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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, \
    raxml_work = op.abspath(op.join(op.dirname(phy_file), "raxml_work"))
    mkdir(raxml_work)
    raxml_cl = RaxmlCommandline(cmd=RAXML_BIN("raxmlHPC"), \
        sequences=phy_file, algorithm="a", model="GTRGAMMA", \
        parsimony_seed=12345, rapid_bootstrap_seed=12345, \
        num_replicates=100, name="aln", \
        working_dir=raxml_work, **kwargs)
 
    logging.debug("Building ML tree using RAxML: %s" % raxml_cl)
    stdout, stderr = raxml_cl()
    raxml_work = op.abspath(op.join(op.dirname(phy_file), "raxml_work"))
    mkdir(raxml_work)
    raxml_cl = RaxmlCommandline(cmd=RAXML_BIN("raxmlHPC"), \
    sequences=phy_file, algorithm="h", model="GTRGAMMA", \
    name="SH", starting_tree=reftree, bipartition_filename=querytree, \
    working_dir=raxml_work)
 
    logging.debug("Running SH test in RAxML: %s" % raxml_cl)
    o, stderr = raxml_cl()

src/b/i/biopython-1.63/Tests/test_raxml_tool.py   biopython(Download)
 
from Bio import Phylo
from Bio.Phylo.Applications import RaxmlCommandline
from Bio import MissingExternalDependencyError
 
    def test_raxml(self):
        """Run RAxML using the wrapper."""
        cmd = RaxmlCommandline(raxml_exe,
                               sequences=EX_PHYLIP, model="PROTCATWAG",
                               name="test")
        # The parsimony seed should be set automatically
        self.assertTrue('-p' in str(cmd))
        # Smoke test
        try:
            out, err = cmd()

src/b/i/biopython-HEAD/Tests/test_raxml_tool.py   biopython(Download)
 
from Bio import Phylo
from Bio.Phylo.Applications import RaxmlCommandline
from Bio import MissingExternalDependencyError
 
    def test_raxml(self):
        """Run RAxML using the wrapper."""
        cmd = RaxmlCommandline(raxml_exe,
                               sequences=EX_PHYLIP, model="PROTCATWAG",
                               name="test")
        # The parsimony seed should be set automatically
        self.assertTrue('-p' in str(cmd))
        # Smoke test
        try:
            out, err = cmd()