# HG changeset patch # User devteam # Date 1498171983 14400 # Node ID 0145969324c4e0eecbcbb77ac0e12a2ed90cca9f # Parent 7a2a604ae9c877759b2336de0fcf5b2856393313 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 diff -r 7a2a604ae9c8 -r 0145969324c4 gops_subtract.py --- a/gops_subtract.py Thu Feb 11 12:11:59 2016 -0500 +++ b/gops_subtract.py Thu Jun 22 18:53:03 2017 -0400 @@ -11,14 +11,18 @@ -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval """ +from __future__ import print_function + import fileinput import sys + +from bx.cookbook import doc_optparse from bx.intervals.io import GenomicInterval, NiceReaderWrapper from bx.intervals.operations.subtract import subtract -from bx.cookbook import doc_optparse from bx.tabular.io import ParseError from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped -from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff + +from utils.gff_util import convert_bed_coords_to_gff, GFFFeature, GFFReaderWrapper assert sys.version_info[:2] >= ( 2, 4 ) @@ -81,16 +85,17 @@ out_file.write( "%s\n" % "\t".join( feature.fields ) ) else: out_file.write( "%s\n" % feature ) - except ParseError, exc: + except ParseError as exc: out_file.close() fail( "Invalid file format: %s" % str( exc ) ) out_file.close() if g1.skipped > 0: - print skipped( g1, filedesc=" of 2nd dataset" ) + print(skipped( g1, filedesc=" of 2nd dataset" )) if g2.skipped > 0: - print skipped( g2, filedesc=" of 1st dataset" ) + print(skipped( g2, filedesc=" of 1st dataset" )) + if __name__ == "__main__": main() diff -r 7a2a604ae9c8 -r 0145969324c4 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 22 18:53:03 2017 -0400 @@ -0,0 +1,20 @@ + + + + + bx-python + galaxy-ops + + + +----- + +**Screencasts!** + +See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). + +.. _Screencasts: https://galaxyproject.org/learn/interval-operations/ + +----- + + diff -r 7a2a604ae9c8 -r 0145969324c4 operation_filter.py --- a/operation_filter.py Thu Feb 11 12:11:59 2016 -0500 +++ b/operation_filter.py Thu Jun 22 18:53:03 2017 -0400 @@ -1,8 +1,7 @@ # runs after the job (and after the default post-filter) +from galaxy.jobs.handler import JOB_ERROR from galaxy.tools.parameters import DataToolParameter -from galaxy.jobs.handler import JOB_ERROR - # Older py compatibility try: set() @@ -14,7 +13,7 @@ dbkeys = set() data_param_names = set() data_params = 0 - for name, param in page_param_map.iteritems(): + for name, param in page_param_map.items(): if isinstance( param, DataToolParameter ): # for each dataset parameter if param_values.get(name, None) is not None: @@ -53,7 +52,6 @@ try: if stderr and len( stderr ) > 0: raise Exception( stderr ) - except Exception: data.blurb = JOB_ERROR data.state = JOB_ERROR diff -r 7a2a604ae9c8 -r 0145969324c4 subtract.xml --- a/subtract.xml Thu Feb 11 12:11:59 2016 -0500 +++ b/subtract.xml Thu Jun 22 18:53:03 2017 -0400 @@ -1,110 +1,95 @@ - the intervals of two datasets - - bx-python - galaxy-ops - - gops_subtract.py - $input1 $input2 $output - - #if isinstance( $input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): - -1 1,4,5,7 --gff1 - #else: - -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} - #end if + the intervals of two datasets + + macros.xml + + + + - - - - - - - - +#if $input2.is_of_type('gff') + -2 1,4,5,7 --gff2 +#else: + -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +-m $min +$returntype + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ]]> diff -r 7a2a604ae9c8 -r 0145969324c4 tool_dependencies.xml --- a/tool_dependencies.xml Thu Feb 11 12:11:59 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ - - - - - - - - - diff -r 7a2a604ae9c8 -r 0145969324c4 utils/__init__.pyc Binary file utils/__init__.pyc has changed diff -r 7a2a604ae9c8 -r 0145969324c4 utils/gff_util.py --- a/utils/gff_util.py Thu Feb 11 12:11:59 2016 -0500 +++ b/utils/gff_util.py Thu Jun 22 18:53:03 2017 -0400 @@ -1,11 +1,12 @@ """ Provides utilities for working with GFF files. """ +import copy -import copy from bx.intervals.io import GenomicInterval, GenomicIntervalReader, MissingFieldError, NiceReaderWrapper -from bx.tabular.io import Header, Comment, ParseError -from utils.odict import odict +from bx.tabular.io import Comment, Header, ParseError + +from .odict import odict class GFFInterval( GenomicInterval ): @@ -144,7 +145,7 @@ self.default_strand, fix_strand=self.fix_strand ) return interval - def next( self ): + def __next__( self ): """ Returns next GFFFeature. """ # @@ -177,10 +178,10 @@ while not self.seed_interval: try: self.seed_interval = GenomicIntervalReader.next( self ) - except ParseError, e: + except ParseError as e: handle_parse_error( e ) # TODO: When no longer supporting python 2.4 use finally: - #finally: + # finally: raw_size += len( self.current_line ) # If header or comment, clear seed interval and return it with its size. @@ -205,19 +206,19 @@ try: interval = GenomicIntervalReader.next( self ) raw_size += len( self.current_line ) - except StopIteration, e: + except StopIteration as e: # No more intervals to read, but last feature needs to be # returned. interval = None raw_size += len( self.current_line ) break - except ParseError, e: + except ParseError as e: handle_parse_error( e ) raw_size += len( self.current_line ) continue # TODO: When no longer supporting python 2.4 use finally: - #finally: - #raw_size += len( self.current_line ) + # finally: + # raw_size += len( self.current_line ) # Ignore comments. if isinstance( interval, Comment ): @@ -263,6 +264,7 @@ convert_gff_coords_to_bed( feature ) return feature + next = __next__ # This line should be removed once the bx-python port to Python3 is finished def convert_bed_coords_to_gff( interval ): @@ -374,7 +376,9 @@ # -- Get function that generates line/feature key. -- - get_transcript_id = lambda fields: parse_gff_attributes( fields[8] )[ 'transcript_id' ] + def get_transcript_id(fields): + return parse_gff_attributes( fields[8] )[ 'transcript_id' ] + if strict: # Strict GTF parsing uses transcript_id only to group lines into feature. key_fn = get_transcript_id @@ -382,7 +386,8 @@ # Use lenient parsing where chromosome + transcript_id is the key. This allows # transcripts with same ID on different chromosomes; this occurs in some popular # datasources, such as RefGenes in UCSC. - key_fn = lambda fields: fields[0] + '_' + get_transcript_id( fields ) + def key_fn(fields): + return fields[0] + '_' + get_transcript_id( fields ) # Aggregate intervals by transcript_id and collect comments. feature_intervals = odict() diff -r 7a2a604ae9c8 -r 0145969324c4 utils/gff_util.pyc Binary file utils/gff_util.pyc has changed diff -r 7a2a604ae9c8 -r 0145969324c4 utils/odict.pyc Binary file utils/odict.pyc has changed