def __init__(self, args):
unixpath.checkFile(args.i)
unixpath.checkFile(args.v)
self.infile = args.i
self.outfile = ""
self.variants = []
self.xlsx = args.v
self.__readVariants__(args)
def __init__(self, args):
unixpath.checkFile(args.d)
self.indir = unixpath.checkDir(args.p)
self.infile = args.d
self.outfile = args.o
self.species = {}
self.__readDeathBooks__()
self.__readPopulationFiles__()
self.__write__()
def __init__(self, args):
unixpath.checkFile(args.i)
self.comments = set()
self.diag = {}
self.header = {}
self.infile = args.i
self.outfile = args.o
self.__readInfile__()
self.__writeFile__()
def __init__(self, args):
for i in [args.i, args.t, args.d]:
unixpath.checkFile(i)
self.infile = args.d
self.outfile = os.path.join(
os.path.split(self.infile)[0], "madsenMergedDiagnoses.csv")
self.refs = {}
self.taxa = {}
self.__setRefs__(args.i)
self.__setTaxa__(args.t)
def __init__(self, args):
self.infile = args.i
self.taxafile = args.t
self.outfile = args.o
self.delete = set()
self.new = {}
self.updated = set()
for i in [self.infile, self.taxafile]:
unixpath.checkFile(i)
self.__setTaxa__()
def __init__(self, args):
for i in [args.a, args.i]:
unixpath.checkFile(i)
self.accounts = {}
self.accountfile = args.a
self.counts = {}
self.infile = args.i
self.outfile = args.o
self.__setAccounts__()
self.__countRecords__()
self.__write__()
def __init__(self, args):
for i in [args.i, args.n]:
unixpath.checkFile(i)
self.min = 50
self.outfile = args.o
self.records = {}
self.rows = []
print()
self.__setCounts__(args.i, False)
self.__setCounts__(args.n, True)
self.__filter__()
self.__write__()
def main():
start = datetime.now()
parser = ArgumentParser("This script will make a histogram of species \
occurances for each species in a given database.")
parser.add_argument("--min", type = int, default = 50,
help = "The minimum number of records required for each species (default = 50).")
parser.add_argument("infile", help = "Path to input file. Output svg will be written in same directory.")
args = parser.parse_args()
checkFile(args.infile)
outfile = args.infile[:args.infile.rfind(".")] + ".svg"
title = getTitle(args.infile, args.min)
freq = getSpeciesCounts(args.infile, args.min)
speciesHist(outfile, freq, title, args.min)
printRuntime(start)
def __init__(self, args):
for i in [args.i, args.t]:
unixpath.checkFile(i)
self.infile = args.i
self.outfile = os.path.join(
os.path.split(self.infile)[0],
"compressed_literature_compilation.csv")
self.header = {}
self.records = {}
self.taxa = {}
self.names = []
self.__setTaxa__(args.t)
self.__readFile__()
self.__writeRecords__()
def __init__(self, args):
unixpath.checkFile(args.a)
unixpath.checkFile(args.n)
pyplot.style.use("seaborn-deep")
self.bins = [20, 30, 40, 50, 60, 70, 80, 90, 100, 110]
self.col = "RecordsWithDenominators"
self.label = ["all records", "necropsies"]
self.legend = "upper right"
self.max = 100
self.min = 20
self.outfile = os.path.join(os.path.split(args.a)[0], "speciesTotals.svg")
print()
self.all = self.__setCounts__(args.a)
self.necropsy = self.__setCounts__(args.n)
