galaxy-commits August 2013

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commit/galaxy-central: dannon: Add missing os import to cli_shell/rsh
by commits-noreply＠bitbucket.org 30 Aug '13

30 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/facc879fe054/ Changeset: facc879fe054 User: dannon Date: 2013-08-30 05:00:04 Summary: Add missing os import to cli_shell/rsh Affected #: 1 file diff -r 5e3567cdc08984012b6b26162a4ebe75e77e942b -r facc879fe0543f25e6b4d65e3e5d5efe716ff455 lib/galaxy/jobs/runners/cli_shell/rsh.py --- a/lib/galaxy/jobs/runners/cli_shell/rsh.py +++ b/lib/galaxy/jobs/runners/cli_shell/rsh.py @@ -2,10 +2,11 @@ Interface for remote shell commands (rsh, rcp) and derivatives that use the same syntax (ssh, scp) """ +import logging +import os +import subprocess +import tempfile import time -import logging -import tempfile -import subprocess from galaxy.util.bunch import Bunch from galaxy.jobs.runners.cli_shell import BaseShellExec Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: data_transfer workflow execute was using replacement_dict (which didn't exist in scope) instead of specifying it empty
by commits-noreply＠bitbucket.org 30 Aug '13

30 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5e3567cdc089/ Changeset: 5e3567cdc089 User: dannon Date: 2013-08-30 04:58:30 Summary: data_transfer workflow execute was using replacement_dict (which didn't exist in scope) instead of specifying it empty Affected #: 1 file diff -r 1cd27d43ab14111326ab9601c7d818e6b15a3e74 -r 5e3567cdc08984012b6b26162a4ebe75e77e942b lib/galaxy/jobs/deferred/data_transfer.py --- a/lib/galaxy/jobs/deferred/data_transfer.py +++ b/lib/galaxy/jobs/deferred/data_transfer.py @@ -367,7 +367,7 @@ outputs[ step.id ] = out_data for pja in step.post_job_actions: if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(self.app, self.sa_session, pja, job, replacement_dict) + ActionBox.execute(self.app, self.sa_session, pja, job, replacement_dict=None) else: job.add_post_job_action(pja) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Broken exception in transfer manager using error vs response['error']
by commits-noreply＠bitbucket.org 30 Aug '13

30 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1cd27d43ab14/ Changeset: 1cd27d43ab14 User: dannon Date: 2013-08-30 04:55:56 Summary: Broken exception in transfer manager using error vs response['error'] Affected #: 1 file diff -r a1abf7b75d3e28ee0dc800a2ba13498e45d70ca2 -r 1cd27d43ab14111326ab9601c7d818e6b15a3e74 lib/galaxy/jobs/transfer_manager.py --- a/lib/galaxy/jobs/transfer_manager.py +++ b/lib/galaxy/jobs/transfer_manager.py @@ -90,7 +90,7 @@ raise Exception( dict( code=128, message='Did not receive valid response from transfer daemon for state' ) ) if 'error' in response: # Response was valid but Request resulted in an error - raise Exception( error ) + raise Exception( response['error']) else: # Request was valid response['result']['transfer_job_id'] = tj.id Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 30 Aug '13

30 Aug '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5623c1027c64/ Changeset: 5623c1027c64 User: dannon Date: 2013-08-30 04:35:20 Summary: Cleanup imports in sniff.py Affected #: 1 file diff -r ce2528c40e4d89642bc98c2aff7bdc6f524e4f03 -r 5623c1027c6490b84fb35a6dd3897337153f8ec5 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -1,12 +1,21 @@ """ File format detector """ -import logging, sys, os, csv, tempfile, shutil, re, zipfile, gzip +import gzip +import logging +import os +import re import registry +import shutil +import sys +import tempfile +import zipfile + +from encodings import search_function as encodings_search_function + from galaxy import util -from galaxy.datatypes.checkers import * -from encodings import search_function as encodings_search_function -from binary import Binary +from galaxy.datatypes.checkers import check_binary, check_html, is_gzip +from galaxy.datatypes.binary import Binary log = logging.getLogger(__name__) @@ -405,5 +414,5 @@ pass if __name__ == '__main__': - import doctest, sys + import doctest doctest.testmod(sys.modules[__name__]) https://bitbucket.org/galaxy/galaxy-central/commits/53f78e82f398/ Changeset: 53f78e82f398 User: dannon Date: 2013-08-30 04:36:33 Summary: Flag duplicated code in workflows API (basically copied straight from controllers/workflow.py) -- needs refactor. Affected #: 1 file diff -r 5623c1027c6490b84fb35a6dd3897337153f8ec5 -r 53f78e82f398067349d2c37c1e0281846be72a31 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -453,6 +453,11 @@ ### ----------------------------------- ### ## RPARK EDIT ## + + # TODO: This is duplicated from + # lib/galaxy/webapps/controllres/workflow.py -- refactor and + # eliminate copied code. + # Get user annotation. step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) annotation_str = "" https://bitbucket.org/galaxy/galaxy-central/commits/a1abf7b75d3e/ Changeset: a1abf7b75d3e User: dannon Date: 2013-08-30 04:38:22 Summary: Clarify in maf_utilities that there now no longer exists a duplicate method in datatypes/sequence.py. Affected #: 1 file diff -r 53f78e82f398067349d2c37c1e0281846be72a31 -r a1abf7b75d3e28ee0dc800a2ba13498e45d70ca2 lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py +++ b/lib/galaxy/tools/util/maf_utilities.py @@ -187,7 +187,6 @@ except: return build_maf_index( maf_file, species = species ) -#*** ANYCHANGE TO THIS METHOD HERE OR IN galaxy.datatypes.sequences MUST BE PROPAGATED *** def build_maf_index_species_chromosomes( filename, index_species = None ): species = [] species_chromosomes = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Remove unused 'chunks' variable calculation from get_sequences_per_file
by commits-noreply＠bitbucket.org 30 Aug '13

30 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce2528c40e4d/ Changeset: ce2528c40e4d User: dannon Date: 2013-08-30 04:32:20 Summary: Remove unused 'chunks' variable calculation from get_sequences_per_file Affected #: 1 file diff -r 31b4f32c38443343612b54cc879739bf7bc019f4 -r ce2528c40e4d89642bc98c2aff7bdc6f524e4f03 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -116,8 +116,6 @@ elif split_params['split_mode'] == 'to_size': # loop through the sections and calculate the number of sequences chunk_size = long(split_params['split_size']) - - chunks = total_sequences / chunk_size rem = total_sequences % chunk_size sequences_per_file = [chunk_size for i in range(total_sequences / chunk_size)] # TODO: Should we invest the time in a better way to handle small remainders? Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Import cleanup in sequence.py, remove import *.
by commits-noreply＠bitbucket.org 30 Aug '13

30 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31b4f32c3844/ Changeset: 31b4f32c3844 User: dannon Date: 2013-08-30 04:31:42 Summary: Import cleanup in sequence.py, remove import *. Affected #: 1 file diff -r d265a8a713092d3ba3fbca4d8db2cb93006d502f -r 31b4f32c38443343612b54cc879739bf7bc019f4 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -2,18 +2,19 @@ Sequence classes """ +import data import gzip -import data import logging +import os import re import string -import os from cgi import escape + +from galaxy import eggs, util +from galaxy.datatypes import metadata +from galaxy.datatypes.checkers import is_gzip +from galaxy.datatypes.sniff import get_test_fname, get_headers from galaxy.datatypes.metadata import MetadataElement -from galaxy.datatypes import metadata -import galaxy.model -from galaxy import eggs, util -from sniff import * eggs.require("simplejson") import simplejson @@ -30,7 +31,7 @@ class SequenceSplitLocations( data.Text ): """ Class storing information about a sequence file composed of multiple gzip files concatenated as - one OR an uncompressed file. In the GZIP case, each sub-file's location is stored in start and end. + one OR an uncompressed file. In the GZIP case, each sub-file's location is stored in start and end. The format of the file is JSON:: @@ -174,7 +175,7 @@ directories.append(dir) return dir - # we know how many splits and how many sequences in each. What remains is to write out instructions for the + # we know how many splits and how many sequences in each. What remains is to write out instructions for the # splitting of all the input files. To decouple the format of those instructions from this code, the exact format of # those instructions is delegated to scripts start_sequence=0 @@ -197,7 +198,7 @@ start_sequence += sequences_per_file[part_no] return directories write_split_files = classmethod(write_split_files) - + def split( cls, input_datasets, subdir_generator_function, split_params): """Split a generic sequence file (not sensible or possible, see subclasses).""" if split_params is None: @@ -217,7 +218,7 @@ return None raise NotImplementedError("Can't split generic alignment files") - + class Fasta( Sequence ): """Class representing a FASTA sequence""" file_ext = "fasta" @@ -225,13 +226,13 @@ def sniff( self, filename ): """ Determines whether the file is in fasta format - - A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. - The first character of the description line is a greater-than (">") symbol in the first column. + + A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. + The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters - + For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml - + Rules for sniffing as True: We don't care about line length (other than empty lines). @@ -247,7 +248,7 @@ This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta We will only check that the first purported sequence is correctly formatted. - + >>> fname = get_test_fname( 'sequence.maf' ) >>> Fasta().sniff( fname ) False @@ -255,7 +256,7 @@ >>> Fasta().sniff( fname ) True """ - + try: fh = open( filename ) while True: @@ -410,7 +411,7 @@ def sniff( self, filename ): """ - Color-space sequence: + Color-space sequence: >2_15_85_F3 T213021013012303002332212012112221222112212222 @@ -444,7 +445,7 @@ except: pass return False - + def set_meta( self, dataset, **kwd ): if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: dataset.metadata.data_lines = None @@ -474,7 +475,7 @@ if line and line.startswith( '#' ) and not sequences: # We don't count comment lines for sequence data types continue - if line and line.startswith( '@' ): + if line and line.startswith( '@' ): if seq_counter >= 4: # count previous block # blocks should be 4 lines long @@ -515,7 +516,7 @@ # Check the sequence line, make sure it contains only G/C/A/T/N if not bases_regexp.match( headers[1][0] ): return False - return True + return True return False except: return False @@ -556,7 +557,7 @@ output_name = data['output_name'] start_sequence = long(args['start_sequence']) sequence_count = long(args['num_sequences']) - + if 'toc_file' in args: toc_file = simplejson.load(open(args['toc_file'], 'r')) commands = Sequence.get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count) @@ -588,7 +589,7 @@ class Maf( Alignment ): """Class describing a Maf alignment""" file_ext = "maf" - + #Readonly and optional, users can't unset it, but if it is not set, we are generally ok; if required use a metadata validator in the tool definition MetadataElement( name="blocks", default=0, desc="Number of blocks", readonly=True, optional=True, visible=False, no_value=0 ) MetadataElement( name="species_chromosomes", desc="Species Chromosomes", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True ) @@ -608,7 +609,7 @@ return #this is not a MAF file dataset.metadata.species = species dataset.metadata.blocks = blocks - + #write species chromosomes to a file chrom_file = dataset.metadata.species_chromosomes if not chrom_file: @@ -618,7 +619,7 @@ chrom_out.write( "%s\t%s\n" % ( spec, "\t".join( chroms ) ) ) chrom_out.close() dataset.metadata.species_chromosomes = chrom_file - + index_file = dataset.metadata.maf_index if not index_file: index_file = dataset.metadata.spec['maf_index'].param.new_file( dataset = dataset ) @@ -665,18 +666,18 @@ def sniff( self, filename ): """ Determines wether the file is in maf format - - The .maf format is line-oriented. Each multiple alignment ends with a blank line. - Each sequence in an alignment is on a single line, which can get quite long, but - there is no length limit. Words in a line are delimited by any white space. - Lines starting with # are considered to be comments. Lines starting with ## can + + The .maf format is line-oriented. Each multiple alignment ends with a blank line. + Each sequence in an alignment is on a single line, which can get quite long, but + there is no length limit. Words in a line are delimited by any white space. + Lines starting with # are considered to be comments. Lines starting with ## can be ignored by most programs, but contain meta-data of one form or another. - - The first line of a .maf file begins with ##maf. This word is followed by white-space-separated + + The first line of a .maf file begins with ##maf. This word is followed by white-space-separated variable=value pairs. There should be no white space surrounding the "=". - + For complete details see http://genome.ucsc.edu/FAQ/FAQformat#format5 - + >>> fname = get_test_fname( 'sequence.maf' ) >>> Maf().sniff( fname ) True @@ -696,11 +697,11 @@ class MafCustomTrack( data.Text ): file_ext = "mafcustomtrack" - + MetadataElement( name="vp_chromosome", default='chr1', desc="Viewport Chromosome", readonly=True, optional=True, visible=False, no_value='' ) MetadataElement( name="vp_start", default='1', desc="Viewport Start", readonly=True, optional=True, visible=False, no_value='' ) MetadataElement( name="vp_end", default='100', desc="Viewport End", readonly=True, optional=True, visible=False, no_value='' ) - + def set_meta( self, dataset, overwrite = True, **kwd ): """ Parses and sets viewport metadata from MAF file. @@ -723,7 +724,7 @@ forward_strand_end = max( forward_strand_end, ref_comp.forward_strand_end ) if i > max_block_check: break - + if forward_strand_end > forward_strand_start: dataset.metadata.vp_chromosome = chrom dataset.metadata.vp_start = forward_strand_start @@ -734,7 +735,7 @@ class Axt( data.Text ): """Class describing an axt alignment""" - + # gvk- 11/19/09 - This is really an alignment, but we no longer have tools that use this data type, and it is # here simply for backward compatibility ( although it is still in the datatypes registry ). Subclassing # from data.Text eliminates managing metadata elements inherited from the Alignemnt class. @@ -744,21 +745,21 @@ def sniff( self, filename ): """ Determines whether the file is in axt format - - axt alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab + + axt alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. - + Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. - + The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields. - + The sequence lines contain the sequence of the primary assembly (line 2) and aligning assembly (line 3) with inserts. Repeats are indicated by lower-case letters. - + For complete details see http://genome.ucsc.edu/goldenPath/help/axt.html - + >>> fname = get_test_fname( 'alignment.axt' ) >>> Axt().sniff( fname ) True @@ -797,12 +798,12 @@ def sniff( self, filename ): """ Determines whether the file is in lav format - + LAV is an alignment format developed by Webb Miller's group. It is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav. - + For complete details see http://www.bioperl.org/wiki/LAV_alignment_format - + >>> fname = get_test_fname( 'alignment.lav' ) >>> Lav().sniff( fname ) True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 30 Aug '13

30 Aug '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce558696ab74/ Changeset: ce558696ab74 User: dannon Date: 2013-08-30 04:28:04 Summary: Strip COPIED_FROM method in datatypes/sequence.py from maf_utilities; avoid circular import. Affected #: 1 file diff -r 638e011bd72d029f08d4f51ea32f6f47ec80b87f -r ce558696ab749b5500e027d3b601a5b715fdac3c lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -12,13 +12,19 @@ from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes import metadata import galaxy.model -from galaxy import util +from galaxy import eggs, util from sniff import * -import pkg_resources -pkg_resources.require("simplejson") +eggs.require("simplejson") import simplejson +try: + eggs.require( "bx-python" ) + import bx.align.maf +except: + pass + + log = logging.getLogger(__name__) class SequenceSplitLocations( data.Text ): @@ -579,90 +585,6 @@ """Class representing a Color Space FASTQ sequence ( e.g a SOLiD variant )""" file_ext = "fastqcssanger" -try: - from galaxy import eggs - import pkg_resources; pkg_resources.require( "bx-python" ) - import bx.align.maf -except: - pass - -#trying to import maf_utilities here throws an ImportError due to a circular import between jobs and tools: -#from galaxy.tools.util.maf_utilities import build_maf_index_species_chromosomes -#Traceback (most recent call last): -# File "./scripts/paster.py", line 27, in <module> -# command.run() -# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/command.py", line 78, in run -# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/command.py", line 117, in invoke -# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/command.py", line 212, in run -# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/serve.py", line 227, in command -# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/serve.py", line 250, in loadapp -# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 193, in loadapp -# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 213, in loadobj -# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 237, in loadcontext -# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 267, in _loadconfig -# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 397, in get_context -# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 439, in _context_from_explicit -# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 18, in import_string -# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/pkg_resources.py", line 1912, in load -# entry = __import__(self.module_name, globals(),globals(), ['__name__']) -# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/web/buildapp.py", line 18, in <module> -# from galaxy import config, jobs, util, tools -# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/jobs/__init__.py", line 3, in <module> -# from galaxy import util, model -# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/model/__init__.py", line 13, in <module> -# import galaxy.datatypes.registry -# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/datatypes/registry.py", line 6, in <module> -# import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo -# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/datatypes/sequence.py", line 344, in <module> -# from galaxy.tools.util.maf_utilities import build_maf_index_species_chromosomes -# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/tools/__init__.py", line 15, in <module> -# from galaxy import util, jobs, model -#ImportError: cannot import name jobs -#so we'll copy and paste for now...terribly icky -#*** ANYCHANGE TO THIS METHOD HERE OR IN maf_utilities MUST BE PROPAGATED *** -def COPIED_build_maf_index_species_chromosomes( filename, index_species = None ): - species = [] - species_chromosomes = {} - indexes = bx.interval_index_file.Indexes() - blocks = 0 - try: - maf_reader = bx.align.maf.Reader( open( filename ) ) - while True: - pos = maf_reader.file.tell() - block = maf_reader.next() - if block is None: - break - blocks += 1 - for c in block.components: - spec = c.src - chrom = None - if "." in spec: - spec, chrom = spec.split( ".", 1 ) - if spec not in species: - species.append( spec ) - species_chromosomes[spec] = [] - if chrom and chrom not in species_chromosomes[spec]: - species_chromosomes[spec].append( chrom ) - if index_species is None or spec in index_species: - forward_strand_start = c.forward_strand_start - forward_strand_end = c.forward_strand_end - try: - forward_strand_start = int( forward_strand_start ) - forward_strand_end = int( forward_strand_end ) - except ValueError: - continue #start and end are not integers, can't add component to index, goto next component - #this likely only occurs when parse_e_rows is True? - #could a species exist as only e rows? should the - if forward_strand_end > forward_strand_start: - #require positive length; i.e. certain lines have start = end = 0 and cannot be indexed - indexes.add( c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size ) - except Exception, e: - #most likely a bad MAF - log.debug( 'Building MAF index on %s failed: %s' % ( filename, e ) ) - return ( None, [], {}, 0 ) - return ( indexes, species, species_chromosomes, blocks ) - - class Maf( Alignment ): """Class describing a Maf alignment""" file_ext = "maf" @@ -679,7 +601,9 @@ Parses and sets species, chromosomes, index from MAF file. """ #these metadata values are not accessable by users, always overwrite - indexes, species, species_chromosomes, blocks = COPIED_build_maf_index_species_chromosomes( dataset.file_name ) + #Imported here to avoid circular dependency + from galaxy.tools.util.maf_utilities import build_maf_index_species_chromosomes + indexes, species, species_chromosomes, blocks = build_maf_index_species_chromosomes( dataset.file_name ) if indexes is None: return #this is not a MAF file dataset.metadata.species = species https://bitbucket.org/galaxy/galaxy-central/commits/d265a8a71309/ Changeset: d265a8a71309 User: dannon Date: 2013-08-30 04:28:23 Summary: Whitespace cleanup in datatypes/sequence.py Affected #: 1 file diff -r ce558696ab749b5500e027d3b601a5b715fdac3c -r d265a8a713092d3ba3fbca4d8db2cb93006d502f lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -30,7 +30,7 @@ class SequenceSplitLocations( data.Text ): """ Class storing information about a sequence file composed of multiple gzip files concatenated as - one OR an uncompressed file. In the GZIP case, each sub-file's location is stored in start and end. + one OR an uncompressed file. In the GZIP case, each sub-file's location is stored in start and end. The format of the file is JSON:: @@ -174,7 +174,7 @@ directories.append(dir) return dir - # we know how many splits and how many sequences in each. What remains is to write out instructions for the + # we know how many splits and how many sequences in each. What remains is to write out instructions for the # splitting of all the input files. To decouple the format of those instructions from this code, the exact format of # those instructions is delegated to scripts start_sequence=0 @@ -197,7 +197,7 @@ start_sequence += sequences_per_file[part_no] return directories write_split_files = classmethod(write_split_files) - + def split( cls, input_datasets, subdir_generator_function, split_params): """Split a generic sequence file (not sensible or possible, see subclasses).""" if split_params is None: @@ -217,7 +217,7 @@ return None raise NotImplementedError("Can't split generic alignment files") - + class Fasta( Sequence ): """Class representing a FASTA sequence""" file_ext = "fasta" @@ -225,13 +225,13 @@ def sniff( self, filename ): """ Determines whether the file is in fasta format - - A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. - The first character of the description line is a greater-than (">") symbol in the first column. + + A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. + The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters - + For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml - + Rules for sniffing as True: We don't care about line length (other than empty lines). @@ -247,7 +247,7 @@ This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta We will only check that the first purported sequence is correctly formatted. - + >>> fname = get_test_fname( 'sequence.maf' ) >>> Fasta().sniff( fname ) False @@ -255,7 +255,7 @@ >>> Fasta().sniff( fname ) True """ - + try: fh = open( filename ) while True: @@ -410,7 +410,7 @@ def sniff( self, filename ): """ - Color-space sequence: + Color-space sequence: >2_15_85_F3 T213021013012303002332212012112221222112212222 @@ -444,7 +444,7 @@ except: pass return False - + def set_meta( self, dataset, **kwd ): if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: dataset.metadata.data_lines = None @@ -474,7 +474,7 @@ if line and line.startswith( '#' ) and not sequences: # We don't count comment lines for sequence data types continue - if line and line.startswith( '@' ): + if line and line.startswith( '@' ): if seq_counter >= 4: # count previous block # blocks should be 4 lines long @@ -515,7 +515,7 @@ # Check the sequence line, make sure it contains only G/C/A/T/N if not bases_regexp.match( headers[1][0] ): return False - return True + return True return False except: return False @@ -556,7 +556,7 @@ output_name = data['output_name'] start_sequence = long(args['start_sequence']) sequence_count = long(args['num_sequences']) - + if 'toc_file' in args: toc_file = simplejson.load(open(args['toc_file'], 'r')) commands = Sequence.get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count) @@ -588,7 +588,7 @@ class Maf( Alignment ): """Class describing a Maf alignment""" file_ext = "maf" - + #Readonly and optional, users can't unset it, but if it is not set, we are generally ok; if required use a metadata validator in the tool definition MetadataElement( name="blocks", default=0, desc="Number of blocks", readonly=True, optional=True, visible=False, no_value=0 ) MetadataElement( name="species_chromosomes", desc="Species Chromosomes", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True ) @@ -608,7 +608,7 @@ return #this is not a MAF file dataset.metadata.species = species dataset.metadata.blocks = blocks - + #write species chromosomes to a file chrom_file = dataset.metadata.species_chromosomes if not chrom_file: @@ -618,7 +618,7 @@ chrom_out.write( "%s\t%s\n" % ( spec, "\t".join( chroms ) ) ) chrom_out.close() dataset.metadata.species_chromosomes = chrom_file - + index_file = dataset.metadata.maf_index if not index_file: index_file = dataset.metadata.spec['maf_index'].param.new_file( dataset = dataset ) @@ -665,18 +665,18 @@ def sniff( self, filename ): """ Determines wether the file is in maf format - - The .maf format is line-oriented. Each multiple alignment ends with a blank line. - Each sequence in an alignment is on a single line, which can get quite long, but - there is no length limit. Words in a line are delimited by any white space. - Lines starting with # are considered to be comments. Lines starting with ## can + + The .maf format is line-oriented. Each multiple alignment ends with a blank line. + Each sequence in an alignment is on a single line, which can get quite long, but + there is no length limit. Words in a line are delimited by any white space. + Lines starting with # are considered to be comments. Lines starting with ## can be ignored by most programs, but contain meta-data of one form or another. - - The first line of a .maf file begins with ##maf. This word is followed by white-space-separated + + The first line of a .maf file begins with ##maf. This word is followed by white-space-separated variable=value pairs. There should be no white space surrounding the "=". - + For complete details see http://genome.ucsc.edu/FAQ/FAQformat#format5 - + >>> fname = get_test_fname( 'sequence.maf' ) >>> Maf().sniff( fname ) True @@ -696,11 +696,11 @@ class MafCustomTrack( data.Text ): file_ext = "mafcustomtrack" - + MetadataElement( name="vp_chromosome", default='chr1', desc="Viewport Chromosome", readonly=True, optional=True, visible=False, no_value='' ) MetadataElement( name="vp_start", default='1', desc="Viewport Start", readonly=True, optional=True, visible=False, no_value='' ) MetadataElement( name="vp_end", default='100', desc="Viewport End", readonly=True, optional=True, visible=False, no_value='' ) - + def set_meta( self, dataset, overwrite = True, **kwd ): """ Parses and sets viewport metadata from MAF file. @@ -723,7 +723,7 @@ forward_strand_end = max( forward_strand_end, ref_comp.forward_strand_end ) if i > max_block_check: break - + if forward_strand_end > forward_strand_start: dataset.metadata.vp_chromosome = chrom dataset.metadata.vp_start = forward_strand_start @@ -734,7 +734,7 @@ class Axt( data.Text ): """Class describing an axt alignment""" - + # gvk- 11/19/09 - This is really an alignment, but we no longer have tools that use this data type, and it is # here simply for backward compatibility ( although it is still in the datatypes registry ). Subclassing # from data.Text eliminates managing metadata elements inherited from the Alignemnt class. @@ -744,21 +744,21 @@ def sniff( self, filename ): """ Determines whether the file is in axt format - - axt alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab + + axt alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. - + Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. - + The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields. - + The sequence lines contain the sequence of the primary assembly (line 2) and aligning assembly (line 3) with inserts. Repeats are indicated by lower-case letters. - + For complete details see http://genome.ucsc.edu/goldenPath/help/axt.html - + >>> fname = get_test_fname( 'alignment.axt' ) >>> Axt().sniff( fname ) True @@ -797,12 +797,12 @@ def sniff( self, filename ): """ Determines whether the file is in lav format - + LAV is an alignment format developed by Webb Miller's group. It is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav. - + For complete details see http://www.bioperl.org/wiki/LAV_alignment_format - + >>> fname = get_test_fname( 'alignment.lav' ) >>> Lav().sniff( fname ) True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Fix maf_utilities formatting, removing windows terminators.
by commits-noreply＠bitbucket.org 30 Aug '13

30 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/638e011bd72d/ Changeset: 638e011bd72d User: dannon Date: 2013-08-30 04:08:18 Summary: Fix maf_utilities formatting, removing windows terminators. Affected #: 1 file diff -r bec1baa9d2db009abd16778093fb15b96bde0950 -r 638e011bd72d029f08d4f51ea32f6f47ec80b87f lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py +++ b/lib/galaxy/tools/util/maf_utilities.py @@ -1,17 +1,17 @@ -#!/usr/bin/env python -""" -Provides wrappers and utilities for working with MAF files and alignments. -""" -#Dan Blankenberg -import pkg_resources; pkg_resources.require( "bx-python" ) -import bx.align.maf -import bx.intervals -import bx.interval_index_file +#!/usr/bin/env python +""" +Provides wrappers and utilities for working with MAF files and alignments. +""" +#Dan Blankenberg +import pkg_resources; pkg_resources.require( "bx-python" ) +import bx.align.maf +import bx.intervals +import bx.interval_index_file import sys, os, string, tempfile import logging -from copy import deepcopy - -assert sys.version_info[:2] >= ( 2, 4 ) +from copy import deepcopy + +assert sys.version_info[:2] >= ( 2, 4 ) log = logging.getLogger(__name__) @@ -26,7 +26,7 @@ chrom = fields.pop( 0 ) else: chrom = spec - return spec, chrom + return spec, chrom def src_merge( spec, chrom, contig = None ): if None in [ spec, chrom ]: @@ -45,140 +45,140 @@ print >> sys.stderr, "Fatal Error: %s" % msg sys.exit() -#an object corresponding to a reference layered alignment -class RegionAlignment( object ): - - DNA_COMPLEMENT = string.maketrans( "ACGTacgt", "TGCAtgca" ) - MAX_SEQUENCE_SIZE = sys.maxint #Maximum length of sequence allowed - - def __init__( self, size, species = [] ): - assert size <= self.MAX_SEQUENCE_SIZE, "Maximum length allowed for an individual sequence has been exceeded (%i > %i)." % ( size, self.MAX_SEQUENCE_SIZE ) - self.size = size - self.sequences = {} - if not isinstance( species, list ): - species = [species] - for spec in species: - self.add_species( spec ) - - #add a species to the alignment - def add_species( self, species ): - #make temporary sequence files - self.sequences[species] = tempfile.TemporaryFile() - self.sequences[species].write( "-" * self.size ) - - #returns the names for species found in alignment, skipping names as requested - def get_species_names( self, skip = [] ): - if not isinstance( skip, list ): skip = [skip] - names = self.sequences.keys() - for name in skip: - try: names.remove( name ) - except: pass - return names - - #returns the sequence for a species - def get_sequence( self, species ): - self.sequences[species].seek( 0 ) - return self.sequences[species].read() - - #returns the reverse complement of the sequence for a species - def get_sequence_reverse_complement( self, species ): - complement = [base for base in self.get_sequence( species ).translate( self.DNA_COMPLEMENT )] - complement.reverse() - return "".join( complement ) - - #sets a position for a species - def set_position( self, index, species, base ): - if len( base ) != 1: raise Exception( "A genomic position can only have a length of 1." ) - return self.set_range( index, species, base ) - #sets a range for a species - def set_range( self, index, species, bases ): - if index >= self.size or index < 0: raise Exception( "Your index (%i) is out of range (0 - %i)." % ( index, self.size - 1 ) ) - if len( bases ) == 0: raise Exception( "A set of genomic positions can only have a positive length." ) - if species not in self.sequences.keys(): self.add_species( species ) - self.sequences[species].seek( index ) - self.sequences[species].write( bases ) - - #Flush temp file of specified species, or all species - def flush( self, species = None ): - if species is None: - species = self.sequences.keys() - elif not isinstance( species, list ): - species = [species] - for spec in species: - self.sequences[spec].flush() - -class GenomicRegionAlignment( RegionAlignment ): - - def __init__( self, start, end, species = [] ): - RegionAlignment.__init__( self, end - start, species ) - self.start = start - self.end = end - -class SplicedAlignment( object ): - - DNA_COMPLEMENT = string.maketrans( "ACGTacgt", "TGCAtgca" ) - - def __init__( self, exon_starts, exon_ends, species = [] ): - if not isinstance( exon_starts, list ): - exon_starts = [exon_starts] - if not isinstance( exon_ends, list ): - exon_ends = [exon_ends] - assert len( exon_starts ) == len( exon_ends ), "The number of starts does not match the number of sizes." - self.exons = [] - for i in range( len( exon_starts ) ): - self.exons.append( GenomicRegionAlignment( exon_starts[i], exon_ends[i], species ) ) - - #returns the names for species found in alignment, skipping names as requested - def get_species_names( self, skip = [] ): - if not isinstance( skip, list ): skip = [skip] - names = [] - for exon in self.exons: - for name in exon.get_species_names( skip = skip ): - if name not in names: - names.append( name ) - return names - - #returns the sequence for a species - def get_sequence( self, species ): - sequence = tempfile.TemporaryFile() - for exon in self.exons: - if species in exon.get_species_names(): - sequence.write( exon.get_sequence( species ) ) - else: - sequence.write( "-" * exon.size ) - sequence.seek( 0 ) - return sequence.read() - - #returns the reverse complement of the sequence for a species - def get_sequence_reverse_complement( self, species ): - complement = [base for base in self.get_sequence( species ).translate( self.DNA_COMPLEMENT )] - complement.reverse() - return "".join( complement ) - - #Start and end of coding region - @property - def start( self ): - return self.exons[0].start - @property - def end( self ): - return self.exons[-1].end - -#Open a MAF index using a UID -def maf_index_by_uid( maf_uid, index_location_file ): - for line in open( index_location_file ): - try: - #read each line, if not enough fields, go to next line - if line[0:1] == "#" : continue - fields = line.split('\t') - if maf_uid == fields[1]: - try: - maf_files = fields[4].replace( "\n", "" ).replace( "\r", "" ).split( "," ) - return bx.align.maf.MultiIndexed( maf_files, keep_open = True, parse_e_rows = False ) - except Exception, e: - raise Exception( 'MAF UID (%s) found, but configuration appears to be malformed: %s' % ( maf_uid, e ) ) - except: - pass - return None +#an object corresponding to a reference layered alignment +class RegionAlignment( object ): + + DNA_COMPLEMENT = string.maketrans( "ACGTacgt", "TGCAtgca" ) + MAX_SEQUENCE_SIZE = sys.maxint #Maximum length of sequence allowed + + def __init__( self, size, species = [] ): + assert size <= self.MAX_SEQUENCE_SIZE, "Maximum length allowed for an individual sequence has been exceeded (%i > %i)." % ( size, self.MAX_SEQUENCE_SIZE ) + self.size = size + self.sequences = {} + if not isinstance( species, list ): + species = [species] + for spec in species: + self.add_species( spec ) + + #add a species to the alignment + def add_species( self, species ): + #make temporary sequence files + self.sequences[species] = tempfile.TemporaryFile() + self.sequences[species].write( "-" * self.size ) + + #returns the names for species found in alignment, skipping names as requested + def get_species_names( self, skip = [] ): + if not isinstance( skip, list ): skip = [skip] + names = self.sequences.keys() + for name in skip: + try: names.remove( name ) + except: pass + return names + + #returns the sequence for a species + def get_sequence( self, species ): + self.sequences[species].seek( 0 ) + return self.sequences[species].read() + + #returns the reverse complement of the sequence for a species + def get_sequence_reverse_complement( self, species ): + complement = [base for base in self.get_sequence( species ).translate( self.DNA_COMPLEMENT )] + complement.reverse() + return "".join( complement ) + + #sets a position for a species + def set_position( self, index, species, base ): + if len( base ) != 1: raise Exception( "A genomic position can only have a length of 1." ) + return self.set_range( index, species, base ) + #sets a range for a species + def set_range( self, index, species, bases ): + if index >= self.size or index < 0: raise Exception( "Your index (%i) is out of range (0 - %i)." % ( index, self.size - 1 ) ) + if len( bases ) == 0: raise Exception( "A set of genomic positions can only have a positive length." ) + if species not in self.sequences.keys(): self.add_species( species ) + self.sequences[species].seek( index ) + self.sequences[species].write( bases ) + + #Flush temp file of specified species, or all species + def flush( self, species = None ): + if species is None: + species = self.sequences.keys() + elif not isinstance( species, list ): + species = [species] + for spec in species: + self.sequences[spec].flush() + +class GenomicRegionAlignment( RegionAlignment ): + + def __init__( self, start, end, species = [] ): + RegionAlignment.__init__( self, end - start, species ) + self.start = start + self.end = end + +class SplicedAlignment( object ): + + DNA_COMPLEMENT = string.maketrans( "ACGTacgt", "TGCAtgca" ) + + def __init__( self, exon_starts, exon_ends, species = [] ): + if not isinstance( exon_starts, list ): + exon_starts = [exon_starts] + if not isinstance( exon_ends, list ): + exon_ends = [exon_ends] + assert len( exon_starts ) == len( exon_ends ), "The number of starts does not match the number of sizes." + self.exons = [] + for i in range( len( exon_starts ) ): + self.exons.append( GenomicRegionAlignment( exon_starts[i], exon_ends[i], species ) ) + + #returns the names for species found in alignment, skipping names as requested + def get_species_names( self, skip = [] ): + if not isinstance( skip, list ): skip = [skip] + names = [] + for exon in self.exons: + for name in exon.get_species_names( skip = skip ): + if name not in names: + names.append( name ) + return names + + #returns the sequence for a species + def get_sequence( self, species ): + sequence = tempfile.TemporaryFile() + for exon in self.exons: + if species in exon.get_species_names(): + sequence.write( exon.get_sequence( species ) ) + else: + sequence.write( "-" * exon.size ) + sequence.seek( 0 ) + return sequence.read() + + #returns the reverse complement of the sequence for a species + def get_sequence_reverse_complement( self, species ): + complement = [base for base in self.get_sequence( species ).translate( self.DNA_COMPLEMENT )] + complement.reverse() + return "".join( complement ) + + #Start and end of coding region + @property + def start( self ): + return self.exons[0].start + @property + def end( self ): + return self.exons[-1].end + +#Open a MAF index using a UID +def maf_index_by_uid( maf_uid, index_location_file ): + for line in open( index_location_file ): + try: + #read each line, if not enough fields, go to next line + if line[0:1] == "#" : continue + fields = line.split('\t') + if maf_uid == fields[1]: + try: + maf_files = fields[4].replace( "\n", "" ).replace( "\r", "" ).split( "," ) + return bx.align.maf.MultiIndexed( maf_files, keep_open = True, parse_e_rows = False ) + except Exception, e: + raise Exception( 'MAF UID (%s) found, but configuration appears to be malformed: %s' % ( maf_uid, e ) ) + except: + pass + return None #return ( index, temp_index_filename ) for user maf, if available, or build one and return it, return None when no tempfile is created def open_or_build_maf_index( maf_file, index_filename, species = None ): @@ -186,27 +186,27 @@ return ( bx.align.maf.Indexed( maf_file, index_filename = index_filename, keep_open = True, parse_e_rows = False ), None ) except: return build_maf_index( maf_file, species = species ) - + #*** ANYCHANGE TO THIS METHOD HERE OR IN galaxy.datatypes.sequences MUST BE PROPAGATED *** def build_maf_index_species_chromosomes( filename, index_species = None ): species = [] species_chromosomes = {} - indexes = bx.interval_index_file.Indexes() + indexes = bx.interval_index_file.Indexes() blocks = 0 try: maf_reader = bx.align.maf.Reader( open( filename ) ) while True: pos = maf_reader.file.tell() block = maf_reader.next() - if block is None: - break + if block is None: + break blocks += 1 for c in block.components: spec = c.src chrom = None if "." in spec: spec, chrom = spec.split( ".", 1 ) - if spec not in species: + if spec not in species: species.append( spec ) species_chromosomes[spec] = [] if chrom and chrom not in species_chromosomes[spec]: @@ -229,17 +229,17 @@ log.debug( 'Building MAF index on %s failed: %s' % ( filename, e ) ) return ( None, [], {}, 0 ) return ( indexes, species, species_chromosomes, blocks ) - -#builds and returns ( index, index_filename ) for specified maf_file -def build_maf_index( maf_file, species = None ): + +#builds and returns ( index, index_filename ) for specified maf_file +def build_maf_index( maf_file, species = None ): indexes, found_species, species_chromosomes, blocks = build_maf_index_species_chromosomes( maf_file, species ) if indexes is not None: - fd, index_filename = tempfile.mkstemp() - out = os.fdopen( fd, 'w' ) - indexes.write( out ) - out.close() + fd, index_filename = tempfile.mkstemp() + out = os.fdopen( fd, 'w' ) + indexes.write( out ) + out.close() return ( bx.align.maf.Indexed( maf_file, index_filename = index_filename, keep_open = True, parse_e_rows = False ), index_filename ) - return ( None, None ) + return ( None, None ) def component_overlaps_region( c, region ): if c is None: return False @@ -276,7 +276,7 @@ start = end - slice_len slice_start = min( start, slice_start ) slice_end = max( end, slice_end ) - + if slice_start < slice_end: block = block.slice( slice_start, slice_end ) if block.text_size > mincols: @@ -287,7 +287,7 @@ block.remove_all_gap_columns() return block return None - + def orient_block_by_region( block, src, region, force_strand = None ): #loop through components matching src, #make sure each of these components overlap region @@ -295,12 +295,12 @@ #if force_strand / region.strand not in strand cache, reverse complement ### we could have 2 sequences with same src, overlapping region, on different strands, this would cause no reverse_complementing strands = [ c.strand for c in iter_components_by_src( block, src ) if component_overlaps_region( c, region ) ] - if strands and ( force_strand is None and region.strand not in strands ) or ( force_strand is not None and force_strand not in strands ): + if strands and ( force_strand is None and region.strand not in strands ) or ( force_strand is not None and force_strand not in strands ): block = block.reverse_complement() return block def get_oriented_chopped_blocks_for_region( index, src, region, species = None, mincols = 0, force_strand = None ): - for block, idx, offset in get_oriented_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols, force_strand ): + for block, idx, offset in get_oriented_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols, force_strand ): yield block def get_oriented_chopped_blocks_with_index_offset_for_region( index, src, region, species = None, mincols = 0, force_strand = None ): for block, idx, offset in get_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols ): @@ -331,8 +331,8 @@ else: #no more components to add, yield this block yield new_block - - #divide components by species + + #divide components by species spec_dict = {} if not species: species = [] @@ -347,7 +347,7 @@ spec_dict[ spec ] = [] for c in iter_components_by_src_start( block, spec ): spec_dict[ spec ].append( c ) - + empty_block = bx.align.Alignment( score=block.score, attributes=deepcopy( block.attributes ) ) #should we copy attributes? empty_block.text_size = block.text_size #call recursive function to split into each combo of spec/blocks @@ -356,68 +356,69 @@ yield value -#generator yielding only chopped and valid blocks for a specified region -def get_chopped_blocks_for_region( index, src, region, species = None, mincols = 0 ): - for block, idx, offset in get_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols ): - yield block -def get_chopped_blocks_with_index_offset_for_region( index, src, region, species = None, mincols = 0 ): - for block, idx, offset in index.get_as_iterator_with_index_and_offset( src, region.start, region.end ): - block = chop_block_by_region( block, src, region, species, mincols ) - if block is not None: - yield block, idx, offset - -#returns a filled region alignment for specified regions -def get_region_alignment( index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): - if species is not None: alignment = RegionAlignment( end - start, species ) - else: alignment = RegionAlignment( end - start, primary_species ) - return fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand, species, mincols, overwrite_with_gaps ) - -#reduces a block to only positions exisiting in the src provided -def reduce_block_by_primary_genome( block, species, chromosome, region_start ): - #returns ( startIndex, {species:texts} - #where texts' contents are reduced to only positions existing in the primary genome - src = "%s.%s" % ( species, chromosome ) - ref = block.get_component_by_src( src ) - start_offset = ref.start - region_start - species_texts = {} - for c in block.components: - species_texts[ c.src.split( '.' )[0] ] = list( c.text ) - #remove locations which are gaps in the primary species, starting from the downstream end - for i in range( len( species_texts[ species ] ) - 1, -1, -1 ): - if species_texts[ species ][i] == '-': - for text in species_texts.values(): - text.pop( i ) - for spec, text in species_texts.items(): - species_texts[spec] = ''.join( text ) - return ( start_offset, species_texts ) - -#fills a region alignment -def fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): - region = bx.intervals.Interval( start, end ) - region.chrom = chrom - region.strand = strand - primary_src = "%s.%s" % ( primary_species, chrom ) - - #Order blocks overlaping this position by score, lowest first - blocks = [] - for block, idx, offset in index.get_as_iterator_with_index_and_offset( primary_src, start, end ): - score = float( block.score ) - for i in range( 0, len( blocks ) ): - if score < blocks[i][0]: - blocks.insert( i, ( score, idx, offset ) ) - break - else: - blocks.append( ( score, idx, offset ) ) - +#generator yielding only chopped and valid blocks for a specified region +def get_chopped_blocks_for_region( index, src, region, species = None, mincols = 0 ): + for block, idx, offset in get_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols ): + yield block +def get_chopped_blocks_with_index_offset_for_region( index, src, region, species = None, mincols = 0 ): + for block, idx, offset in index.get_as_iterator_with_index_and_offset( src, region.start, region.end ): + block = chop_block_by_region( block, src, region, species, mincols ) + if block is not None: + yield block, idx, offset + +#returns a filled region alignment for specified regions +def get_region_alignment( index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): + if species is not None: alignment = RegionAlignment( end - start, species ) + else: alignment = RegionAlignment( end - start, primary_species ) + return fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand, species, mincols, overwrite_with_gaps ) + +#reduces a block to only positions exisiting in the src provided +def reduce_block_by_primary_genome( block, species, chromosome, region_start ): + #returns ( startIndex, {species:texts} + #where texts' contents are reduced to only positions existing in the primary genome + src = "%s.%s" % ( species, chromosome ) + ref = block.get_component_by_src( src ) + start_offset = ref.start - region_start + species_texts = {} + for c in block.components: + species_texts[ c.src.split( '.' )[0] ] = list( c.text ) + #remove locations which are gaps in the primary species, starting from the downstream end + for i in range( len( species_texts[ species ] ) - 1, -1, -1 ): + if species_texts[ species ][i] == '-': + for text in species_texts.values(): + text.pop( i ) + for spec, text in species_texts.items(): + species_texts[spec] = ''.join( text ) + return ( start_offset, species_texts ) + +#fills a region alignment +def fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): + region = bx.intervals.Interval( start, end ) + region.chrom = chrom + region.strand = strand + primary_src = "%s.%s" % ( primary_species, chrom ) + + #Order blocks overlaping this position by score, lowest first + blocks = [] + for block, idx, offset in index.get_as_iterator_with_index_and_offset( primary_src, start, end ): + score = float( block.score ) + for i in range( 0, len( blocks ) ): + if score < blocks[i][0]: + blocks.insert( i, ( score, idx, offset ) ) + break + else: + blocks.append( ( score, idx, offset ) ) + #gap_chars_tuple = tuple( GAP_CHARS ) - gap_chars_str = ''.join( GAP_CHARS ) - #Loop through ordered blocks and layer by increasing score - for block_dict in blocks: for block in iter_blocks_split_by_species( block_dict[1].get_at_offset( block_dict[2] ) ): #need to handle each occurance of sequence in block seperately + gap_chars_str = ''.join( GAP_CHARS ) + #Loop through ordered blocks and layer by increasing score + for block_dict in blocks: + for block in iter_blocks_split_by_species( block_dict[1].get_at_offset( block_dict[2] ) ): #need to handle each occurance of sequence in block seperately if component_overlaps_region( block.get_component_by_src( primary_src ), region ): block = chop_block_by_region( block, primary_src, region, species, mincols ) #chop block block = orient_block_by_region( block, primary_src, region ) #orient block - start_offset, species_texts = reduce_block_by_primary_genome( block, primary_species, chrom, start ) - for spec, text in species_texts.items(): + start_offset, species_texts = reduce_block_by_primary_genome( block, primary_species, chrom, start ) + for spec, text in species_texts.items(): #we should trim gaps from both sides, since these are not positions in this species genome (sequence) text = text.rstrip( gap_chars_str ) gap_offset = 0 @@ -433,169 +434,169 @@ else: for i, char in enumerate( text ): if char not in GAP_CHARS: - alignment.set_position( start_offset + gap_offset + i, spec, char ) - return alignment - -#returns a filled spliced region alignment for specified region with start and end lists -def get_spliced_region_alignment( index, primary_species, chrom, starts, ends, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): - #create spliced alignment object - if species is not None: alignment = SplicedAlignment( starts, ends, species ) - else: alignment = SplicedAlignment( starts, ends, [primary_species] ) - for exon in alignment.exons: - fill_region_alignment( exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols, overwrite_with_gaps ) - return alignment - -#loop through string array, only return non-commented lines -def line_enumerator( lines, comment_start = '#' ): - i = 0 - for line in lines: - if not line.startswith( comment_start ): - i += 1 - yield ( i, line ) - -#read a GeneBed file, return list of starts, ends, raw fields -def get_starts_ends_fields_from_gene_bed( line ): - #Starts and ends for exons - starts = [] - ends = [] - - fields = line.split() - #Requires atleast 12 BED columns - if len(fields) < 12: - raise Exception( "Not a proper 12 column BED line (%s)." % line ) - chrom = fields[0] - tx_start = int( fields[1] ) - tx_end = int( fields[2] ) - name = fields[3] - strand = fields[5] - if strand != '-': strand='+' #Default strand is + - cds_start = int( fields[6] ) - cds_end = int( fields[7] ) - - #Calculate and store starts and ends of coding exons - region_start, region_end = cds_start, cds_end - exon_starts = map( int, fields[11].rstrip( ',\n' ).split( ',' ) ) - exon_starts = map( ( lambda x: x + tx_start ), exon_starts ) - exon_ends = map( int, fields[10].rstrip( ',' ).split( ',' ) ) - exon_ends = map( ( lambda x, y: x + y ), exon_starts, exon_ends ); - for start, end in zip( exon_starts, exon_ends ): - start = max( start, region_start ) - end = min( end, region_end ) - if start < end: - starts.append( start ) - ends.append( end ) - return ( starts, ends, fields ) - -def iter_components_by_src( block, src ): - for c in block.components: - if c.src == src: - yield c - -def get_components_by_src( block, src ): - return [ value for value in iter_components_by_src( block, src ) ] - -def iter_components_by_src_start( block, src ): - for c in block.components: - if c.src.startswith( src ): - yield c - -def get_components_by_src_start( block, src ): - return [ value for value in iter_components_by_src_start( block, src ) ] + alignment.set_position( start_offset + gap_offset + i, spec, char ) + return alignment + +#returns a filled spliced region alignment for specified region with start and end lists +def get_spliced_region_alignment( index, primary_species, chrom, starts, ends, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): + #create spliced alignment object + if species is not None: alignment = SplicedAlignment( starts, ends, species ) + else: alignment = SplicedAlignment( starts, ends, [primary_species] ) + for exon in alignment.exons: + fill_region_alignment( exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols, overwrite_with_gaps ) + return alignment + +#loop through string array, only return non-commented lines +def line_enumerator( lines, comment_start = '#' ): + i = 0 + for line in lines: + if not line.startswith( comment_start ): + i += 1 + yield ( i, line ) + +#read a GeneBed file, return list of starts, ends, raw fields +def get_starts_ends_fields_from_gene_bed( line ): + #Starts and ends for exons + starts = [] + ends = [] + + fields = line.split() + #Requires atleast 12 BED columns + if len(fields) < 12: + raise Exception( "Not a proper 12 column BED line (%s)." % line ) + chrom = fields[0] + tx_start = int( fields[1] ) + tx_end = int( fields[2] ) + name = fields[3] + strand = fields[5] + if strand != '-': strand='+' #Default strand is + + cds_start = int( fields[6] ) + cds_end = int( fields[7] ) + + #Calculate and store starts and ends of coding exons + region_start, region_end = cds_start, cds_end + exon_starts = map( int, fields[11].rstrip( ',\n' ).split( ',' ) ) + exon_starts = map( ( lambda x: x + tx_start ), exon_starts ) + exon_ends = map( int, fields[10].rstrip( ',' ).split( ',' ) ) + exon_ends = map( ( lambda x, y: x + y ), exon_starts, exon_ends ); + for start, end in zip( exon_starts, exon_ends ): + start = max( start, region_start ) + end = min( end, region_end ) + if start < end: + starts.append( start ) + ends.append( end ) + return ( starts, ends, fields ) + +def iter_components_by_src( block, src ): + for c in block.components: + if c.src == src: + yield c + +def get_components_by_src( block, src ): + return [ value for value in iter_components_by_src( block, src ) ] + +def iter_components_by_src_start( block, src ): + for c in block.components: + if c.src.startswith( src ): + yield c + +def get_components_by_src_start( block, src ): + return [ value for value in iter_components_by_src_start( block, src ) ] def sort_block_components_by_block( block1, block2 ): #orders the components in block1 by the index of the component in block2 #block1 must be a subset of block2 #occurs in-place return block1.components.sort( cmp = lambda x, y: block2.components.index( x ) - block2.components.index( y ) ) - + def get_species_in_maf( maf_filename ): species = [] for block in bx.align.maf.Reader( open( maf_filename ) ): for spec in get_species_in_block( block ): if spec not in species: species.append( spec ) - return species - -def parse_species_option( species ): - if species: - species = species.split( ',' ) - if 'None' not in species: - return species - return None #provided species was '', None, or had 'None' in it - -def remove_temp_index_file( index_filename ): - try: os.unlink( index_filename ) - except: pass - -#Below are methods to deal with FASTA files - -def get_fasta_header( component, attributes = {}, suffix = None ): - header = ">%s(%s):%i-%i|" % ( component.src, component.strand, component.get_forward_strand_start(), component.get_forward_strand_end() ) - for key, value in attributes.iteritems(): - header = "%s%s=%s|" % ( header, key, value ) - if suffix: - header = "%s%s" % ( header, suffix ) - else: - header = "%s%s" % ( header, src_split( component.src )[ 0 ] ) - return header - -def get_attributes_from_fasta_header( header ): - if not header: return {} - attributes = {} - header = header.lstrip( '>' ) - header = header.strip() - fields = header.split( '|' ) - try: - region = fields[0] - region = region.split( '(', 1 ) - temp = region[0].split( '.', 1 ) - attributes['species'] = temp[0] - if len( temp ) == 2: - attributes['chrom'] = temp[1] - else: - attributes['chrom'] = temp[0] - region = region[1].split( ')', 1 ) - attributes['strand'] = region[0] - region = region[1].lstrip( ':' ).split( '-' ) - attributes['start'] = int( region[0] ) - attributes['end'] = int( region[1] ) - except: - #fields 0 is not a region coordinate - pass - if len( fields ) > 2: - for i in xrange( 1, len( fields ) - 1 ): - prop = fields[i].split( '=', 1 ) - if len( prop ) == 2: - attributes[ prop[0] ] = prop[1] - if len( fields ) > 1: - attributes['__suffix__'] = fields[-1] - return attributes - -def iter_fasta_alignment( filename ): - class fastaComponent: - def __init__( self, species, text = "" ): - self.species = species - self.text = text - def extend( self, text ): - self.text = self.text + text.replace( '\n', '' ).replace( '\r', '' ).strip() - #yields a list of fastaComponents for a FASTA file - f = open( filename, 'rb' ) - components = [] - #cur_component = None - while True: - line = f.readline() - if not line: - if components: - yield components - return - line = line.strip() - if not line: - if components: - yield components - components = [] - elif line.startswith( '>' ): - attributes = get_attributes_from_fasta_header( line ) - components.append( fastaComponent( attributes['species'] ) ) - elif components: - components[-1].extend( line ) - + return species + +def parse_species_option( species ): + if species: + species = species.split( ',' ) + if 'None' not in species: + return species + return None #provided species was '', None, or had 'None' in it + +def remove_temp_index_file( index_filename ): + try: os.unlink( index_filename ) + except: pass + +#Below are methods to deal with FASTA files + +def get_fasta_header( component, attributes = {}, suffix = None ): + header = ">%s(%s):%i-%i|" % ( component.src, component.strand, component.get_forward_strand_start(), component.get_forward_strand_end() ) + for key, value in attributes.iteritems(): + header = "%s%s=%s|" % ( header, key, value ) + if suffix: + header = "%s%s" % ( header, suffix ) + else: + header = "%s%s" % ( header, src_split( component.src )[ 0 ] ) + return header + +def get_attributes_from_fasta_header( header ): + if not header: return {} + attributes = {} + header = header.lstrip( '>' ) + header = header.strip() + fields = header.split( '|' ) + try: + region = fields[0] + region = region.split( '(', 1 ) + temp = region[0].split( '.', 1 ) + attributes['species'] = temp[0] + if len( temp ) == 2: + attributes['chrom'] = temp[1] + else: + attributes['chrom'] = temp[0] + region = region[1].split( ')', 1 ) + attributes['strand'] = region[0] + region = region[1].lstrip( ':' ).split( '-' ) + attributes['start'] = int( region[0] ) + attributes['end'] = int( region[1] ) + except: + #fields 0 is not a region coordinate + pass + if len( fields ) > 2: + for i in xrange( 1, len( fields ) - 1 ): + prop = fields[i].split( '=', 1 ) + if len( prop ) == 2: + attributes[ prop[0] ] = prop[1] + if len( fields ) > 1: + attributes['__suffix__'] = fields[-1] + return attributes + +def iter_fasta_alignment( filename ): + class fastaComponent: + def __init__( self, species, text = "" ): + self.species = species + self.text = text + def extend( self, text ): + self.text = self.text + text.replace( '\n', '' ).replace( '\r', '' ).strip() + #yields a list of fastaComponents for a FASTA file + f = open( filename, 'rb' ) + components = [] + #cur_component = None + while True: + line = f.readline() + if not line: + if components: + yield components + return + line = line.strip() + if not line: + if components: + yield components + components = [] + elif line.startswith( '>' ): + attributes = get_attributes_from_fasta_header( line ) + components.append( fastaComponent( attributes['species'] ) ) + elif components: + components[-1].extend( line ) + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Irods get_data was using wrong varname for reading(count)
by commits-noreply＠bitbucket.org 29 Aug '13

29 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bec1baa9d2db/ Changeset: bec1baa9d2db User: dannon Date: 2013-08-29 18:21:50 Summary: Irods get_data was using wrong varname for reading(count) Affected #: 1 file diff -r 444c5b5b451b50eacba3ba1d08d83e16c1027fa5 -r bec1baa9d2db009abd16778093fb15b96bde0950 lib/galaxy/objectstore/rods.py --- a/lib/galaxy/objectstore/rods.py +++ b/lib/galaxy/objectstore/rods.py @@ -210,7 +210,7 @@ if count == -1: return h.read() else: - return f.read( count ) + return h.read( count ) # TODO: make sure implicit close is okay, DiskObjectStore actually # reads data into a var, closes, and returns the var Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Log, then raise the IOError exception that occur in DiskObjectStore.update_from_file() as per discussion 08/05/2013-08/12/2013.
by commits-noreply＠bitbucket.org 29 Aug '13

29 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/444c5b5b451b/ Changeset: 444c5b5b451b User: dan Date: 2013-08-29 17:52:41 Summary: Log, then raise the IOError exception that occur in DiskObjectStore.update_from_file() as per discussion 08/05/2013-08/12/2013. Affected #: 1 file diff -r 533fb8fcc330c52646529659a246e1c50dc18e6a -r 444c5b5b451b50eacba3ba1d08d83e16c1027fa5 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -344,6 +344,7 @@ except IOError, ex: log.critical('Error copying %s to %s: %s' % (file_name, self._get_filename(obj, **kwargs), ex)) + raise ex def get_object_url(self, obj, **kwargs): return None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits August 2013