1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/bbda064ee4b6/ changeset: bbda064ee4b6 user: jgoecks date: 2011-12-06 15:34:19 summary: Add automatic conversions for SAM to BAM and SAM to summary tree. Enable SAM datasets to be visualized in Trackster. affected #: 8 files

diff -r c28e9ef4036aca6a897db2aa93517577b0afddda -r bbda064ee4b6ffff2d867a389b81d884c772aa12 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -139,7 +139,10 @@ <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/><datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/><datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/> - <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/> + <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"> + <converter file="sam_to_bam.xml" target_datatype="bam"/> + <converter file="sam_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + </datatype><datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/><datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>

diff -r c28e9ef4036aca6a897db2aa93517577b0afddda -r bbda064ee4b6ffff2d867a389b81d884c772aa12 lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py +++ /dev/null @@ -1,34 +0,0 @@ -#!/usr/bin/env python - -from __future__ import division - -import sys, os -sys.stderr = open(os.devnull, 'w') # suppress stderr as cython produces warning on some systems: - # csamtools.so:6: RuntimeWarning: __builtin__.file size changed - -from galaxy import eggs -import pkg_resources - -if sys.version_info[:2] == (2, 4): - pkg_resources.require( "ctypes" ) -pkg_resources.require( "pysam" ) - -from pysam import csamtools -from galaxy.visualization.tracks.summary import * - -def main(): - - input_fname = sys.argv[1] - index_fname = sys.argv[2] - out_fname = sys.argv[3] - - bamfile = csamtools.Samfile( filename=input_fname, mode='rb', index_filename=index_fname ) - - st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) - for read in bamfile.fetch(): - st.insert_range(bamfile.getrname(read.rname), read.pos, read.pos + read.rlen) - - st.write(out_fname) - -if __name__ == "__main__": - main()

diff -r c28e9ef4036aca6a897db2aa93517577b0afddda -r bbda064ee4b6ffff2d867a389b81d884c772aa12 lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml +++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml @@ -1,6 +1,6 @@ <tool id="CONVERTER_bam_to_summary_tree_0" name="Convert BAM to Summary Tree" version="1.0.0" hidden="true"><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> - <command interpreter="python">bam_to_summary_tree_converter.py $input1 $bai $output1</command> + <command interpreter="python">sam_or_bam_to_summary_tree_converter.py --bam $input1 $bai $output1</command><inputs><page><param format="bam" name="input1" type="data" label="Choose BAM file"/>

diff -r c28e9ef4036aca6a897db2aa93517577b0afddda -r bbda064ee4b6ffff2d867a389b81d884c772aa12 lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py --- /dev/null +++ b/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python + +from __future__ import division + +import sys, os, optparse +sys.stderr = open(os.devnull, 'w') # suppress stderr as cython produces warning on some systems: + # csamtools.so:6: RuntimeWarning: __builtin__.file size changed + +from galaxy import eggs +import pkg_resources + +if sys.version_info[:2] == (2, 4): + pkg_resources.require( "ctypes" ) +pkg_resources.require( "pysam" ) + +from pysam import csamtools +from galaxy.visualization.tracks.summary import * + +def main(): + parser = optparse.OptionParser() + parser.add_option( '-S', '--sam', action="store_true", dest="is_sam" ) + parser.add_option( '-B', '--bam', action="store_true", dest="is_bam" ) + options, args = parser.parse_args() + + if options.is_bam: + input_fname = args[0] + index_fname = args[1] + out_fname = args[2] + samfile = csamtools.Samfile( filename=input_fname, mode='rb', index_filename=index_fname ) + elif options.is_sam: + input_fname = args[0] + out_fname = args[1] + samfile = csamtools.Samfile( filename=input_fname, mode='r' ) + + st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) + for read in samfile.fetch(): + st.insert_range( samfile.getrname( read.rname ), read.pos, read.pos + read.rlen ) + + st.write(out_fname) + +if __name__ == "__main__": + main()

diff -r c28e9ef4036aca6a897db2aa93517577b0afddda -r bbda064ee4b6ffff2d867a389b81d884c772aa12 lib/galaxy/datatypes/converters/sam_to_bam.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/sam_to_bam.xml @@ -0,0 +1,17 @@ +<tool id="CONVERTER_sam_to_bam" name="Convert SAM to BAM" version="1.0.0"> + <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> + <!-- Used on the metadata edit page. --> + <!-- FIXME: conversion will only work if headers for reference sequences are in input file. + To fix this: (a) merge sam_to_bam tool in tools with this conversion (like fasta_to_len + conversion); and (b) define a datatype-specific way to set converter parameters. + --> + <command>samtools view -bS $input1 > $output 2> /dev/null </command> + <inputs> + <param name="input1" type="data" format="sam" label="SAM file"/> + </inputs> + <outputs> + <data name="output" format="bam"/> + </outputs> + <help> + </help> +</tool>

diff -r c28e9ef4036aca6a897db2aa93517577b0afddda -r bbda064ee4b6ffff2d867a389b81d884c772aa12 lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml @@ -0,0 +1,14 @@ +<tool id="CONVERTER_sam_to_summary_tree_0" name="Convert SAM to Summary Tree" version="1.0.0" hidden="true"> +<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> + <command interpreter="python">sam_or_bam_to_summary_tree_converter.py --sam $input1 $output1</command> + <inputs> + <page> + <param format="sam" name="input1" type="data" label="Choose sam file"/> + </page> + </inputs> + <outputs> + <data format="summary_tree" name="output1"/> + </outputs> + <help> + </help> +</tool>

diff -r c28e9ef4036aca6a897db2aa93517577b0afddda -r bbda064ee4b6ffff2d867a389b81d884c772aa12 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -368,7 +368,10 @@ if result != 0: raise Exception('Result %s from %s' % (result, cmd)) merge = staticmethod(merge) - + + def get_track_type( self ): + return "ReadTrack", {"data": "bam", "index": "summary_tree"} + class Pileup( Tabular ): """Tab delimited data in pileup (6- or 10-column) format""" file_ext = "pileup"

diff -r c28e9ef4036aca6a897db2aa93517577b0afddda -r bbda064ee4b6ffff2d867a389b81d884c772aa12 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -725,6 +725,18 @@ max_low, max_high = get_bounds( results, 1, 2 )

return { 'data': results, 'message': message, 'max_low': max_low, 'max_high': max_high } + +class SamDataProvider( BamDataProvider ): + + def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ): + """ Create SamDataProvider. """ + + # HACK: to use BamDataProvider, original dataset must be BAM and + # converted dataset must be BAI. Use BAI from BAM metadata. + if converted_dataset: + self.converted_dataset = converted_dataset.metadata.bam_index + self.original_dataset = converted_dataset + self.dependencies = dependencies

class BBIDataProvider( TracksDataProvider ): """ @@ -957,6 +969,7 @@ "tabix": { Vcf: VcfTabixDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider }, "interval_index": IntervalIndexDataProvider, "bai": BamDataProvider, + "bam": SamDataProvider, "summary_tree": SummaryTreeDataProvider, "bigwig": BigWigDataProvider, "bigbed": BigBedDataProvider

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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