comparison sam_to_bam.py @ 1:93f2e3337a33

Update sam_to_bam to use the fasta_indexes data table.

0:30fdbaccb96b

#!/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

        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

1:93f2e3337a33

#!/usr/bin/env python
"""
Converts SAM data to sorted BAM data.
usage: sam_to_bam.py [options]
   --input1: SAM file to be converted
   --index: path of the indexed reference genome
   --ref_file: Reference file if choosing from history
   --output1: output dataset in bam format
"""

import optparse, os, sys, subprocess, tempfile, shutil

def stop_err( msg ):
    sys.stderr.write( '%s\n' % msg )
    sys.exit()

def __main__():
    #Parse Command Line
    parser = optparse.OptionParser()
    parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
    
    parser.add_option( '', '--index', dest='index', help='The path of the indexed reference genome' )
    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' )
    ( options, args ) = parser.parse_args()

    # output version # of tool
    try:
        tmp = tempfile.NamedTemporaryFile().name

        else:
            raise Exception
    except:
        sys.stdout.write( 'Could not determine Samtools version\n' )

    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' % options.index
        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( 'Indexed genome %s not present, request it by reporting this error.' % options.index )
    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