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Bio.Phylo.Applications.FastTreeCommandline

All Samples(8)  |  Call(6)  |  Derive(0)  |  Import(2)


src/b/i/biopython-1.63/Tests/test_Fasttree_tool.py   biopython(Download)
from Bio import SeqIO
from Bio import Phylo
from Bio.Phylo.Applications import FastTreeCommandline
from Bio.Phylo.Applications import _Fasttree
from Bio.Application import ApplicationError

input_file = "does_not_exist.fasta"
assert not os.path.isfile(input_file)
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
    stdout, stderr = cline()

assert os.path.isfile(input_file)
assert len(list(SeqIO.parse(input_file, "fasta")))==1
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
    stdout, stderr = cline()

input_file = "Medline/pubmed_result1.txt"
assert os.path.isfile(input_file)
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
    stdout, stderr = cline()


src/b/i/biopython-HEAD/Tests/test_Fasttree_tool.py   biopython(Download)
from Bio import SeqIO
from Bio import Phylo
from Bio.Phylo.Applications import FastTreeCommandline
from Bio.Phylo.Applications import _Fasttree
from Bio.Application import ApplicationError

input_file = "does_not_exist.fasta"
assert not os.path.isfile(input_file)
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
    stdout, stderr = cline()

assert os.path.isfile(input_file)
assert len(list(SeqIO.parse(input_file, "fasta")))==1
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
    stdout, stderr = cline()

input_file = "Medline/pubmed_result1.txt"
assert os.path.isfile(input_file)
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
    stdout, stderr = cline()