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src/j/c/jcvi-HEAD/apps/phylo.py jcvi(Download)
from Bio.Emboss.Applications import FSeqBootCommandline, FDNADistCommandline, \ FNeighborCommandline, FConsenseCommandline from Bio.Phylo.Applications import PhymlCommandline, RaxmlCommandline from jcvi.apps.ks import AbstractCommandline, find_first_isoform, \
AlignIO.write(alignment, file(phy_file, "w"), "phylip-relaxed") phyml_cl = PhymlCommandline(cmd=PHYML_BIN("phyml"), input=phy_file, **kwargs) logging.debug("Building ML tree using PhyML: %s" % phyml_cl) stdout, stderr = phyml_cl()
src/b/i/biopython-1.63/Tests/test_phyml_tool.py biopython(Download)
from Bio import Phylo from Bio.Phylo.Applications import PhymlCommandline from Bio import MissingExternalDependencyError
def test_phyml(self): """Run PhyML using the wrapper.""" cmd = PhymlCommandline(phyml_exe, input=EX_PHYLIP, datatype='aa') # Smoke test try: out, err = cmd()
src/b/i/biopython-HEAD/Tests/test_phyml_tool.py biopython(Download)
from Bio import Phylo from Bio.Phylo.Applications import PhymlCommandline from Bio import MissingExternalDependencyError
def test_phyml(self): """Run PhyML using the wrapper.""" cmd = PhymlCommandline(phyml_exe, input=EX_PHYLIP, datatype='aa') # Smoke test try: out, err = cmd()