comparison BSseeker2/bs_utils/utils.py @ 1:8b26adf64adc draft default tip

V2.0.5

0:e6df770c0e58

def show_version() :
    print ""
    print "     BS-Seeker2 v2.0.3 - May 19, 2013     "
    print ""



"""

aligner_options_prefixes = { BOWTIE  : '--bt-',
                             BOWTIE2 : '--bt2-',
                             SOAP    : '--soap-',
                             RMAP    : '--rmap-' }

aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or default_path))
                    for aligner, default_path in
                           [(BOWTIE,'~/bowtie-0.12.7/'),
                            (BOWTIE2, '~/bowtie-0.12.7/'),
                            (SOAP, '~/soap2.21release/'),
                            (RMAP, '~/rmap_v2.05/bin')
                            ])


reference_genome_path = os.path.join(os.path.split(globals()['__file__'])[0],'reference_genomes')

def split_file(filename, output_prefix, nlines):
    """ Splits a file (equivalend to UNIX split -l ) """
    fno = 0
    lno = 0
    INPUT = open(filename, 'r')
    output = None
    for l in INPUT:
        if lno == 0:
            fno += 1
            if output is not None: output.close()

def run_in_parallel(commands):

    commands = [(cmd[0], open(cmd[1], 'w')) if type(cmd) is tuple else (cmd, None) for cmd in commands]

    logm('Starting commands:\n' + '\n'.join([cmd for cmd, stdout in commands]))
    for i, proc in enumerate([subprocess.Popen(args = shlex.split(cmd), stdout = stdout) for cmd, stdout in commands]):
        return_code = proc.wait()
        logm('Finished: ' + commands[i][0])
        if return_code != 0:
            error('%s \nexit with an error code: %d. Please, check the log files.' % (commands[i], return_code))

1:8b26adf64adc

def show_version() :
    print ""
    print "     BS-Seeker2 v2.0.5 - Nov 5, 2013     "
    print ""



"""

aligner_options_prefixes = { BOWTIE  : '--bt-',
                             BOWTIE2 : '--bt2-',
                             SOAP    : '--soap-',
                             RMAP    : '--rmap-' }

#aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or default_path))
#                    for aligner, default_path in
#                           [(BOWTIE,'~/bowtie/'),
#                            (BOWTIE2, '~/bowtie2/'),
#                            (SOAP, '~/soap/'),
#                            (RMAP, '~/rmap/bin')
#                            ])
aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or "None"))
                    for aligner in [(BOWTIE), (BOWTIE2), (SOAP), (RMAP)])

reference_genome_path = os.path.join(os.path.split(globals()['__file__'])[0],'reference_genomes')

def split_file(filename, output_prefix, nlines):
    """ Splits a file (equivalend to UNIX split -l ) """
    fno = 0
    lno = 0
    if filename.endswith(".gz") :
        INPUT = gzip.open(filename, 'rb')
    else :
        INPUT = open(filename, 'r')
    output = None
    for l in INPUT:
        if lno == 0:
            fno += 1
            if output is not None: output.close()

def run_in_parallel(commands):

    commands = [(cmd[0], open(cmd[1], 'w')) if type(cmd) is tuple else (cmd, None) for cmd in commands]

    #logm('Starting commands:\n' + '\n'.join([cmd for cmd, stdout in commands]))
    logm('Starting commands:')
    for cmd, stdout in commands :
        logm("Launched: "+cmd)
    for i, proc in enumerate([subprocess.Popen(args = shlex.split(cmd), stdout = stdout) for cmd, stdout in commands]):
        return_code = proc.wait()
        logm('Finished: ' + commands[i][0])
        if return_code != 0:
            error('%s \nexit with an error code: %d. Please, check the log files.' % (commands[i], return_code))