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src/b/i/biopython-HEAD/Bio/motifs/applications/_xxmotif.py   biopython(Download)
 
import os
from Bio.Application import AbstractCommandline, _Option, _Switch, _Argument
 
 
        self.parameters = \
          [
          _Argument(["outdir", "OUTDIR"],
                   "output directory for all results",
                   filename = True,
                   is_required = True,
                   # XXmotif currently does not accept spaces in the outdir name
                   checker_function = lambda x: " " not in x),
          _Argument(["seqfile", "SEQFILE"],

src/b/i/biopython-1.63/Bio/motifs/applications/_xxmotif.py   biopython(Download)
 
import os
from Bio.Application import AbstractCommandline, _Option, _Switch, _Argument
 
 
        self.parameters = \
          [
          _Argument(["outdir", "OUTDIR"],
                   "output directory for all results",
                   filename = True,
                   is_required = True,
                   # XXmotif currently does not accept spaces in the outdir name
                   checker_function = lambda x: " " not in x),
          _Argument(["seqfile", "SEQFILE"],

src/w/l/wLib-1.1.0/external/Motif/Applications/_XXmotif.py   wLib(Download)
 
import os
from Bio.Application import AbstractCommandline, _Option, _Switch, _Argument
 
 
        self.parameters = \
          [
          _Argument(["outdir", "OUTDIR"],
                   "output directory for all results",
                   filename = True,
                   is_required = True,
                   # XXmotif currently does not accept spaces in the outdir name
                   checker_function = lambda x: " " not in x),
          _Argument(["seqfile", "SEQFILE"],

src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_samtools.py   biopython(Download)
from __future__ import print_function
__docformat__ = "epytext en"
from Bio.Application import _Option, _Argument, _Switch
from Bio.Application import AbstractCommandline, _ArgumentList
from Bio.Application import _StaticArgument
            _Switch(["-1", "fast_bam"],
                    "Use zlib compression level 1 to compress the output"),
            _Argument(["input", "input_file"],
                      "Input File Name", filename=True, is_required=True),
            _Argument(["region"], "Region", is_required=False),
    def __init__(self, cmd="samtools", **kwargs):
        self.program_name = cmd
        self.parameters = [
            _StaticArgument("reheader"),
            _Argument(["input_header", "header_sam", "sam_file"],
                      "Sam file with header",
                      filename=True, is_required=True),
            _Argument(["input_bam", "input_file", "bam_file"],

src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_bwa.py   biopython(Download)
__docformat__ = "epytext en"
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
from Bio.Application import _StaticArgument
 
                            "Prefix of the output database [same as db filename]",
                            equate=False, is_required=False),
                    _Argument(["infile"], "Input file name", filename=True, is_required=True),
                    _Switch(["-c", "c"],
                            "Build color-space index. The input fasta should be in nucleotide space.")
                [
                    _StaticArgument("aln"),
                    _Argument(["reference"], "Reference file name",
                              filename=True, is_required=True),
                    _Argument(["read_file"], "Read file name",
                [
                    _StaticArgument("samse"),
                    _Argument(["reference"], "Reference file name", filename=True, is_required=True),
                    _Argument(["sai_file"], "Sai file name", filename=True, is_required=True),
                    _Argument(["read_file"], "Read  file name", filename=True, is_required=True),

src/b/i/biopython-1.63/Bio/Sequencing/Applications/_bwa.py   biopython(Download)
__docformat__ = "epytext en"
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
from Bio.Application import _StaticArgument
 
                            "Prefix of the output database [same as db filename]",
                            equate=False, is_required=False),
                    _Argument(["infile"], "Input file name", filename=True, is_required=True),
                    _Switch(["-c", "c"],
                            "Build color-space index. The input fasta should be in nucleotide space.")
                [
                    _StaticArgument("aln"),
                    _Argument(["reference"], "Reference file name",
                              filename=True, is_required=True),
                    _Argument(["read_file"], "Read file name",
                [
                    _StaticArgument("samse"),
                    _Argument(["reference"], "Reference file name", filename=True, is_required=True),
                    _Argument(["sai_file"], "Sai file name", filename=True, is_required=True),
                    _Argument(["read_file"], "Read  file name", filename=True, is_required=True),

src/b/i/biopython-HEAD/Bio/Align/Applications/_Dialign.py   biopython(Download)
__docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
 
 
                    "'exclude fragments' - list of fragments can be "
                    "specified that are NOT considered for pairwise alignment"),
            _Argument(["input"],
                      "Input file name. Must be FASTA format",
                      filename=True,

src/b/i/biopython-1.63/Bio/Align/Applications/_Dialign.py   biopython(Download)
__docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
 
 
                    "'exclude fragments' - list of fragments can be "
                    "specified that are NOT considered for pairwise alignment"),
            _Argument(["input"],
                      "Input file name. Must be FASTA format",
                      filename=True,

src/b/i/biopython-HEAD/Bio/Phylo/Applications/_Fasttree.py   biopython(Download)
__docformat__ = "restructuredtext en"
 
from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline
 
 
                equate=False,
                ),
             _Argument(['input'],
                """Enter <input file>
 

src/b/i/biopython-HEAD/Bio/Align/Applications/_Probcons.py   biopython(Download)
__docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline
 
 
                    "order (default: off)"),
            #Input file name
            _Argument(["input"],
                      "Input file name. Must be multiple FASTA alignment "+
                      "(MFA) format",

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