Bio.Emboss.Applications.WaterCommandline

All Samples(14) | Call(12) | Derive(0) | Import(2)

src/b/i/biopython-1.63/Tests/test_Emboss.py biopython(Download)

from Bio._py3k import StringIO
 
from Bio.Emboss.Applications import WaterCommandline, NeedleCommandline
from Bio.Emboss.Applications import SeqretCommandline, SeqmatchallCommandline
from Bio import SeqIO

    def test_water_file(self):
        """water with the asis trick, output to a file."""
        #Setup, try a mixture of keyword arguments and later additions:
        cline = WaterCommandline(cmd=exes["water"],
                                 gapopen="10", gapextend="0.5")

    def test_water_piped(self):
        """water with asis trick, output piped to stdout."""
        cline = WaterCommandline(cmd=exes["water"],
                                 asequence="asis:ACCCGGGCGCGGT",
                                 bsequence="asis:ACCCGAGCGCGGT",

        if os.path.isfile(out_file):
            os.remove(out_file)
        cline = WaterCommandline(cmd=exes["water"])
        cline.set_parameter("-asequence", "asis:%s" % query)
        cline.set_parameter("-bsequence", in_file)

        if os.path.isfile(out_file):
            os.remove(out_file)
        cline = WaterCommandline(cmd=exes["water"])
        cline.set_parameter("asequence", "asis:%s" % query)
        cline.set_parameter("bsequence", in_file)

src/b/i/biopython-HEAD/Tests/test_Emboss.py biopython(Download)

from Bio._py3k import StringIO
 
from Bio.Emboss.Applications import WaterCommandline, NeedleCommandline
from Bio.Emboss.Applications import SeqretCommandline, SeqmatchallCommandline
from Bio import SeqIO

    def test_water_file(self):
        """water with the asis trick, output to a file."""
        #Setup, try a mixture of keyword arguments and later additions:
        cline = WaterCommandline(cmd=exes["water"],
                                 gapopen="10", gapextend="0.5")

    def test_water_piped(self):
        """water with asis trick, output piped to stdout."""
        cline = WaterCommandline(cmd=exes["water"],
                                 asequence="asis:ACCCGGGCGCGGT",
                                 bsequence="asis:ACCCGAGCGCGGT",

        if os.path.isfile(out_file):
            os.remove(out_file)
        cline = WaterCommandline(cmd=exes["water"])
        cline.set_parameter("-asequence", "asis:%s" % query)
        cline.set_parameter("-bsequence", in_file)

        if os.path.isfile(out_file):
            os.remove(out_file)
        cline = WaterCommandline(cmd=exes["water"])
        cline.set_parameter("asequence", "asis:%s" % query)
        cline.set_parameter("bsequence", in_file)