Mercurial > repos > devteam > concat
changeset 0:8aa939ace6ba
Imported from capsule None
| author | devteam |
|---|---|
| date | Tue, 01 Apr 2014 10:53:46 -0400 |
| parents | |
| children | 855580142a12 |
| files | concat.xml gops_concat.py operation_filter.py test-data/1.bed test-data/1.interval test-data/2.bed test-data/gops_concat_out1.bed test-data/gops_concat_out2.bed tool_dependencies.xml |
| diffstat | 9 files changed, 586 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/concat.xml Tue Apr 01 10:53:46 2014 -0400 @@ -0,0 +1,63 @@ +<tool id="gops_concat_1" name="Concatenate" version="1.0.1"> + <description>two datasets into one dataset</description> + <requirements> + <requirement type="package" version="0.7.1">bx-python</requirement> + <requirement type="package" version="1.0.0">galaxy-ops</requirement> + </requirements> + <command interpreter="python">gops_concat.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} $sameformat</command> + <inputs> + <param format="interval" name="input1" type="data" help="First dataset"> + <label>Concatenate</label> + </param> + <param format="interval" name="input2" type="data" help="Second dataset"> + <label>with</label> + </param> + <param name="sameformat" type="boolean" truevalue="--sameformat" falsevalue="" label="Both datasets are same filetype?" checked="true" help="If unchecked Second dataset will be forced into format of First dataset"> + </param> + </inputs> + <outputs> + <data format="input" name="output" metadata_source="input1" /> + </outputs> + <code file="operation_filter.py"/> + <tests> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="sameformat" value="true" /> + <output name="output" file="gops_concat_out1.bed" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="1.interval" /> + <param name="sameformat" value="false" /> + <output name="output" file="gops_concat_out2.bed" /> + </test> + </tests> + <help> + +.. class:: infomark + +**TIP:** If your dataset does not appear in the pulldown menu -> 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** + +- **Both datasets are exactly the same filetype** will preserve all extra fields in both files. Leaving this unchecked will force the second dataset to use the same column assignments for chrom, start, end and strand, but will fill extra fields with a period(.). In both cases, the output fields are truncated or padded with fields of periods to maintain a truly tabular output. + +----- + +**Example** + +.. image:: ${static_path}/operation_icons/gops_concatenate.gif + +</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gops_concat.py Tue Apr 01 10:53:46 2014 -0400 @@ -0,0 +1,74 @@ +#!/usr/bin/env python +""" +Concatenate two bed files. The concatenated files are returned in the +same format as the first. If --sameformat is specified, then all +columns will be treated as the same, and all fields will be saved, +although the output will be trimmed to match the primary input. In +addition, if --sameformat is specified, missing fields will be padded +with a period(.). + +usage: %prog in_file_1 in_file_2 out_file + -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in first file + -2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in second file + -s, --sameformat: All files are precisely the same format. +""" + +import sys, traceback, fileinput +from warnings import warn +from bx.intervals import * +from bx.intervals.io import * +from bx.intervals.operations.concat import * +from bx.cookbook import doc_optparse +from galaxy.tools.util.galaxyops import * + +assert sys.version_info[:2] >= ( 2, 4 ) + +def main(): + sameformat=False + 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 ) + chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) + if options.sameformat: sameformat = True + in_file_1, in_file_2, out_fname = args + except: + doc_optparse.exception() + + g1 = NiceReaderWrapper( fileinput.FileInput( in_file_1 ), + chrom_col=chr_col_1, + start_col=start_col_1, + end_col=end_col_1, + strand_col=strand_col_1, + fix_strand=True ) + + g2 = NiceReaderWrapper( fileinput.FileInput( in_file_2 ), + chrom_col=chr_col_2, + start_col=start_col_2, + end_col=end_col_2, + strand_col=strand_col_2, + fix_strand=True ) + + out_file = open( out_fname, "w" ) + + try: + for line in concat( [g1, g2], sameformat=sameformat ): + if type( line ) is GenomicInterval: + out_file.write( "%s\n" % "\t".join( line.fields ) ) + else: + out_file.write( "%s\n" % line ) + except ParseError, exc: + out_file.close() + fail( "Invalid file format: %s" % str( exc ) ) + + out_file.close() + + if g1.skipped > 0: + print skipped( g1, filedesc=" of 1st dataset" ) + if g2.skipped > 0: + print skipped( g2, filedesc=" of 2nd dataset" ) + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/operation_filter.py Tue Apr 01 10:53:46 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
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_concat_out2.bed Tue Apr 01 10:53:46 2014 -0400 @@ -0,0 +1,70 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - +chr1 4348187 4348589 . . + +chr1 4488177 4488442 . . + +chr1 4774091 4774440 . . + +chr1 4800122 4800409 . . + +chr1 4878925 4879277 . . +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 01 10:53:46 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>