root/galaxy-central/tools/metag_tools/blat_wrapper.py

#!/usr/bin/env python

import os, sys, tempfile

assert sys.version_info[:2] >= (2.4)

def stop_err( msg ):
    sys.stderr.write( "%s\n" % msg )
    sys.exit()
    
def check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ):
    nib_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR
    nib_path = ''
    nibs = {}
    for i, line in enumerate( file( nib_file ) ):
        line = line.rstrip( '\r\n' )
        if line and not line.startswith( "#" ):
            fields = line.split( '\t' )
            if len( fields ) < 3:
                continue
            if fields[0] == 'seq':
                nibs[( fields[1] )] = fields[2]
    if nibs.has_key( dbkey ):
        nib_path = nibs[( dbkey )]
    return nib_path

def check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR ):
    twobit_file = "%s/twobit.loc" % GALAXY_DATA_INDEX_DIR
    twobit_path = ''
    twobits = {}
    for i, line in enumerate( file( twobit_file ) ):
        line = line.rstrip( '\r\n' )
        if line and not line.startswith( "#" ): 
            fields = line.split( '\t' )
            if len( fields ) < 2:
                continue
            twobits[( fields[0] )] = fields[1]
    if twobits.has_key( dbkey ):
        twobit_path = twobits[( dbkey )]
    return twobit_path

def __main__():
    # I/O
    source_format = sys.argv[1]        # 0: dbkey; 1: upload file
    target_file = sys.argv[2]
    query_file = sys.argv[3]
    output_file = sys.argv[4]
    min_iden = sys.argv[5]
    tile_size = sys.argv[6]
    one_off = sys.argv[7]
    
    try:
        float(min_iden)    
    except:
        stop_err('Invalid value for minimal identity.')
    
    try:  
        test = int(tile_size)
        assert test >= 6 and test <= 18
    except:
        stop_err('Invalid value for tile size. DNA word size must be between 6 and 18.')
        
    try:
        test = int(one_off)
        assert test >= 0 and test <= int(tile_size)
    except:
        stop_err('Invalid value for mismatch numbers in the word')
        
    GALAXY_DATA_INDEX_DIR = sys.argv[8]

    all_files = []
    if source_format == '0':
        # check target genome
        dbkey = target_file
        nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR )
        twobit_path = check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR )
        if not os.path.exists( nib_path ) and not os.path.exists( twobit_path ):
            stop_err("No sequences are available for %s, request them by reporting this error." % dbkey)
    
        # check the query file, see whether all of them are legitimate sequence
        if nib_path and os.path.isdir( nib_path ):
            compress_files = os.listdir(nib_path)
            target_path = nib_path
        elif twobit_path:
            compress_files = [twobit_path]
            target_path = ""
        else:
            stop_err("Requested genome build has no available sequence.")
            
        for file in compress_files:
            file = "%s/%s" % ( target_path, file )
            file = os.path.normpath(file)
            all_files.append(file)
    else:
        all_files = [target_file]
        
    for detail_file_path in all_files:
        output_tempfile = tempfile.NamedTemporaryFile().name
        command = "blat %s %s %s -oneOff=%s -tileSize=%s -minIdentity=%s -mask=lower -noHead -out=pslx 2>&1" % ( detail_file_path, query_file, output_tempfile, one_off, tile_size, min_iden )
        os.system( command )
        os.system( 'cat %s >> %s' % ( output_tempfile, output_file ) )
        os.remove( output_tempfile )
        
if __name__ == '__main__': __main__()