details: http://www.bx.psu.edu/hg/galaxy/rev/b7a3a82b71ce changeset: 2636:b7a3a82b71ce user: James Taylor <james@jamestaylor.org> date: Fri Aug 28 15:07:48 2009 -0400 description: Merge 0 file(s) affected in this change: diffs (44 lines): diff -r 3df00582ca44 -r b7a3a82b71ce lib/galaxy/datatypes/images.py --- a/lib/galaxy/datatypes/images.py Fri Aug 28 15:06:41 2009 -0400 +++ b/lib/galaxy/datatypes/images.py Fri Aug 28 15:07:48 2009 -0400 @@ -9,6 +9,7 @@ from galaxy.datatypes.sniff import * from urllib import urlencode, quote_plus import zipfile +import os, subprocess, tempfile log = logging.getLogger(__name__) @@ -240,6 +241,26 @@ """Class describing a BAM binary file""" file_ext = "bam" MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True ) + def init_meta( self, dataset, copy_from=None ): + data.Binary.init_meta( self, dataset, copy_from=copy_from ) + def set_meta( self, dataset, overwrite = True, **kwd ): + """ + Sets index for BAM file. + """ + index_file = dataset.metadata.bam_index + if not index_file: + index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset ) + tmp_dir = tempfile.gettempdir() + tmpf1 = tempfile.NamedTemporaryFile(dir=tmp_dir) + try: + subprocess.check_call(['cd', tmp_dir], shell=True) + subprocess.check_call('cp %s %s' % (dataset.file_name, tmpf1.name), shell=True) + subprocess.check_call('samtools index %s' % tmpf1.name, shell=True) + subprocess.check_call('cp %s.bai %s' % (tmpf1.name, index_file.file_name), shell=True) + except subprocess.CalledProcessError: + sys.stderr.write('There was a problem creating the index for the BAM file\n') + tmpf1.close() + dataset.metadata.bam_index = index_file def set_peek( self, dataset ): if not dataset.dataset.purged: export_url = "/history_add_to?" + urlencode({'history_id':dataset.history_id,'ext':'bam','name':'bam alignments','info':'Alignments file','dbkey':dataset.dbkey}) @@ -256,4 +277,3 @@ def get_mime(self): """Returns the mime type of the datatype""" return 'application/octet-stream' - \ No newline at end of file