) minimum 5) maximum
+"""
+import sys, traceback, fileinput
+from warnings import warn
+from bx.intervals import *
+from bx.intervals.io import *
+from bx.intervals.operations.find_clusters import *
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def main():
+    distance = 0
+    minregions = 2
+    output = 1
+    upstream_pad = 0
+    downstream_pad = 0
+
+    options, args = doc_optparse.parse( __doc__ )
+    try:
+        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
+        if options.distance: distance = int( options.distance )
+        if options.overlap: distance = -1 * int( options.overlap )
+        if options.output: output = int( options.output )
+        if options.minregions: minregions = int( options.minregions )
+        in_fname, out_fname = args
+    except:
+        doc_optparse.exception()
+
+    g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
+                            chrom_col=chr_col_1,
+                            start_col=start_col_1,
+                            end_col=end_col_1,
+                            strand_col=strand_col_1,
+                            fix_strand=True )
+
+    # Get the cluster tree
+    try:
+        clusters, extra = find_clusters( g1, mincols=distance, minregions=minregions)
+    except ParseError, exc:
+        fail( "Invalid file format: %s" % str( exc ) )
+
+    f1 = open( in_fname, "r" )
+    out_file = open( out_fname, "w" )
+    
+    # If "merge"
+    if output == 1:
+        fields = ["."  for x in range(max(g1.chrom_col, g1.start_col, g1.end_col)+1)]
+        for chrom, tree in clusters.items():
+            for start, end, lines in tree.getregions():
+                fields[g1.chrom_col] = chrom
+                fields[g1.start_col] = str(start)
+                fields[g1.end_col] = str(end)
+                out_file.write( "%s\n" % "\t".join( fields ) )
+
+    # If "filtered" we preserve order of file and comments, etc.
+    if output == 2:
+        linenums = dict()
+        for chrom, tree in clusters.items():
+            for linenum in tree.getlines():
+                linenums[linenum] = 0
+        linenum = -1
+        f1.seek(0)
+        for line in f1.readlines():
+            linenum += 1
+            if linenum in linenums or linenum in extra:
+                out_file.write( "%s\n" % line.rstrip( "\n\r" ) )
+
+    # If "clustered" we output original intervals, but near each other (i.e. clustered)
+    if output == 3:
+        linenums = list()
+        f1.seek(0)
+        fileLines = f1.readlines()
+        for chrom, tree in clusters.items():
+            for linenum in tree.getlines():
+                out_file.write( "%s\n" % fileLines[linenum].rstrip( "\n\r" ) )
+
+    # If "minimum" we output the smallest interval in each cluster
+    if output == 4 or output == 5:
+        linenums = list()
+        f1.seek(0)
+        fileLines = f1.readlines()
+        for chrom, tree in clusters.items():
+            regions = tree.getregions()
+            for start, end, lines in tree.getregions():
+                outsize = -1
+                outinterval = None
+                for line in lines:
+                    # three nested for loops?
+                    # should only execute this code once per line
+                    fileline = fileLines[line].rstrip("\n\r")
+                    try:
+                        cluster_interval = GenomicInterval( g1, fileline.split("\t"), 
+                                                            g1.chrom_col, 
+                                                            g1.start_col,
+                                                            g1.end_col, 
+                                                            g1.strand_col, 
+                                                            g1.default_strand,
+                                                            g1.fix_strand )
+                    except Exception, exc:
+                        print >> sys.stderr, str( exc )
+                        f1.close()
+                        sys.exit()
+                    interval_size = cluster_interval.end - cluster_interval.start
+                    if outsize == -1 or \
+                       ( outsize > interval_size and output == 4 ) or \
+                       ( outsize < interval_size and output == 5 ) :
+                        outinterval = cluster_interval
+                        outsize = interval_size
+                out_file.write( "%s\n" % outinterval )
+
+    f1.close()
+    out_file.close()
+    
+    if g1.skipped > 0:
+        print skipped( g1, filedesc="" )
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/operation_filter.py	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,99 @@
+# runs after the job (and after the default post-filter)
+import os
+from galaxy import eggs
+from galaxy import jobs
+from galaxy.tools.parameters import DataToolParameter
+
+from galaxy.jobs.handler import JOB_ERROR
+
+# Older py compatibility
+try:
+    set()
+except:
+    from sets import Set as set
+
+#def exec_before_process(app, inp_data, out_data, param_dict, tool=None):
+#    """Sets the name of the data"""
+#    dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] ) 
+#    if len(dbkeys) != 1:
+#        raise Exception, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>'
+
+def validate_input( trans, error_map, param_values, page_param_map ):
+    dbkeys = set()
+    data_param_names = set()
+    data_params = 0
+    for name, param in page_param_map.iteritems():
+        if isinstance( param, DataToolParameter ):
+            # for each dataset parameter
+            if param_values.get(name, None) != None:
+                dbkeys.add( param_values[name].dbkey )
+                data_params += 1
+                # check meta data
+                try:
+                    param = param_values[name]
+                    if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ):
+                        # TODO: currently cannot validate GFF inputs b/c they are not derived from interval.
+                        pass
+                    else: # Validate interval datatype.
+                        startCol = int( param.metadata.startCol )
+                        endCol = int( param.metadata.endCol )
+                        chromCol = int( param.metadata.chromCol )
+                        if param.metadata.strandCol is not None:
+                            strandCol = int ( param.metadata.strandCol )
+                        else:
+                            strandCol = 0
+                except:
+                    error_msg = "The attributes of this dataset are not properly set. " + \
+                    "Click the pencil icon in the history item to set the chrom, start, end and strand columns."
+                    error_map[name] = error_msg
+            data_param_names.add( name )
+    if len( dbkeys ) > 1:
+        for name in data_param_names:
+            error_map[name] = "All datasets must belong to same genomic build, " \
+                "this dataset is linked to build '%s'" % param_values[name].dbkey
+    if data_params != len(data_param_names):
+        for name in data_param_names:
+            error_map[name] = "A dataset of the appropriate type is required"
+
+# Commented out by INS, 5/30/2007.  What is the PURPOSE of this?
+def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
+    """Verify the output data after each run"""
+    items = out_data.items()
+
+    for name, data in items:
+        try:
+            if stderr and len( stderr ) > 0:
+                raise Exception( stderr )
+
+        except Exception, exc:
+            data.blurb = JOB_ERROR
+            data.state = JOB_ERROR
+
+## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
+##     pass
+
+
+def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
+    exec_after_process(
+        app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
+
+    # strip strand column if clusters were merged
+    items = out_data.items()
+    for name, data in items:
+        if param_dict['returntype'] == True:
+            data.metadata.chromCol = 1
+            data.metadata.startCol = 2
+            data.metadata.endCol = 3
+        # merge always clobbers strand
+        data.metadata.strandCol = None
+            
+
+def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
+    exec_after_process(
+        app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
+
+    # strip strand column if clusters were merged
+    if param_dict["returntype"] == '1':
+        items = out_data.items()
+        for name, data in items:
+            data.metadata.strandCol = None
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/5.bed	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,134 @@
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+chr7	116656241	116656364	CCDS5772.1_cds_10_0_chr7_116656242_r	0	-
+chr7	116660840	116660940	CCDS5772.1_cds_11_0_chr7_116660841_r	0	-
+chr7	116661360	116661465	CCDS5772.1_cds_12_0_chr7_116661361_r	0	-
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
+chr7	116738257	116738368	CCDS5773.1_cds_1_0_chr7_116738258_f	0	+
+chr7	116743038	116743147	CCDS5773.1_cds_2_0_chr7_116743039_f	0	+
+chr7	116764903	116765119	CCDS5773.1_cds_3_0_chr7_116764904_f	0	+
+chr7	116768280	116768370	CCDS5773.1_cds_4_0_chr7_116768281_f	0	+
+chr7	116769252	116769416	CCDS5773.1_cds_5_0_chr7_116769253_f	0	+
+chr7	116770552	116770678	CCDS5773.1_cds_6_0_chr7_116770553_f	0	+
+chr7	116774104	116774351	CCDS5773.1_cds_7_0_chr7_116774105_f	0	+
+chr7	116776020	116776113	CCDS5773.1_cds_8_0_chr7_116776021_f	0	+
+chr7	116782645	116782828	CCDS5773.1_cds_9_0_chr7_116782646_f	0	+
+chr7	116793468	116793660	CCDS5773.1_cds_10_0_chr7_116793469_f	0	+
+chr7	116821743	116821838	CCDS5773.1_cds_11_0_chr7_116821744_f	0	+
+chr7	116824357	116824444	CCDS5773.1_cds_12_0_chr7_116824358_f	0	+
+chr7	116825938	116826662	CCDS5773.1_cds_13_0_chr7_116825939_f	0	+
+chr7	116828934	116829063	CCDS5773.1_cds_14_0_chr7_116828935_f	0	+
+chr7	116836830	116836868	CCDS5773.1_cds_15_0_chr7_116836831_f	0	+
+chr7	116837536	116837787	CCDS5773.1_cds_16_0_chr7_116837537_f	0	+
+chr7	116840678	116840758	CCDS5773.1_cds_17_0_chr7_116840679_f	0	+
+chr7	116844523	116844674	CCDS5773.1_cds_18_0_chr7_116844524_f	0	+
+chr7	116845585	116845813	CCDS5773.1_cds_19_0_chr7_116845586_f	0	+
+chr7	116848617	116848718	CCDS5773.1_cds_20_0_chr7_116848618_f	0	+
+chr7	116861526	116861775	CCDS5773.1_cds_21_0_chr7_116861527_f	0	+
+chr7	116876442	116876598	CCDS5773.1_cds_22_0_chr7_116876443_f	0	+
+chr7	116886846	116886936	CCDS5773.1_cds_23_0_chr7_116886847_f	0	+
+chr7	116898692	116898865	CCDS5773.1_cds_24_0_chr7_116898693_f	0	+
+chr7	116899463	116899569	CCDS5773.1_cds_25_0_chr7_116899464_f	0	+
+chr7	116900912	116901113	CCDS5773.1_cds_26_0_chr7_116900913_f	0	+
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-
+chr7	116952022	116952124	CCDS5774.1_cds_1_0_chr7_116952023_r	0	-
+chr7	116953508	116953641	CCDS5774.1_cds_2_0_chr7_116953509_r	0	-
+chr7	116955071	116955135	CCDS5774.1_cds_3_0_chr7_116955072_r	0	-
+chr7	116958551	116958737	CCDS5774.1_cds_4_0_chr7_116958552_r	0	-
+chr7	116959056	116959262	CCDS5774.1_cds_5_0_chr7_116959057_r	0	-
+chr7	116962093	116962272	CCDS5774.1_cds_6_0_chr7_116962094_r	0	-
+chr7	116968917	116969105	CCDS5774.1_cds_7_0_chr7_116968918_r	0	-
+chr7	116969273	116969426	CCDS5774.1_cds_8_0_chr7_116969274_r	0	-
+chr7	116979835	116979935	CCDS5774.1_cds_9_0_chr7_116979836_r	0	-
+chr7	116980017	116980104	CCDS5774.1_cds_10_0_chr7_116980018_r	0	-
+chr7	116990559	116990639	CCDS5774.1_cds_11_0_chr7_116990560_r	0	-
+chr7	116991879	116991975	CCDS5774.1_cds_12_0_chr7_116991880_r	0	-
+chr7	116994439	116994715	CCDS5774.1_cds_13_0_chr7_116994440_r	0	-
+chr7	117001063	117001181	CCDS5774.1_cds_14_0_chr7_117001064_r	0	-
+chr7	117011515	117011770	CCDS5774.1_cds_15_0_chr7_117011516_r	0	-
+chr7	117014445	117014596	CCDS5774.1_cds_16_0_chr7_117014446_r	0	-
+chr7	117016866	117016966	CCDS5774.1_cds_17_0_chr7_117016867_r	0	-
+chr7	117018255	117018459	CCDS5774.1_cds_18_0_chr7_117018256_r	0	-
+chr7	117025132	117026786	CCDS5774.1_cds_19_0_chr7_117025133_r	0	-
+chr7	117044769	117044994	CCDS5774.1_cds_20_0_chr7_117044770_r	0	-
+chr7	117095213	117095321	CCDS5774.1_cds_21_0_chr7_117095214_r	0	-
+chr7	117107339	117107420	CCDS5774.1_cds_22_0_chr7_117107340_r	0	-
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
+chr5	131424558	131424600	CCDS4149.1_cds_1_0_chr5_131424559_f	0	+
+chr5	131425903	131425993	CCDS4149.1_cds_2_0_chr5_131425904_f	0	+
+chr5	131426117	131426159	CCDS4149.1_cds_3_0_chr5_131426118_f	0	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gops-cluster-1.bed	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,22 @@
+chr7	115468538	115468624
+chr7	115483024	115483277
+chr7	115484165	115484501
+chr7	115485764	115485980
+chr7	115486322	115486481
+chr7	115491298	115491487
+chr7	115733786	115733936
+chr7	115739975	115740164
+chr7	116187545	116187696
+chr7	116333766	116333849
+chr7	116353565	116353725
+chr7	116363797	116363852
+chr7	116364495	116364611
+chr7	116365889	116365965
+chr7	116370085	116370240
+chr7	116372439	116372537
+chr7	116404866	116404981
+chr7	116423325	116423398
+chr7	116424838	116424941
+chr7	116443791	116443942
+chr7	116453088	116453181
+chr7	116455927	116456067
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gops-cluster-2.bed	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,44 @@
+chr7	115468538	115468624	CCDS5763.1_cds_1_0_chr7_115468539_f	0	+
+chr7	115483024	115483277	CCDS5763.1_cds_2_0_chr7_115483025_f	0	+
+chr7	115484165	115484501	CCDS5763.1_cds_3_0_chr7_115484166_f	0	+
+chr7	115485764	115485980	CCDS5763.1_cds_4_0_chr7_115485765_f	0	+
+chr7	115486322	115486481	CCDS5763.1_cds_5_0_chr7_115486323_f	0	+
+chr7	115491298	115491487	CCDS5763.1_cds_6_0_chr7_115491299_f	0	+
+chr7	115468538	115468624	CCDS5764.1_cds_0_0_chr7_115468539_f	0	+
+chr7	115483024	115483277	CCDS5764.1_cds_1_0_chr7_115483025_f	0	+
+chr7	115484165	115484501	CCDS5764.1_cds_2_0_chr7_115484166_f	0	+
+chr7	115485764	115485980	CCDS5764.1_cds_3_0_chr7_115485765_f	0	+
+chr7	115486322	115486481	CCDS5764.1_cds_4_0_chr7_115486323_f	0	+
+chr7	115491298	115491487	CCDS5764.1_cds_5_0_chr7_115491299_f	0	+
+chr7	115733786	115733936	CCDS5766.1_cds_0_0_chr7_115733787_f	0	+
+chr7	115739975	115740126	CCDS5766.1_cds_2_0_chr7_115739976_f	0	+
+chr7	115733786	115733936	CCDS5765.1_cds_0_0_chr7_115733787_f	0	+
+chr7	115739975	115740164	CCDS5765.1_cds_1_0_chr7_115739976_f	0	+
+chr7	116187545	116187696	CCDS5770.1_cds_0_0_chr7_116187546_f	0	+
+chr7	116333766	116333849	CCDS5770.1_cds_1_0_chr7_116333767_f	0	+
+chr7	116353565	116353725	CCDS5770.1_cds_2_0_chr7_116353566_f	0	+
+chr7	116363797	116363852	CCDS5770.1_cds_3_0_chr7_116363798_f	0	+
+chr7	116364495	116364611	CCDS5770.1_cds_4_0_chr7_116364496_f	0	+
+chr7	116365889	116365965	CCDS5770.1_cds_5_0_chr7_116365890_f	0	+
+chr7	116370085	116370240	CCDS5770.1_cds_7_0_chr7_116370086_f	0	+
+chr7	116372439	116372537	CCDS5770.1_cds_8_0_chr7_116372440_f	0	+
+chr7	116404866	116404981	CCDS5770.1_cds_9_0_chr7_116404867_f	0	+
+chr7	116423325	116423398	CCDS5770.1_cds_10_0_chr7_116423326_f	0	+
+chr7	116424838	116424941	CCDS5770.1_cds_11_0_chr7_116424839_f	0	+
+chr7	116443791	116443942	CCDS5770.1_cds_12_0_chr7_116443792_f	0	+
+chr7	116453088	116453181	CCDS5770.1_cds_13_0_chr7_116453089_f	0	+
+chr7	116455927	116456067	CCDS5770.1_cds_14_0_chr7_116455928_f	0	+
+chr7	116187545	116187696	CCDS5769.1_cds_0_0_chr7_116187546_f	0	+
+chr7	116333766	116333849	CCDS5769.1_cds_1_0_chr7_116333767_f	0	+
+chr7	116353565	116353725	CCDS5769.1_cds_2_0_chr7_116353566_f	0	+
+chr7	116363797	116363852	CCDS5769.1_cds_3_0_chr7_116363798_f	0	+
+chr7	116364495	116364611	CCDS5769.1_cds_4_0_chr7_116364496_f	0	+
+chr7	116365889	116365965	CCDS5769.1_cds_5_0_chr7_116365890_f	0	+
+chr7	116370085	116370240	CCDS5769.1_cds_6_0_chr7_116370086_f	0	+
+chr7	116372439	116372537	CCDS5769.1_cds_7_0_chr7_116372440_f	0	+
+chr7	116404866	116404981	CCDS5769.1_cds_8_0_chr7_116404867_f	0	+
+chr7	116423325	116423398	CCDS5769.1_cds_9_0_chr7_116423326_f	0	+
+chr7	116424838	116424941	CCDS5769.1_cds_10_0_chr7_116424839_f	0	+
+chr7	116443791	116443942	CCDS5769.1_cds_11_0_chr7_116443792_f	0	+
+chr7	116453088	116453181	CCDS5769.1_cds_12_0_chr7_116453089_f	0	+
+chr7	116455927	116456067	CCDS5769.1_cds_13_0_chr7_116455928_f	0	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gops-cluster-3.bed	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,44 @@
+chr7	115468538	115468624	CCDS5763.1_cds_1_0_chr7_115468539_f	0	+
+chr7	115468538	115468624	CCDS5764.1_cds_0_0_chr7_115468539_f	0	+
+chr7	115483024	115483277	CCDS5763.1_cds_2_0_chr7_115483025_f	0	+
+chr7	115483024	115483277	CCDS5764.1_cds_1_0_chr7_115483025_f	0	+
+chr7	115484165	115484501	CCDS5763.1_cds_3_0_chr7_115484166_f	0	+
+chr7	115484165	115484501	CCDS5764.1_cds_2_0_chr7_115484166_f	0	+
+chr7	115485764	115485980	CCDS5763.1_cds_4_0_chr7_115485765_f	0	+
+chr7	115485764	115485980	CCDS5764.1_cds_3_0_chr7_115485765_f	0	+
+chr7	115486322	115486481	CCDS5763.1_cds_5_0_chr7_115486323_f	0	+
+chr7	115486322	115486481	CCDS5764.1_cds_4_0_chr7_115486323_f	0	+
+chr7	115491298	115491487	CCDS5763.1_cds_6_0_chr7_115491299_f	0	+
+chr7	115491298	115491487	CCDS5764.1_cds_5_0_chr7_115491299_f	0	+
+chr7	115733786	115733936	CCDS5766.1_cds_0_0_chr7_115733787_f	0	+
+chr7	115733786	115733936	CCDS5765.1_cds_0_0_chr7_115733787_f	0	+
+chr7	115739975	115740126	CCDS5766.1_cds_2_0_chr7_115739976_f	0	+
+chr7	115739975	115740164	CCDS5765.1_cds_1_0_chr7_115739976_f	0	+
+chr7	116187545	116187696	CCDS5770.1_cds_0_0_chr7_116187546_f	0	+
+chr7	116187545	116187696	CCDS5769.1_cds_0_0_chr7_116187546_f	0	+
+chr7	116333766	116333849	CCDS5770.1_cds_1_0_chr7_116333767_f	0	+
+chr7	116333766	116333849	CCDS5769.1_cds_1_0_chr7_116333767_f	0	+
+chr7	116353565	116353725	CCDS5770.1_cds_2_0_chr7_116353566_f	0	+
+chr7	116353565	116353725	CCDS5769.1_cds_2_0_chr7_116353566_f	0	+
+chr7	116363797	116363852	CCDS5770.1_cds_3_0_chr7_116363798_f	0	+
+chr7	116363797	116363852	CCDS5769.1_cds_3_0_chr7_116363798_f	0	+
+chr7	116364495	116364611	CCDS5770.1_cds_4_0_chr7_116364496_f	0	+
+chr7	116364495	116364611	CCDS5769.1_cds_4_0_chr7_116364496_f	0	+
+chr7	116365889	116365965	CCDS5770.1_cds_5_0_chr7_116365890_f	0	+
+chr7	116365889	116365965	CCDS5769.1_cds_5_0_chr7_116365890_f	0	+
+chr7	116370085	116370240	CCDS5770.1_cds_7_0_chr7_116370086_f	0	+
+chr7	116370085	116370240	CCDS5769.1_cds_6_0_chr7_116370086_f	0	+
+chr7	116372439	116372537	CCDS5770.1_cds_8_0_chr7_116372440_f	0	+
+chr7	116372439	116372537	CCDS5769.1_cds_7_0_chr7_116372440_f	0	+
+chr7	116404866	116404981	CCDS5770.1_cds_9_0_chr7_116404867_f	0	+
+chr7	116404866	116404981	CCDS5769.1_cds_8_0_chr7_116404867_f	0	+
+chr7	116423325	116423398	CCDS5770.1_cds_10_0_chr7_116423326_f	0	+
+chr7	116423325	116423398	CCDS5769.1_cds_9_0_chr7_116423326_f	0	+
+chr7	116424838	116424941	CCDS5770.1_cds_11_0_chr7_116424839_f	0	+
+chr7	116424838	116424941	CCDS5769.1_cds_10_0_chr7_116424839_f	0	+
+chr7	116443791	116443942	CCDS5770.1_cds_12_0_chr7_116443792_f	0	+
+chr7	116443791	116443942	CCDS5769.1_cds_11_0_chr7_116443792_f	0	+
+chr7	116453088	116453181	CCDS5770.1_cds_13_0_chr7_116453089_f	0	+
+chr7	116453088	116453181	CCDS5769.1_cds_12_0_chr7_116453089_f	0	+
+chr7	116455927	116456067	CCDS5770.1_cds_14_0_chr7_116455928_f	0	+
+chr7	116455927	116456067	CCDS5769.1_cds_13_0_chr7_116455928_f	0	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gops_cluster_bigint.bed	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,135 @@
+chr7	115444712	115444739	CCDS5763.1_cds_0_0_chr7_115444713_f	0	+
+chr7	115468538	115468624	CCDS5763.1_cds_1_0_chr7_115468539_f	0	+
+chr7	115483024	115483277	CCDS5763.1_cds_2_0_chr7_115483025_f	0	+
+chr7	115484165	115484501	CCDS5763.1_cds_3_0_chr7_115484166_f	0	+
+chr7	115485764	115485980	CCDS5763.1_cds_4_0_chr7_115485765_f	0	+
+chr7	115486322	115486481	CCDS5763.1_cds_5_0_chr7_115486323_f	0	+
+chr7	115491298	115491487	CCDS5763.1_cds_6_0_chr7_115491299_f	0	+
+chr7	115468538	115468624	CCDS5764.1_cds_0_0_chr7_115468539_f	0	+
+chr7	115483024	115483277	CCDS5764.1_cds_1_0_chr7_115483025_f	0	+
+chr7	115484165	115484501	CCDS5764.1_cds_2_0_chr7_115484166_f	0	+
+chr7	115485764	115485980	CCDS5764.1_cds_3_0_chr7_115485765_f	0	+
+chr7	115486322	115486481	CCDS5764.1_cds_4_0_chr7_115486323_f	0	+
+chr7	115491298	115491487	CCDS5764.1_cds_5_0_chr7_115491299_f	0	+
+chr7	115733786	115733936	CCDS5766.1_cds_0_0_chr7_115733787_f	0	+
+chr7	115734264	115734452	CCDS5766.1_cds_1_0_chr7_115734265_f	0	+
+chr7	115739975	115740126	CCDS5766.1_cds_2_0_chr7_115739976_f	0	+
+chr7	115733786	115733936	CCDS5765.1_cds_0_0_chr7_115733787_f	0	+
+chr7	115739975	115740164	CCDS5765.1_cds_1_0_chr7_115739976_f	0	+
+chr7	115759067	115759097	CCDS5767.1_cds_0_0_chr7_115759068_f	0	+
+chr7	115760529	115760694	CCDS5767.1_cds_1_0_chr7_115760530_f	0	+
+chr7	115792950	115793292	CCDS5767.1_cds_2_0_chr7_115792951_f	0	+
+chr7	116096616	116096655	CCDS5768.1_cds_0_0_chr7_116096617_f	0	+
+chr7	116122131	116122195	CCDS5768.1_cds_1_0_chr7_116122132_f	0	+
+chr7	116126998	116127050	CCDS5768.1_cds_2_0_chr7_116126999_f	0	+
+chr7	116132776	116132840	CCDS5768.1_cds_3_0_chr7_116132777_f	0	+
+chr7	116138181	116138388	CCDS5768.1_cds_4_0_chr7_116138182_f	0	+
+chr7	116140267	116140347	CCDS5768.1_cds_5_0_chr7_116140268_f	0	+
+chr7	116144237	116144316	CCDS5768.1_cds_6_0_chr7_116144238_f	0	+
+chr7	116146073	116146145	CCDS5768.1_cds_7_0_chr7_116146074_f	0	+
+chr7	116150064	116150127	CCDS5768.1_cds_8_0_chr7_116150065_f	0	+
+chr7	116151731	116151872	CCDS5768.1_cds_9_0_chr7_116151732_f	0	+
+chr7	116187545	116187696	CCDS5770.1_cds_0_0_chr7_116187546_f	0	+
+chr7	116333766	116333849	CCDS5770.1_cds_1_0_chr7_116333767_f	0	+
+chr7	116353565	116353725	CCDS5770.1_cds_2_0_chr7_116353566_f	0	+
+chr7	116363797	116363852	CCDS5770.1_cds_3_0_chr7_116363798_f	0	+
+chr7	116364495	116364611	CCDS5770.1_cds_4_0_chr7_116364496_f	0	+
+chr7	116365889	116365965	CCDS5770.1_cds_5_0_chr7_116365890_f	0	+
+chr7	116368128	116368197	CCDS5770.1_cds_6_0_chr7_116368129_f	0	+
+chr7	116370085	116370240	CCDS5770.1_cds_7_0_chr7_116370086_f	0	+
+chr7	116372439	116372537	CCDS5770.1_cds_8_0_chr7_116372440_f	0	+
+chr7	116404866	116404981	CCDS5770.1_cds_9_0_chr7_116404867_f	0	+
+chr7	116423325	116423398	CCDS5770.1_cds_10_0_chr7_116423326_f	0	+
+chr7	116424838	116424941	CCDS5770.1_cds_11_0_chr7_116424839_f	0	+
+chr7	116443791	116443942	CCDS5770.1_cds_12_0_chr7_116443792_f	0	+
+chr7	116453088	116453181	CCDS5770.1_cds_13_0_chr7_116453089_f	0	+
+chr7	116455927	116456067	CCDS5770.1_cds_14_0_chr7_116455928_f	0	+
+chr7	116456865	116456985	CCDS5770.1_cds_15_0_chr7_116456866_f	0	+
+chr7	116187545	116187696	CCDS5769.1_cds_0_0_chr7_116187546_f	0	+
+chr7	116333766	116333849	CCDS5769.1_cds_1_0_chr7_116333767_f	0	+
+chr7	116353565	116353725	CCDS5769.1_cds_2_0_chr7_116353566_f	0	+
+chr7	116363797	116363852	CCDS5769.1_cds_3_0_chr7_116363798_f	0	+
+chr7	116364495	116364611	CCDS5769.1_cds_4_0_chr7_116364496_f	0	+
+chr7	116365889	116365965	CCDS5769.1_cds_5_0_chr7_116365890_f	0	+
+chr7	116370085	116370240	CCDS5769.1_cds_6_0_chr7_116370086_f	0	+
+chr7	116372439	116372537	CCDS5769.1_cds_7_0_chr7_116372440_f	0	+
+chr7	116404866	116404981	CCDS5769.1_cds_8_0_chr7_116404867_f	0	+
+chr7	116423325	116423398	CCDS5769.1_cds_9_0_chr7_116423326_f	0	+
+chr7	116424838	116424941	CCDS5769.1_cds_10_0_chr7_116424839_f	0	+
+chr7	116443791	116443942	CCDS5769.1_cds_11_0_chr7_116443792_f	0	+
+chr7	116453088	116453181	CCDS5769.1_cds_12_0_chr7_116453089_f	0	+
+chr7	116455927	116456067	CCDS5769.1_cds_13_0_chr7_116455928_f	0	+
+chr7	116463766	116463862	CCDS5769.1_cds_14_0_chr7_116463767_f	0	+
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-
+chr7	116531616	116531881	CCDS5771.1_cds_1_0_chr7_116531617_r	0	-
+chr7	116549075	116549353	CCDS5771.1_cds_2_0_chr7_116549076_r	0	-
+chr7	116554571	116554798	CCDS5771.1_cds_3_0_chr7_116554572_r	0	-
+chr7	116556911	116556994	CCDS5771.1_cds_4_0_chr7_116556912_r	0	-
+chr7	116597600	116597753	CCDS5772.1_cds_0_0_chr7_116597601_r	0	-
+chr7	116601356	116601470	CCDS5772.1_cds_1_0_chr7_116601357_r	0	-
+chr7	116602616	116602722	CCDS5772.1_cds_2_0_chr7_116602617_r	0	-
+chr7	116613942	116614052	CCDS5772.1_cds_3_0_chr7_116613943_r	0	-
+chr7	116615015	116615072	CCDS5772.1_cds_4_0_chr7_116615016_r	0	-
+chr7	116616073	116616149	CCDS5772.1_cds_5_0_chr7_116616074_r	0	-
+chr7	116616990	116617115	CCDS5772.1_cds_6_0_chr7_116616991_r	0	-
+chr7	116618730	116618865	CCDS5772.1_cds_7_0_chr7_116618731_r	0	-
+chr7	116619702	116619814	CCDS5772.1_cds_8_0_chr7_116619703_r	0	-
+chr7	116654167	116654279	CCDS5772.1_cds_9_0_chr7_116654168_r	0	-
+chr7	116656241	116656364	CCDS5772.1_cds_10_0_chr7_116656242_r	0	-
+chr7	116660840	116660940	CCDS5772.1_cds_11_0_chr7_116660841_r	0	-
+chr7	116661360	116661465	CCDS5772.1_cds_12_0_chr7_116661361_r	0	-
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
+chr7	116738257	116738368	CCDS5773.1_cds_1_0_chr7_116738258_f	0	+
+chr7	116743038	116743147	CCDS5773.1_cds_2_0_chr7_116743039_f	0	+
+chr7	116764903	116765119	CCDS5773.1_cds_3_0_chr7_116764904_f	0	+
+chr7	116768280	116768370	CCDS5773.1_cds_4_0_chr7_116768281_f	0	+
+chr7	116769252	116769416	CCDS5773.1_cds_5_0_chr7_116769253_f	0	+
+chr7	116770552	116770678	CCDS5773.1_cds_6_0_chr7_116770553_f	0	+
+chr7	116774104	116774351	CCDS5773.1_cds_7_0_chr7_116774105_f	0	+
+chr7	116776020	116776113	CCDS5773.1_cds_8_0_chr7_116776021_f	0	+
+chr7	116782645	116782828	CCDS5773.1_cds_9_0_chr7_116782646_f	0	+
+chr7	116793468	116793660	CCDS5773.1_cds_10_0_chr7_116793469_f	0	+
+chr7	116821743	116821838	CCDS5773.1_cds_11_0_chr7_116821744_f	0	+
+chr7	116824357	116824444	CCDS5773.1_cds_12_0_chr7_116824358_f	0	+
+chr7	116825938	116826662	CCDS5773.1_cds_13_0_chr7_116825939_f	0	+
+chr7	116828934	116829063	CCDS5773.1_cds_14_0_chr7_116828935_f	0	+
+chr7	116836830	116836868	CCDS5773.1_cds_15_0_chr7_116836831_f	0	+
+chr7	116837536	116837787	CCDS5773.1_cds_16_0_chr7_116837537_f	0	+
+chr7	116840678	116840758	CCDS5773.1_cds_17_0_chr7_116840679_f	0	+
+chr7	116844523	116844674	CCDS5773.1_cds_18_0_chr7_116844524_f	0	+
+chr7	116845585	116845813	CCDS5773.1_cds_19_0_chr7_116845586_f	0	+
+chr7	116848617	116848718	CCDS5773.1_cds_20_0_chr7_116848618_f	0	+
+chr7	116861526	116861775	CCDS5773.1_cds_21_0_chr7_116861527_f	0	+
+chr7	116876442	116876598	CCDS5773.1_cds_22_0_chr7_116876443_f	0	+
+chr7	116886846	116886936	CCDS5773.1_cds_23_0_chr7_116886847_f	0	+
+chr7	116898692	116898865	CCDS5773.1_cds_24_0_chr7_116898693_f	0	+
+chr7	116899463	116899569	CCDS5773.1_cds_25_0_chr7_116899464_f	0	+
+chr7	116900912	116901113	CCDS5773.1_cds_26_0_chr7_116900913_f	0	+
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-
+chr7	116952022	116952124	CCDS5774.1_cds_1_0_chr7_116952023_r	0	-
+chr7	116953508	116953641	CCDS5774.1_cds_2_0_chr7_116953509_r	0	-
+chr7	116955071	116955135	CCDS5774.1_cds_3_0_chr7_116955072_r	0	-
+chr7	116958551	116958737	CCDS5774.1_cds_4_0_chr7_116958552_r	0	-
+chr7	116959056	116959262	CCDS5774.1_cds_5_0_chr7_116959057_r	0	-
+chr7	116962093	116962272	CCDS5774.1_cds_6_0_chr7_116962094_r	0	-
+chr7	116968917	116969105	CCDS5774.1_cds_7_0_chr7_116968918_r	0	-
+chr7	116969273	116969426	CCDS5774.1_cds_8_0_chr7_116969274_r	0	-
+chr7	116979835	116979935	CCDS5774.1_cds_9_0_chr7_116979836_r	0	-
+chr7	116980017	116980104	CCDS5774.1_cds_10_0_chr7_116980018_r	0	-
+chr7	116990559	116990639	CCDS5774.1_cds_11_0_chr7_116990560_r	0	-
+chr7	116991879	116991975	CCDS5774.1_cds_12_0_chr7_116991880_r	0	-
+chr7	116994439	116994715	CCDS5774.1_cds_13_0_chr7_116994440_r	0	-
+chr7	117001063	117001181	CCDS5774.1_cds_14_0_chr7_117001064_r	0	-
+chr7	117011515	117011770	CCDS5774.1_cds_15_0_chr7_117011516_r	0	-
+chr7	117014445	117014596	CCDS5774.1_cds_16_0_chr7_117014446_r	0	-
+chr7	117016866	117016966	CCDS5774.1_cds_17_0_chr7_117016867_r	0	-
+chr7	117018255	117018459	CCDS5774.1_cds_18_0_chr7_117018256_r	0	-
+chr7	117025132	117026786	CCDS5774.1_cds_19_0_chr7_117025133_r	0	-
+chr7	117044769	117044994	CCDS5774.1_cds_20_0_chr7_117044770_r	0	-
+chr7	117095213	117095321	CCDS5774.1_cds_21_0_chr7_117095214_r	0	-
+chr7	117107339	117107420	CCDS5774.1_cds_22_0_chr7_117107340_r	0	-
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
+chr5	131424558	131424600	CCDS4149.1_cds_1_0_chr5_131424559_f	0	+
+chr5	131425903	131425993	CCDS4149.1_cds_2_0_chr5_131425904_f	0	+
+chr5	131426117	131426159	CCDS4149.1_cds_3_0_chr5_131426118_f	0	+
+chrM	4294967295	4294967322	CCDS4149.1_cds_4_0_chr5_4294967296_f	0	+
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="bx-python" version="0.7.1">
+      <repository changeset_revision="41eb9d9f667d" name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="galaxy-ops" version="1.0.0">
+      <repository changeset_revision="4e39032e4ec6" name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>