Python Bunch.output方法代码示例

# 需要导入模块: from galaxy.util.bunch import Bunch [as 别名]
# 或者: from galaxy.util.bunch.Bunch import output [as 别名]
def __main__():
    #Parse Command Line
    parser = optparse.OptionParser()
    parser.add_option( '', '--threads', dest='threads', help='The number of threads to use' )
    parser.add_option( '', '--ref_name', dest='ref_name', help='The reference name to change all output matches to' )
    parser.add_option( '', '--ref_source', dest='ref_source', help='Whether the reference is self, cached or from the history' )
    parser.add_option( '', '--ref_sequences', dest='ref_sequences', help='Number of sequences in the reference dataset' )
    parser.add_option( '', '--mirror', dest='mirror', help='Do or do not report mirror image of all gap-free alignments' )
    parser.add_option( '', '--source_select', dest='source_select', help='Whether to used pre-set or cached reference file' )
    parser.add_option( '', '--input1', dest='input1', help='The name of the reference file if using history or reference base name if using cached' )
    parser.add_option( '', '--input2', dest='input2', help='The reads file to align' )
    parser.add_option( '', '--strand', dest='strand', help='Which strand of the read to search, if specifying all parameters' )
    parser.add_option( '', '--match_reward', dest='match_reward', help='Score values for a match (reward)' )
    parser.add_option( '', '--match_penalty', dest='match_penalty', help='Score values for a mismatch (penalty), same as reward when not specified (but reward is)' )
    parser.add_option( '', '--gapped', dest='gapped', help='Perform gapped extension of HSPs (or seeds if gapped-free extension is not performed) after first reducing them to anchor points' )
    parser.add_option( '', '--gap_open', dest='gap_open', help='Score penalties for opening a gap' )
    parser.add_option( '', '--gap_extend', dest='gap_extend', help='Score penalties for extending a gap' )
    parser.add_option( '', '--ambiguous', dest='ambiguous', help='Treat as ambiguous nucleotides' )
    parser.add_option( '', '--step', dest='step', help='Offset between the starting positions of successive target words considered for potential seeds' )
    parser.add_option( '', '--masking', dest='masking', help='Dynamically mask the target sequence by excluding any positions that appear in too many alignments from further consideration for seeds' )
    parser.add_option( '', '--seed', dest='seed', help='Offset between the starting positions of successive target words considered for potential seeds' )
    parser.add_option( '', '--match_length', dest='match_length', help='Seeds require bp word of this length with matches in all positions' )
    parser.add_option( '', '--transition', dest='transition', help='Transition settings, affects the number of allowed transition substitutions in each seed' )
    parser.add_option( '', '--xdrop', dest='xdrop', help='Find HSPs using the xdrop extension method with the given termination threshold instead of using the exact match method' )
    parser.add_option( '', '--hspthresh', dest='hspthresh', help='Score threshold for the x-drop extension method' )
    parser.add_option( '', '--entropy', dest='entropy', help='Whether to adjust for entropy when qualifying HSPs in the x-drop extension method' )
    parser.add_option( '', '--chain', dest='chain', help='Perform chaining of HSPs with no penalties' )
    parser.add_option( '', '--ydrop', dest='ydrop', help='Set the threshold for terminating gapped extension' )
    parser.add_option( '', '--ytrim', dest='ytrim', help='Trim back to peak score if y-drop extension encounters end of sequence' )
    parser.add_option( '', '--gappedthresh', dest='gappedthresh', help='Threshold for gapped extension.  Alignments scoring lower are discarded.' )
    parser.add_option( '', '--filter', dest='filter', help='Filter alignments.' )
    parser.add_option( '', '--identity_min', dest='identity_min', help='Minimum for filtering alignments by their percent identity.' )
    parser.add_option( '', '--identity_max', dest='identity_max', help='Maximum for filtering alignments by their percent identity.' )
    parser.add_option( '', '--coverage_min', dest='coverage_min', help='Minimum for filtering alignments by how much of the input sequence they cover.' )
    parser.add_option( '', '--coverage_max', dest='coverage_max', help='Maximum for filtering alignments by how much of the input sequence they cover.' )
    parser.add_option( '', '--nmatch_min', dest='nmatch_min', help='Minimum for filtering alignments by how many bases they match.' )
    parser.add_option( '', '--nmismatch_max', dest='nmismatch_max', help='Maximum for filtering alignments by the number of mismatches.' )
    parser.add_option( '', '--trivial', dest='trivial', help='Do or do not output a trivial self-alignment block if the target and query sequences are identical.' )
    parser.add_option( '', '--inner', dest='inner', help='Perform additional alignment between the gapped alignment blocks using (presumably) more sensitive alignment parameters.' )
    parser.add_option( '', '--shortcuts_for_yasra', dest='shortcuts_for_yasra', help='Shortcut options to support the Yasra mapping assembler' )
    parser.add_option( '', '--out_format', dest='format', help='The format of the output file (sam, diffs, or tabular (general))' )
    parser.add_option( '', '--output', dest='output', help='The output file' )
    parser.add_option( '', '--lastzSeqsFileDir', dest='lastzSeqsFileDir', help='Directory of local lastz_seqs.loc file' )
    ( options, args ) = parser.parse_args()
    # Output version # of tool
    try:
        tmp = tempfile.NamedTemporaryFile().name
        tmp_stdout = open( tmp, 'wb' )
        proc = subprocess.Popen( args='lastz -v', 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( '%s\n' % stdout )
        else:
            raise Exception
    except:
        sys.stdout.write( 'Could not determine Lastz version\n' )

    if options.ref_name:
        ref_name = '[nickname=%s]' % options.ref_name
    else:
        ref_name = ''
    set_options = ''
    # Commonly-used preset options
    if options.source_select == 'pre_set':
        # Handle ref_source
        if options.ref_source == 'self':
            # --mirror is available only if ref_source selection is --self
            if options.mirror == 'yes':
                set_options += '--nomirror '
    else:
        # Full set of user-specified options
        # Handle ref_source
        if options.ref_source == 'self':
            # --mirror is available only if ref_source selection is --self
            if options.mirror == 'yes':
                set_options += '--nomirror '
        else:
            # Using --self automatically enables this option
            if options.trivial == 'no':
                set_options += '--notrivial '
        # Handle --match
        if options.match_reward not in [ "", "0" ]:
            if options.match_penalty in [ "", "0" ]:
                match_penalty = options.match_reward
            else:
                match_penalty = options.match_penalty
            set_options += '--match=%s,%s ' % ( options.match_reward, match_penalty )
        # Handle --gapped
        if options.gapped == 'yes':
            set_options += '--gapped '
            if options.gap_open not in [ "" ]:
                if options.gap_extend in [ "" ]:
                    set_options += '--gap=%s ' % options.gap_open
                else:
#.........这里部分代码省略.........

# 需要导入模块: from galaxy.util.bunch import Bunch [as 别名]
# 或者: from galaxy.util.bunch.Bunch import output [as 别名]
def __main__():
    #Parse Command Line
    parser = optparse.OptionParser()
    parser.add_option( '', '--ref_name', dest='ref_name', help='The reference name to change all output matches to' )
    parser.add_option( '', '--ref_source', dest='ref_source', help='Whether the reference is cached or from the history' )
    parser.add_option( '', '--ref_sequences', dest='ref_sequences', help='Number of sequences in the reference dataset' )
    parser.add_option( '', '--source_select', dest='source_select', help='Whether to used pre-set or cached reference file' )
    parser.add_option( '', '--input1', dest='input1', help='The name of the reference file if using history or reference base name if using cached' )
    parser.add_option( '', '--input2', dest='input2', help='The reads file to align' )
    parser.add_option( '', '--pre_set_options', dest='pre_set_options', help='Which of the pre set options to use, if using pre-sets' )
    parser.add_option( '', '--strand', dest='strand', help='Which strand of the read to search, if specifying all parameters' )
    parser.add_option( '', '--seed', dest='seed', help='Seeding settings, if specifying all parameters' )
    parser.add_option( '', '--transition', dest='transition', help='Number of transitions to allow in each seed hit, if specifying all parameters' )
    parser.add_option( '', '--gfextend', dest='gfextend', help='Whether to perform gap-free extension of seed hits to HSPs (high scoring segment pairs), if specifying all parameters' )
    parser.add_option( '', '--chain', dest='chain', help='Whether to perform chaining of HSPs, if specifying all parameters' )
    parser.add_option( '', '--O', dest='O', help='Gap opening penalty, if specifying all parameters' )
    parser.add_option( '', '--E', dest='E', help='Gap extension penalty, if specifying all parameters' )
    parser.add_option( '', '--X', dest='X', help='X-drop threshold, if specifying all parameters' )
    parser.add_option( '', '--Y', dest='Y', help='Y-drop threshold, if specifying all parameters' )
    parser.add_option( '', '--K', dest='K', help='Threshold for HSPs, if specifying all parameters' )
    parser.add_option( '', '--L', dest='L', help='Threshold for gapped alignments, if specifying all parameters' )
    parser.add_option( '', '--entropy', dest='entropy', help='Whether to involve entropy when filtering HSPs, if specifying all parameters' )
    parser.add_option( '', '--identity_min', dest='identity_min', help="Minimum identity (don't report matches under this identity)" )
    parser.add_option( '', '--identity_max', dest='identity_max', help="Maximum identity (don't report matches above this identity)" )
    parser.add_option( '', '--coverage', dest='coverage', help="The minimum coverage value (don't report matches covering less than this)" )
    parser.add_option( '', '--unmask', dest='unmask', help='Whether to convert lowercase bases to uppercase' )
    parser.add_option( '', '--out_format', dest='format', help='The format of the output file (sam, diffs, or tabular (general))' )
    parser.add_option( '', '--output', dest='output', help='The output file' )
    parser.add_option( '', '--lastzSeqsFileDir', dest='lastzSeqsFileDir', help='Directory of local lastz_seqs.loc file' )
    ( options, args ) = parser.parse_args()

    # output version # of tool
    try:
        tmp = tempfile.NamedTemporaryFile().name
        tmp_stdout = open( tmp, 'wb' )
        proc = subprocess.Popen( args='lastz -v', 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( '%s\n' % stdout )
        else:
            raise Exception
    except:
        sys.stdout.write( 'Could not determine Lastz version\n' )

    if options.unmask == 'yes':
        unmask = '[unmask]'
    else:
        unmask = ''
    if options.ref_name:
        ref_name = '[nickname=%s]' % options.ref_name
    else:
        ref_name = ''
    # Prepare for commonly-used preset options
    if options.source_select == 'pre_set':
        set_options = '--%s' % options.pre_set_options
    # Prepare for user-specified options
    else:
        set_options = '--%s --%s --gapped --strand=%s --seed=%s --%s O=%s E=%s X=%s Y=%s K=%s L=%s --%s' % \
                    ( options.gfextend, options.chain, options.strand, options.seed, options.transition,
                      options.O, options.E, options.X, options.Y, options.K, options.L, options.entropy )
    # Specify input2 and add [fullnames] modifier if output format is diffs
    if options.format == 'diffs':
        input2 = '%s[fullnames]' % options.input2
    else:
        input2 = options.input2
    if options.format == 'tabular':
        # Change output format to general if it's tabular and add field names for tabular output
        format = 'general-'
        tabular_fields = ':score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle'
    elif options.format == 'sam':
        # We currently ALWAYS suppress SAM headers.
        format = 'sam-'
        tabular_fields = ''
    else:
        format = options.format
        tabular_fields = ''

    # Set up our queues
    lastz_job_queue = LastzJobQueue( WORKERS, slots=SLOTS )
    combine_data_queue = CombineDataQueue( options.output )

    if options.ref_source == 'history':
        # Reference is a fasta dataset from the history, so split job across
        # the number of sequences in the dataset ( this could be a HUGE number )
        try:
            # Ensure there is at least 1 sequence in the dataset ( this may not be necessary ).
            error_msg = "The reference dataset is missing metadata, click the pencil icon in the history item and 'auto-detect' the metadata attributes."
            ref_sequences = int( options.ref_sequences )
            if ref_sequences < 1:
                stop_queues( lastz_job_queue, combine_data_queue )
                stop_err( error_msg )
        except:
            stop_queues( lastz_job_queue, combine_data_queue )
            stop_err( error_msg )
#.........这里部分代码省略.........