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Update BAM set_meta() and groom_dataset_content

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This commit is contained in:
Daniel Blankenberg
2009-12-09 15:44:10 -05:00
parent 4071d88e5c
commit c141dbd7ba
1 changed files with 42 additions and 43 deletions
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lib/galaxy/datatypes/binary.py
+42 -43
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@@ -58,26 +58,32 @@ class Bam( Binary ):
on an output dataset after the content is initially generated.
"""
# Use samtools to sort the Bam file
tmp_dir = tempfile.gettempdir()
# Create a symlink from the temporary directory to the dataset file so that samtools can mess with it.
tmp_dataset_file_name = os.path.join( tmp_dir, os.path.basename( file_name ) )
# Here tmp_dataset_file_name looks something like /tmp/dataset_XX.dat
os.symlink( file_name, tmp_dataset_file_name )
# Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created.
# TODO: This command may also create temporary files <out.prefix>.%d.bam when the
# whole alignment cannot be fitted into memory ( controlled by option -m ). We're
# not handling this case here.
tmp_sorted_dataset_file = tempfile.NamedTemporaryFile( prefix=tmp_dataset_file_name )
tmp_sorted_dataset_file_name = tmp_sorted_dataset_file.name
tmp_sorted_dataset_file.close()
command = "samtools sort %s %s 2>/dev/null" % ( tmp_dataset_file_name, tmp_sorted_dataset_file_name )
proc = subprocess.Popen( args=command, shell=True )
##$ samtools sort
##Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>
## Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created.
## This command may also create temporary files <out.prefix>.%d.bam when the
## whole alignment cannot be fitted into memory ( controlled by option -m ).
#do this in a unique temp directory, because of possible <out.prefix>.%d.bam temp files
tmp_dir = tempfile.mkdtemp()
tmp_sorted_dataset_file_name_prefix = os.path.join( tmp_dir, 'sorted' )
stderr_name = tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "bam_sort_stderr" ).name
samtools_created_sorted_file_name = "%s.bam" % tmp_sorted_dataset_file_name_prefix #samtools accepts a prefix, not a filename, it always adds .bam to the prefix
command = "samtools sort %s %s" % ( file_name, tmp_sorted_dataset_file_name_prefix )
proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
proc.wait()
tmp_sorted_bam_file_name = '%s.bam' % tmp_sorted_dataset_file_name
# Move tmp_sorted_bam_file_name to our output dataset location
shutil.move( tmp_sorted_bam_file_name, file_name )
# Remove all remaining temporary files
os.unlink( tmp_dataset_file_name )
#Did sort succeed?
stderr = open( stderr_name ).read().strip()
if stderr:
raise Exception, "Error Grooming BAM file contents: %s" % stderr
# Move samtools_created_sorted_file_name to our output dataset location
shutil.move( samtools_created_sorted_file_name, file_name )
# Remove temp file and empty temporary directory
os.unlink( stderr_name )
os.rmdir( tmp_dir )
def init_meta( self, dataset, copy_from=None ):
Binary.init_meta( self, dataset, copy_from=copy_from )
def set_meta( self, dataset, overwrite = True, **kwd ):
@@ -86,30 +92,23 @@ class Bam( Binary ):
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()
# Create a symlink from the temporary directory to the dataset file so that samtools can mess with it.
tmp_dataset_file_name = os.path.join( tmp_dir, os.path.basename( dataset.file_name ) )
# Here tmp_dataset_file_name looks something like /tmp/dataset_XX.dat
os.symlink( dataset.file_name, tmp_dataset_file_name )
errors = False
try:
# Create the Bam index
command = 'samtools index %s' % tmp_dataset_file_name
proc = subprocess.Popen( args=command, shell=True )
proc.wait()
except Exception, e:
errors = True
err_msg = 'Error creating index for BAM file (%s)' % str( tmp_dataset_file_name )
log.exception( err_msg )
sys.stderr.write( err_msg + str( e ) )
if not errors:
# Move the temporary index file ~/tmp/dataset_XX.dat.bai to our metadata file
# storage location ~/database/files/_metadata_files/dataset_XX.dat
shutil.move( '%s.bai' % ( tmp_dataset_file_name ), index_file.file_name )
# Remove all remaining temporary files
os.unlink( tmp_dataset_file_name )
# Set the metadata
dataset.metadata.bam_index = index_file
# Create the Bam index
##$ samtools index
##Usage: samtools index <in.bam> [<out.index>]
stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
command = 'samtools index %s %s' % ( dataset.file_name, index_file.file_name )
proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
#Did index succeed?
stderr = open( stderr_name ).read().strip()
if stderr:
raise Exception, "Error Setting BAM Metadata: %s" % stderr
dataset.metadata.bam_index = index_file
# Remove temp file
os.unlink( stderr_name )
def sniff( self, filename ):
# BAM is compressed in the BGZF format, and must not be uncompressed in Galaxy.
# The first 4 bytes of any bam file is 'BAM\1', and the file is binary.