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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)