--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_to_bam.py	Mon Aug 26 14:22:00 2013 -0400
@@ -0,0 +1,197 @@
+#!/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( dir='.' )
+    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__()