def PrepareScoaryCMDline(self):
"""
Prepares arguments to correspond with argparse namespace and runs.
Listens to sys.stdout and updates statusbar while scoary runs
"""
citation=False
RunScoary = True
correction = []
p_value_cutoff = []
for m in self.Scoary_parameters["Cutoffs"]:
if self.Scoary_parameters["Cutoffs"][m][0] == 1:
correction.append(m)
try:
p_value_cutoff.append(float(self.Scoary_parameters["Cutoffs"][m][1]))
except ValueError:
print("Please enter real numbers in the p value fields")
RunScoary = False
break
delimiter = self.Scoary_parameters["Delimiter"]
genes = self.Scoary_parameters["GPA"] if self.Scoary_parameters["GPA"] not in ["","Path to gene presence absence file"] else None
try:
max_hits = int(self.Scoary_parameters["Maxhits"]) if self.Scoary_parameters["Maxhits"] not in [""] else None
except ValueError:
print("Please enter a real number (or nothing) in the max hits field")
max_hits = None
RunScoary = False
try:
permutations = abs(int(self.Scoary_parameters["Permutations"])) if self.Scoary_parameters["Permutations"] not in [""] else 0
except ValueError:
print("Please enter a real number (or nothing) in the max hits field")
permutations = 0
RunScoary = False
newicktree = self.Scoary_parameters["Tree"] if self.Scoary_parameters["Tree"] not in ["", "(Optional) Path to custom tree file"] else None
no_time = True if self.Scoary_parameters["Notime"] == 1 else False
outdir = self.Scoary_parameters["Outdir"] if self.Scoary_parameters["Outdir"] not in ["","(Optional) Output directory"] else "./"
restrict_to = self.Scoary_parameters["Restrict"] if self.Scoary_parameters["Restrict"] not in ["", "(Optional) Path to file naming isolates to include"] else None
start_col = self.Scoary_parameters["Startcol"]
test = False
threads = 1
traits = self.Scoary_parameters["Traits"] if self.Scoary_parameters["Traits"] not in ["","Path to traits/phenotype file"] else None
upgma_tree = True if self.Scoary_parameters["Writetree"] == 1 else False
write_reduced=False
collapse=False
myargs = argparse.Namespace(citation=citation, correction=correction, p_value_cutoff=p_value_cutoff, delimiter=delimiter, genes=genes, max_hits=max_hits, newicktree=newicktree,no_time=no_time,restrict_to=restrict_to,
outdir=outdir,permute=permutations,start_col=start_col,test=test,threads=threads,traits=traits,upgma_tree=upgma_tree,write_reduced=write_reduced,collapse=collapse)
if RunScoary:
try:
sm.main(args=myargs, cutoffs=dict(list(zip(correction, p_value_cutoff))),statusbar=sys.stdout)
except SystemExit as SE:
# Set status bar color to red?
if str(SE) == "0":
print("Analysis complete!")
else:
print("Fatal error: %s" % str(SE))
#!/usr/bin/env python # Scoary - Microbial Pan-GWAS. Associates genes in Roary output with phenotypes # Copyright (C) 2016 Ola Brynildsrud ([email protected]) # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. from scoary import methods if __name__ == '__main__': print("Warning. Since 1.5.0 scoary.py is deprecated. " "Install Scoary using 'pip install scoary instead, and run using " "scoary <options>") methods.main()
#!/usr/bin/env python # Scoary - Microbial Pan-GWAS. Associates genes in Roary output with phenotypes # Copyright (C) 2016 Ola Brynildsrud ([email protected]) # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. from scoary import methods if __name__ == '__main__': print("Warning. Since 1.5.0 scoary.py is deprecated. " \ "Install Scoary using 'pip install git+https://github.com/AdmiralenOla/" \ "Scoary.git' instead") methods.main()
def PrepareScoaryCMDline(self):
"""
Prepares arguments to correspond with argparse namespace and
runs. Listens to sys.stdout and updates statusbar.
"""
citation = False
RunScoary = True
correction = []
p_value_cutoff = []
for m in self.Scoary_parameters["Cutoffs"]:
if self.Scoary_parameters["Cutoffs"][m][0] == 1:
correction.append(m)
try:
p_value_cutoff.append(
float(self.Scoary_parameters["Cutoffs"][m][1]))
except ValueError:
print("Please enter real numbers in the p value " "fields")
RunScoary = False
break
delimiter = self.Scoary_parameters["Delimiter"]
genes = (self.Scoary_parameters["GPA"] if self.Scoary_parameters["GPA"]
not in ["", "Path to gene presence absence file"] else None)
try:
max_hits = (int(self.Scoary_parameters["Maxhits"])
if self.Scoary_parameters["Maxhits"] not in [""] else
None)
except ValueError:
print("Please enter a real number (or nothing) in the max "
"hits field")
max_hits = None
RunScoary = False
try:
permutations = (abs(int(self.Scoary_parameters["Permutations"]))
if self.Scoary_parameters["Permutations"]
not in [""] else 0)
except ValueError:
print("Please enter a real number (or nothing) in the max "
"hits field")
permutations = 0
RunScoary = False
newicktree = (
self.Scoary_parameters["Tree"] if self.Scoary_parameters["Tree"]
not in ["", "(Optional) Path to custom tree file"] else None)
no_time = (True if self.Scoary_parameters["Notime"] == 1 else False)
outdir = (self.Scoary_parameters["Outdir"]
if self.Scoary_parameters["Outdir"]
not in ["", "(Optional) Output directory"] else "./")
restrict_to = (self.Scoary_parameters["Restrict"]
if self.Scoary_parameters["Restrict"] not in [
"", "(Optional) Path to file naming isolates to "
"include"
] else None)
start_col = self.Scoary_parameters["Startcol"]
test = False
threads = 1
traits = (self.Scoary_parameters["Traits"]
if self.Scoary_parameters["Traits"]
not in ["", "Path to traits/phenotype file"] else None)
upgma_tree = (True
if self.Scoary_parameters["Writetree"] == 1 else False)
write_reduced = False
collapse = (True if self.Scoary_parameters["Collapse"] == 1 else False)
no_pairwise = (True if self.Scoary_parameters["No_pairwise"] == 1 else
False)
myargs = argparse.Namespace(citation=citation,
correction=correction,
p_value_cutoff=p_value_cutoff,
delimiter=delimiter,
genes=genes,
grabcols=[],
max_hits=max_hits,
newicktree=newicktree,
no_time=no_time,
restrict_to=restrict_to,
outdir=outdir,
permute=permutations,
start_col=start_col,
test=test,
threads=threads,
traits=traits,
upgma_tree=upgma_tree,
write_reduced=write_reduced,
collapse=collapse,
no_pairwise=no_pairwise)
if RunScoary:
try:
sm.main(args=myargs,
cutoffs=dict(list(zip(correction, p_value_cutoff))),
statusbar=sys.stdout)
except SystemExit as SE:
# Set status bar color to red?
if str(SE) == "0":
print("Analysis complete!")
else:
print("Fatal error: %s" % str(SE))
