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src/b/i/biopython-1.63/Bio/Wise/dnal.py   biopython(Download)
 
#Importing with leading underscore as not intended to be exposed
from Bio._py3k import getoutput as _getoutput
from Bio._py3k import zip
from Bio._py3k import map
def _fgrep_count(pattern, file):
    return int(_getoutput(_CMDLINE_FGREP_COUNT % (pattern, file)))
 
_re_alb_line2coords = re.compile(r"^\[([^:]+):[^\[]+\[([^:]+):")
 

src/b/i/biopython-HEAD/Bio/Wise/dnal.py   biopython(Download)
 
#Importing with leading underscore as not intended to be exposed
from Bio._py3k import getoutput as _getoutput
from Bio._py3k import zip
from Bio._py3k import map
def _fgrep_count(pattern, file):
    return int(_getoutput(_CMDLINE_FGREP_COUNT % (pattern, file)))
 
_re_alb_line2coords = re.compile(r"^\[([^:]+):[^\[]+\[([^:]+):")
 

src/b/i/biopython-1.63/Tests/test_Probcons_tool.py   biopython(Download)
    raise MissingExternalDependencyError("PROBCONS not available on Windows")
else:
    from Bio._py3k import getoutput
    output = getoutput("probcons")
    if "not found" not in output and "probcons" in output.lower():

src/b/i/biopython-HEAD/Tests/test_Probcons_tool.py   biopython(Download)
    raise MissingExternalDependencyError("PROBCONS not available on Windows")
else:
    from Bio._py3k import getoutput
    output = getoutput("probcons")
    if "not found" not in output and "probcons" in output.lower():

src/b/i/biopython-1.63/Tests/test_Fasttree_tool.py   biopython(Download)
                break
else:
    from Bio._py3k import getoutput
    # Checking the -help argument
    output = getoutput("fasttree -help")

src/b/i/biopython-HEAD/Tests/test_Fasttree_tool.py   biopython(Download)
                break
else:
    from Bio._py3k import getoutput
    # Website uses 'FastTree', Nate's system had 'fasttree'
    likely_exes = ["FastTree", "fasttree"]
    for filename in likely_exes:
        # Checking the -help argument
        output = getoutput("%s -help" % filename)

src/b/i/biopython-1.63/Tests/test_Clustalw_tool.py   biopython(Download)
                break
else:
    from Bio._py3k import getoutput
    #Note that clustalw 1.83 and clustalw 2.1 don't obey the --version
    #command, but this does cause them to quit cleanly.  Otherwise they prompt
    #the user for input (causing a lock up).
    output = getoutput("clustalw2 --version")
        clustalw_exe = "clustalw2"
    if not clustalw_exe:
        output = getoutput("clustalw --version")
        if "not found" not in output and "CLUSTAL" in output \
        and "Multiple Sequence Alignments" in output:

src/b/i/biopython-HEAD/Tests/test_Clustalw_tool.py   biopython(Download)
                break
else:
    from Bio._py3k import getoutput
    #Note that clustalw 1.83 and clustalw 2.1 don't obey the --version
    #command, but this does cause them to quit cleanly.  Otherwise they prompt
    #the user for input (causing a lock up).
    output = getoutput("clustalw2 --version")
        clustalw_exe = "clustalw2"
    if not clustalw_exe:
        output = getoutput("clustalw --version")
        if "not found" not in output and "CLUSTAL" in output \
        and "Multiple Sequence Alignments" in output:

src/b/i/biopython-HEAD/Tests/test_BWA_tool.py   biopython(Download)
                break
else:
    from Bio._py3k import getoutput
    output = getoutput("bwa")
 
        bwa_exe = "bwa"
    skip_aln_tests = False
    aln_output = getoutput("bwa aln")
    if "unrecognized" in aln_output:
        skip_aln_tests = True

src/b/i/biopython-1.63/Tests/test_Emboss.py   biopython(Download)
    del path
if sys.platform!="win32":
    from Bio._py3k import getoutput
    for name in exes_wanted:
        #This will "just work" if installed on the path as normal on Unix
        output = getoutput("%s -help" % name)

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