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src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_samtools.py   biopython(Download)
__docformat__ = "epytext en"
from Bio.Application import _Option, _Argument, _Switch
from Bio.Application import AbstractCommandline, _ArgumentList
from Bio.Application import _StaticArgument
 
 
class SamtoolsViewCommandline(AbstractCommandline):
class SamtoolsMpileupCommandline(AbstractCommandline):
    """Command line wrapper for samtools mpileup.
 
    Generate BCF or pileup for one or multiple BAM files, equivalent to:
 
class SamtoolsReheaderCommandline(AbstractCommandline):
    """Command line wrapper for samtools reheader.
 
    Replace the header in in.bam with the header
    in in.header.sam, equivalent to:
class SamtoolsCatCommandline(AbstractCommandline):
    """Command line wrapper for samtools cat.
 
    Concatenate BAMs, equivalent to:
 

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
 
 
class BwaIndexCommandline(AbstractCommandline):
class BwaAlignCommandline(AbstractCommandline):
    """Command line wrapper for Burrows Wheeler Aligner (BWA) aln.
 
    Run a BWA alignment, equivalent to::
 
class BwaSamseCommandline(AbstractCommandline):
    """Command line wrapper for Burrows Wheeler Aligner (BWA) samse.
 
    Generate alignments in the SAM format given single-end reads.
    Equvialent to::
class BwaSampeCommandline(AbstractCommandline):
    """Command line wrapper for Burrows Wheeler Aligner (BWA) sampe.
 
    Generate alignments in the SAM format given paired-end reads. 
    Equivalent to::

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
 
 
class BwaIndexCommandline(AbstractCommandline):
class BwaAlignCommandline(AbstractCommandline):
    """Command line wrapper for Burrows Wheeler Aligner (BWA) aln.
 
    Run a BWA alignment, equivalent to::
 
class BwaSamseCommandline(AbstractCommandline):
    """Command line wrapper for Burrows Wheeler Aligner (BWA) samse.
 
    Generate alignments in the SAM format given single-end reads.
    Equvialent to::
class BwaSampeCommandline(AbstractCommandline):
    """Command line wrapper for Burrows Wheeler Aligner (BWA) sampe.
 
    Generate alignments in the SAM format given paired-end reads. 
    Equivalent to::

src/b/i/biopython-1.63/Bio/Blast/Applications.py   biopython(Download)
from Bio import BiopythonDeprecationWarning
 
from Bio.Application import _Option, AbstractCommandline, _Switch
 
 
class FastacmdCommandline(AbstractCommandline):
class _BlastCommandLine(AbstractCommandline):
    """Base Commandline object for (classic) NCBI BLAST wrappers (PRIVATE).
 
    This is provided for subclassing, it deals with shared options
    common to all the BLAST tools (blastall, rpsblast, blastpgp).
class _NcbibaseblastCommandline(AbstractCommandline):
    """Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE).
 
    This is provided for subclassing, it deals with shared options
    common to all the BLAST tools (blastn, rpsblast, rpsblast, etc

src/b/i/biopython-HEAD/Bio/Phylo/Applications/_Fasttree.py   biopython(Download)
__docformat__ = "restructuredtext en"
 
from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline
 
 
class FastTreeCommandline(AbstractCommandline):
    """Command-line wrapper for FastTree.
 
    Homepage: http://www.microbesonline.org/fasttree/
 

src/b/i/biopython-HEAD/Bio/Align/Applications/_Mafft.py   biopython(Download)
 
import os
from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline
 
 
class MafftCommandline(AbstractCommandline):

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
 
 
class DialignCommandline(AbstractCommandline):

src/b/i/biopython-1.63/Bio/Phylo/Applications/_Fasttree.py   biopython(Download)
__docformat__ = "restructuredtext en"
 
from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline
 
 
class FastTreeCommandline(AbstractCommandline):
    """Command-line wrapper for FastTree.
 
    Homepage: http://www.microbesonline.org/fasttree/
 

src/b/i/biopython-1.63/Bio/Align/Applications/_Mafft.py   biopython(Download)
 
import os
from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline
 
 
class MafftCommandline(AbstractCommandline):

src/b/i/biopython-HEAD/Bio/motifs/applications/_xxmotif.py   biopython(Download)
 
import os
from Bio.Application import AbstractCommandline, _Option, _Switch, _Argument
 
 
class XXmotifCommandline(AbstractCommandline):

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