def fmt(prog):
return br.CustomHelpFormatter(prog)
parser = argparse.ArgumentParser(prog="PhyloBuddy.py", formatter_class=fmt, add_help=False, usage=argparse.SUPPRESS,
description='''\
\033[1mPhyloBuddy\033[m
Put a little bonsai into your phylogeny.
\033[1mUsage examples\033[m:
PhyloBuddy.py "/path/to/tree_file" -<cmd>
PhyloBuddy.py "/path/to/tree_file" -<cmd> | PhyloBuddy.py -<cmd>
PhyloBuddy.py "(A,(B,C));" -f "raw" -<cmd>
''')
br.flags(parser, ("trees", "Supply file path(s) or raw tree string, If piping trees into PhyloBuddy "
"this argument can be left blank."), br.pb_flags, br.pb_modifiers, VERSION)
# This is to allow py.test to work with the -x flag
parser.add_argument("-x", nargs="?")
parser.add_argument("-m", nargs="?")
parser.add_argument("-n", nargs="?")
parser.add_argument("--cov", nargs="?")
parser.add_argument("--cov-report", nargs="?")
in_args = parser.parse_args()
def phylo_to_hash(_phylobuddy, mode='hash'):
if mode != "hash":
return str(_phylobuddy)
_hash = md5("{0}\n".format(str(_phylobuddy).rstrip()).encode()).hexdigest()
return _hash
parser = argparse.ArgumentParser(prog="DbBuddy.py", formatter_class=fmt, add_help=False, usage=argparse.SUPPRESS,
description='''
\033[1mDatabaseBuddy\033[m
Go forth to the servers of sequence, and discover.
\033[1mUsage examples\033[m:
DbBuddy.py -ls (launch empty live session)
DbBuddy.py "<accn1,accn2,accn3,...>" -<cmd>
DbBuddy.py "<search term1, search term2,...>" -<cmd>
DbBuddy.py "<accn1,search term1>" -<cmd>
DbBuddy.py "/path/to/file_of_accns" -<cmd>
''')
br.db_modifiers["database"]["choices"] = Db.DATABASES
br.flags(parser, ("user_input", "Specify accession numbers or search terms, "
"either in a file or as a comma separated list"),
br.db_flags, br.db_modifiers, Db.VERSION)
# This is to allow py.test to work with its own flags
in_args = parser.parse_args([])
def mock_cmdloop(*args):
print(args)
return True
class MockUsage(object):
def __init__(self, *args, **kwargs):
self.args = args
self.kwargs = kwargs
def test_flags(capsys, hf):
contributors = list()
contributors.append(
br.Contributor("Bud", "Suite", "D", commits=10, github="buddysuite"))
contributors.append(
br.Contributor("Sweet", "Water", commits=5, github="sweetwater"))
version = br.Version("BudddySuite",
"3",
"5",
contributors,
release_date={
"day": 13,
"month": 7,
"year": 2016
})
parser = argparse.ArgumentParser(prog="SeqBuddy.py", add_help=False)
pos_dict = ("sequence",
"Supply file path(s) or raw sequence. If piping sequences "
"into SeqBuddy this argument can be left blank.")
flag_dict = {
"annotate": {
"flag":
"ano",
"nargs":
"*",
"metavar":
"args",
"help":
"Add a feature (annotation) to selected sequences. "
"Args: <name>, <location (start1-end1,start2-end2...)>, [strand (+|-)], "
"[qualifier (foo=bar) [qualifier]], [regex_pattern [regex_[pattern]]}"
},
"ave_seq_length": {
"flag":
"asl",
"action":
"append",
"nargs":
"?",
"metavar":
"'clean'",
"help":
"Calculate average sequence length. Specify 'clean' to remove gaps etc "
"first"
}
}
mod_dict = {
"alpha": {
"flag": "a",
"action": "store",
"help": "If you want the file read with a specific alphabet"
},
"in_format": {
"flag":
"f",
"action":
"store",
"help":
"If SeqBuddy can't guess the file format, try specifying it directly"
}
}
br.flags(parser,
_positional=pos_dict,
_flags=flag_dict,
_modifiers=mod_dict,
version=version)
parser.print_help()
out, err = capsys.readouterr()
assert hf.string2hash(out) == "9ea2d4ac842b1712687034ea0abf497b"
def fmt(prog):
return br.CustomHelpFormatter(prog)
parser = argparse.ArgumentParser(prog="alignBuddy", formatter_class=fmt, add_help=False, usage=argparse.SUPPRESS,
description='''\
\033[1mAlignBuddy\033[m
Sequence alignments with a splash of kava.
\033[1mUsage examples\033[m:
AlignBuddy.py "/path/to/align_file" -<cmd>
AlignBuddy.py "/path/to/align_file" -<cmd> | AlignBuddy.py -<cmd>
AlignBuddy.py "/path/to/seq_file" -ga "mafft" -p "--auto --thread 8"
''')
br.flags(parser, ("alignments", "The file(s) you want to start working on"),
br.alb_flags, br.alb_modifiers, VERSION)
# This is to allow py.test to work with its own flags
in_args = parser.parse_args([])
# ###################### argparse_init() ###################### #
def test_argparse_init(capsys, monkeypatch, alb_resources, hf, alb_odd_resources):
monkeypatch.setattr(sys, 'argv', ['AlignBuddy.py', alb_resources.get_one("o p py", "paths"), "-con",
"-o", "stockholm"])
temp_in_args, alignbuddy = Alb.argparse_init()
assert hf.buddy2hash(alignbuddy) == "5d9a03d9e1b4bf72d991257d3a696306"
monkeypatch.setattr(sys, 'argv', ['AlignBuddy.py', alb_resources.get_one("o p py", "paths"), "-con", "-o", "foo"])
with pytest.raises(SystemExit):
Alb.argparse_init()
formatter_class=fmt,
add_help=False,
usage=argparse.SUPPRESS,
description='''\
\033[1mPhyloBuddy\033[m
Put a little bonsai into your phylogeny.
\033[1mUsage examples\033[m:
PhyloBuddy.py "/path/to/tree_file" -<cmd>
PhyloBuddy.py "/path/to/tree_file" -<cmd> | PhyloBuddy.py -<cmd>
PhyloBuddy.py "(A,(B,C));" -f "raw" -<cmd>
''')
br.flags(
parser,
("trees",
"Supply file path(s) or raw tree string, If piping trees into PhyloBuddy "
"this argument can be left blank."), br.pb_flags, br.pb_modifiers,
VERSION)
# This is to allow py.test to work with its own flags
in_args = parser.parse_args([])
def mock_fileexistserror(*args, **kwargs):
raise FileExistsError(args, kwargs)
def mock_filenotfounderror(*args, **kwargs):
raise FileNotFoundError(args, kwargs)