def write(otu_in_group, outfile):
with open(outfile, 'w') as fp:
for group, otus in otu_in_group.iteritems():
otus = sorted(list(otus), cmp=lambda a, b: cmp(int(a), int(b)))
fp.write('%s\t%s\n' % (group, ' '.join(otus)))
if __name__ == '__main__':
params = read_params(sys.argv)
dirname=params['outputdir']
mkdir(dirname)
for_plot = dirname + '/for_plot.txt'
tiff_file = dirname + '/venn.tiff'
png_file = dirname + '/venn.png'
vars = {'for_plot': for_plot,
'tiff_file': tiff_file,
'group_file': params['group_dir']}
otu_in_group = read(params['microbial_profile'], params['group'], vars)
write(otu_in_group, for_plot)
r_job = Rparser()
r_job.open(const.Rscript + '02_venn.R')
r_job.format(vars)
r_job.write(dirname+ '/otu_venn.R')
r_job.run()
image_trans(300,tiff_file, png_file)
help=
"please set method Dissimilarity index, partial match to manhattan euclidean \
canberra bray kulczynski jaccard gower altGower morisita horn\
mountford raup binomial chao cao mahalanobis")
args = parser.parse_args()
params = vars(args)
return params
if __name__ == '__main__':
reload(sys)
sys.setdefaultencoding('utf8')
params = read_params(sys.argv)
tool_default_dir = const.tool_default_dir
mkdir(params['out_dir'])
use_method = params["method"]
pdf_file = params['out_dir'] + "/" + use_method + '_adonis_pcoa.pdf'
png_file = params['out_dir'] + "/" + use_method + '_adonis_pcoa.png'
env = Environment(loader=FileSystemLoader(tool_default_dir),
autoescape=False)
template = env.get_template("t12_adonis_pcoa.R")
Rtxt = template.render(tool_default_dir = tool_default_dir,\
profile_table =params['profile_table'],\
group_file =params['group_file'],\
pdf_file = pdf_file,\
method = use_method)
with open("%s/adonis_pcoa.R" % params["out_dir"], "w") as fqout:
fqout.write(Rtxt)
Rrun("%s/adonis_pcoa.R" % params["out_dir"])
image_trans(pdf_file, png_file)
params = vars(args)
params['group'] = parse_group_file(params['group'])
return params
if __name__ == '__main__':
params = read_params(sys.argv)
outputfile = params['outputfile']
dirname,filename,suffix =get_name(outputfile)
inputfile = params['inputfile']
top = params['top']
title = params['title']
data = pd.DataFrame.from_csv(file=inputfile,sep="\t")
data["sum"] = data.sum(axis=1)
data = data.sort_values(by="sum",ascending=False)
del data["sum"]
data = data.ix[:top]
data.to_csv("%s/for_plot.csv"%dirname,sep="\t")
mkdir(os.path.split(outputfile)[0])
RscriptDir = const.Rscript
r_job = Rparser()
r_job.open("%s/02_barplot.R"%RscriptDir)
vars = {"top":top,
"infile": "%s/for_plot.csv"%dirname,
"pdf_file": outputfile,
"title": title}
r_job.format(vars)
r_job.write("%s/bar_plot.R"%dirname)
r_job.run()
image_trans(300,"%s/%s.pdf"%(dirname,filename),"%s/%s.png"%(dirname,filename))
def read_params(args):
parser = argparse.ArgumentParser(description="group file change")
parser.add_argument(
"-i", "--inputfile", dest="inputfile", metavar="inputfile", type=str, required=True, help="set input file"
)
parser.add_argument(
"-o", "--outputdir", dest="outputdir", metavar="outputdir", type=str, required=True, help="set out put dir"
)
parser.add_argument("-g", "--group", dest="group", metavar="group", type=str, required=True, help="set group file")
args = parser.parse_args()
params = vars(args)
return params
if __name__ == "__main__":
params = read_params(sys.argv)
outputdir = params["outputdir"]
inputfile = params["inputfile"]
pdfoutput = outputdir + "top.pdf"
pngoutput = outputdir + "top.png"
group = params["group"]
vars = {"group": group, "pdfoutput": pdfoutput, "input": inputfile}
r_job = Rparser()
r_job.open(const.Rscript + "02_top.R")
r_job.format(vars)
r_job.write(outputdir + "/top.R")
r_job.run()
image_trans(300, pdfoutput, pngoutput)
parser.set_defaults(with_boxplot=True)
args = parser.parse_args()
params = vars(args)
return params
if __name__ == '__main__':
params = read_params(sys.argv)
mkdir(params['out_dir'])
pdf_file = params['out_dir'] + '/otu_pca.pdf'
png_file = params['out_dir'] + '/otu_pca.png'
vars = {'otu_profile': params['otu_table'],
'group_file': params['group'],
'pdf_file': pdf_file}
r_job = Rparser()
if params['two_legend']:
if params['with_boxplot']:
r_job.open(const.Rscript + '/02_tax_pca_two.R')
else:
r_job.open(const.Rscript + '/02_tax_pca_two.R')
else:
if params['with_boxplot']:
r_job.open(const.Rscript + '/02_tax_pca_with_boxplot.R')
else:
r_job.open(const.Rscript + '/02_tax_pca.R')
r_job.format(vars)
r_job.write(params['out_dir'] + '/tax_pca.R')
r_job.run()
image_trans(300,pdf_file, png_file)
png_file = params['out_dir'] + '/pca.png'
env = Environment(loader=FileSystemLoader(tool_default_dir), autoescape=False)
if params["Kmeans_cluster"]:
if params["with_boxplot"]:
template = env.get_template("1_pca_kmeans_withbox.R")
else:
template = env.get_template("1_pca_kmeans.R")
else:
if params['two_legend']:
if params['with_boxplot']:
template = env.get_template("1_pca_two.R")
else:
template = env.get_template("1_pca_two.R")
else:
if params['with_boxplot']:
template = env.get_template("1_pca_with_boxplot.R")
else:
template = env.get_template("1_pca.R")
Rtxt = template.render(tool_default_dir=tool_default_dir, \
profile_table=params['profile_table'], \
group_file=params['group_file'], \
pdf_file=pdf_file)
with open("%s/pca.R" % (params["out_dir"]), "w") as fqout:
fqout.write(Rtxt)
Rrun("%s/pca.R" % params["out_dir"], )
image_trans(300, pdf_file, png_file)
