/tools/samtools/sam_to_bam.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 197 lines · 150 code · 7 blank · 40 comment · 49 complexity · 6b8395f02f8d20ed800e18b6c452dbb2 MD5 · raw file
- #!/usr/bin/env python
- """
- Converts SAM data to sorted BAM data.
- usage: sam_to_bam.py [options]
- --input1: SAM file to be converted
- --dbkey: dbkey value
- --ref_file: Reference file if choosing from history
- --output1: output dataset in bam format
- --index_dir: GALAXY_DATA_INDEX_DIR
- """
- import optparse, os, sys, subprocess, tempfile, shutil, gzip
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "bx-python" )
- from bx.cookbook import doc_optparse
- from galaxy import util
- def stop_err( msg ):
- sys.stderr.write( '%s\n' % msg )
- sys.exit()
- def check_seq_file( dbkey, cached_seqs_pointer_file ):
- seq_path = ''
- for line in open( cached_seqs_pointer_file ):
- line = line.rstrip( '\r\n' )
- if line and not line.startswith( '#' ) and line.startswith( 'index' ):
- fields = line.split( '\t' )
- if len( fields ) < 3:
- continue
- if fields[1] == dbkey:
- seq_path = fields[2].strip()
- break
- return seq_path
- def __main__():
- #Parse Command Line
- parser = optparse.OptionParser()
- parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
- parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' )
- parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
- parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
- parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
- ( options, args ) = parser.parse_args()
- # output version # of tool
- try:
- tmp = tempfile.NamedTemporaryFile().name
- tmp_stdout = open( tmp, 'wb' )
- proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
- tmp_stdout.close()
- returncode = proc.wait()
- stdout = None
- for line in open( tmp_stdout.name, 'rb' ):
- if line.lower().find( 'version' ) >= 0:
- stdout = line.strip()
- break
- if stdout:
- sys.stdout.write( 'Samtools %s\n' % stdout )
- else:
- raise Exception
- except:
- sys.stdout.write( 'Could not determine Samtools version\n' )
- cached_seqs_pointer_file = '%s/sam_fa_indices.loc' % options.index_dir
- if not os.path.exists( cached_seqs_pointer_file ):
- stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file )
- # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa,
- # and the equCab2.fa file will contain fasta sequences.
- seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file )
- tmp_dir = tempfile.mkdtemp()
- if not options.ref_file or options.ref_file == 'None':
- # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
- # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in
- # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai
- fai_index_file_base = seq_path
- fai_index_file_path = '%s.fai' % seq_path
- if not os.path.exists( fai_index_file_path ):
- #clean up temp files
- if os.path.exists( tmp_dir ):
- shutil.rmtree( tmp_dir )
- stop_err( 'No sequences are available for build (%s), request them by reporting this error.' % options.dbkey )
- else:
- try:
- # Create indexes for history reference ( e.g., ~/database/files/000/dataset_1.dat ) using samtools faidx, which will:
- # - index reference sequence in the FASTA format or extract subsequence from indexed reference sequence
- # - if no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk
- # - if regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format
- # - the input file can be compressed in the RAZF format.
- # IMPORTANT NOTE: a real weakness here is that we are creating indexes for the history dataset
- # every time we run this tool. It would be nice if we could somehow keep track of user's specific
- # index files so they could be re-used.
- fai_index_file_base = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
- # At this point, fai_index_file_path will look something like /tmp/dataset_13.dat
- os.symlink( options.ref_file, fai_index_file_base )
- fai_index_file_path = '%s.fai' % fai_index_file_base
- command = 'samtools faidx %s' % fai_index_file_base
- tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
- tmp_stderr = open( tmp, 'wb' )
- proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
- returncode = proc.wait()
- tmp_stderr.close()
- # get stderr, allowing for case where it's very large
- tmp_stderr = open( tmp, 'rb' )
- stderr = ''
- buffsize = 1048576
- try:
- while True:
- stderr += tmp_stderr.read( buffsize )
- if not stderr or len( stderr ) % buffsize != 0:
- break
- except OverflowError:
- pass
- tmp_stderr.close()
- if returncode != 0:
- raise Exception, stderr
- if os.path.getsize( fai_index_file_path ) == 0:
- raise Exception, 'Index file empty, there may be an error with your reference file or settings.'
- except Exception, e:
- #clean up temp files
- if os.path.exists( tmp_dir ):
- shutil.rmtree( tmp_dir )
- stop_err( 'Error creating indexes from reference (%s), %s' % ( options.ref_file, str( e ) ) )
- try:
- # Extract all alignments from the input SAM file to BAM format ( since no region is specified, all the alignments will be extracted ).
- tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
- tmp_aligns_file_name = tmp_aligns_file.name
- tmp_aligns_file.close()
- command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 )
- tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
- tmp_stderr = open( tmp, 'wb' )
- proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
- returncode = proc.wait()
- tmp_stderr.close()
- # get stderr, allowing for case where it's very large
- tmp_stderr = open( tmp, 'rb' )
- stderr = ''
- buffsize = 1048576
- try:
- while True:
- stderr += tmp_stderr.read( buffsize )
- if not stderr or len( stderr ) % buffsize != 0:
- break
- except OverflowError:
- pass
- tmp_stderr.close()
- if returncode != 0:
- raise Exception, stderr
- except Exception, e:
- #clean up temp files
- if os.path.exists( tmp_dir ):
- shutil.rmtree( tmp_dir )
- stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) )
- try:
- # 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 ).
- tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
- tmp_sorted_aligns_file_name = tmp_sorted_aligns_file.name
- tmp_sorted_aligns_file.close()
- command = 'samtools sort %s %s' % ( tmp_aligns_file_name, tmp_sorted_aligns_file_name )
- tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
- tmp_stderr = open( tmp, 'wb' )
- proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
- returncode = proc.wait()
- tmp_stderr.close()
- # get stderr, allowing for case where it's very large
- tmp_stderr = open( tmp, 'rb' )
- stderr = ''
- buffsize = 1048576
- try:
- while True:
- stderr += tmp_stderr.read( buffsize )
- if not stderr or len( stderr ) % buffsize != 0:
- break
- except OverflowError:
- pass
- tmp_stderr.close()
- if returncode != 0:
- raise Exception, stderr
- except Exception, e:
- #clean up temp files
- if os.path.exists( tmp_dir ):
- shutil.rmtree( tmp_dir )
- stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) )
- # Move tmp_aligns_file_name to our output dataset location
- sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name
- shutil.move( sorted_bam_file, options.output1 )
- #clean up temp files
- if os.path.exists( tmp_dir ):
- shutil.rmtree( tmp_dir )
- # check that there are results in the output file
- if os.path.getsize( options.output1 ) > 0:
- sys.stdout.write( 'SAM file converted to BAM' )
- else:
- stop_err( 'Error creating sorted version of BAM file.' )
- if __name__=="__main__": __main__()