# HG changeset patch # User devteam # Date 1396363999 14400 # Node ID 1e6a9e97fa41a701cd44f845fa21ebb53ab39359 Imported from capsule None diff -r 000000000000 -r 1e6a9e97fa41 basecoverage.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/basecoverage.xml Tue Apr 01 10:53:19 2014 -0400 @@ -0,0 +1,49 @@ + + of all intervals + gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} + + bx-python + galaxy-ops + + + + + + + + + + + + + + + + + + + + + + +.. 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. + +This operation counts the total bases covered by a set of intervals. Bases that are covered by more than one interval are **not** counted more than once towards the total. + +----- + +**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 + +**Example** + +.. image:: ${static_path}/operation_icons/gops_baseCoverage.gif + + + + diff -r 000000000000 -r 1e6a9e97fa41 gops_basecoverage.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gops_basecoverage.py Tue Apr 01 10:53:19 2014 -0400 @@ -0,0 +1,48 @@ +#!/usr/bin/env python +""" +Count total base coverage. + +usage: %prog in_file out_file + -1, --cols1=N,N,N,N: Columns for start, end, strand in first file +""" + +import sys, traceback, fileinput +from warnings import warn +from bx.intervals import * +from bx.intervals.io import * +from bx.intervals.operations.base_coverage import * +from bx.cookbook import doc_optparse +from galaxy.tools.util.galaxyops import * + +assert sys.version_info[:2] >= ( 2, 4 ) + +def main(): + 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 ) + 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 ) + + try: + bases = base_coverage(g1) + except ParseError, exc: + fail( "Invalid file format: %s" % str( exc ) ) + out_file = open( out_fname, "w" ) + out_file.write( "%s\n" % str( bases ) ) + out_file.close() + if g1.skipped > 0: + print skipped( g1, filedesc="" ) + +if __name__ == "__main__": + main() diff -r 000000000000 -r 1e6a9e97fa41 operation_filter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/operation_filter.py Tue Apr 01 10:53:19 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, '

Both Queries must be from the same genome build

' + +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 diff -r 000000000000 -r 1e6a9e97fa41 test-data/1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Tue Apr 01 10:53:19 2014 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 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