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)
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
profile_table = params["profile_table"]
group_file = params["group_file"]
out_dir = params["out_dir"]
top = params["top"]
pdf_file = "%s/heatmap.pdf"%out_dir
png_file = "%s/heatmap.png"%out_dir
mkdir(out_dir)
env = Environment(loader=FileSystemLoader(tool_default_dir), autoescape=False)
template = env.get_template("t06_heatmap.R")
Rtxt = template.render(tool_default_dir = tool_default_dir,\
out_dir = out_dir,\
profile_table = profile_table,\
group_file=group_file,\
pdf_file = pdf_file,\
top=top)
with open("%s/heatmap.R"%(params["out_dir"]),"w") as fqout:
fqout.write(Rtxt)
Rrun("%s/heatmap.R"%(params["out_dir"]))
image_trans(pdf_file,png_file)
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
profile_table = params["profile_table"]
out_dir = params["out_dir"]
out_dir = "%s/%s/"%(out_dir,params["level"])
mkdir(out_dir)
group_file = params["group_file"]
_,_,_,group_num = parse_group(group_file)
pdf_file = "%s/venn.png"%out_dir
png_file = "%s/venn.png"%out_dir
if group_num<6 and group_num>=2:
env = Environment(loader=FileSystemLoader(tool_default_dir),autoescape=False)
template = env.get_template("t07_venn_flower.R")
Rtext = template.render(tool_default_dir = tool_default_dir,\
png_file=png_file,\
group_file = group_file,\
profile_table = profile_table)
with open(out_dir + 'venn_flower.R', 'w') as fp:
fp.write(Rtext)
Rrun("%s/venn_flower.R"%out_dir)
# image_trans(300,pdf_file,png_file)
else:
pass
help="set profile table file")
parser.add_argument('-o', '--out_dir', dest='out_dir', metavar='out_dir', type=str, required=True,
help="set out put dir")
parser.add_argument('-g','--group_file',dest='group_file',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)
bin_default_dir = const.bin_default_dir
out_dir = params['out_dir']
profile_table = params['profile_table']
pdf_file = out_dir+"top.pdf"
png_file = out_dir+"top.png"
group_file = params['group_file']
vars = {'group_file': group_file,
'pdf_file':pdf_file,
"profile_table":profile_table
}
env = Environment(loader=FileSystemLoader("%s/02.taxonomy/"%bin_default_dir),autoescape=False)
template = env.get_template("207_top.R")
Rtext = template.render(tool_default_dir=const.tool_default_dir,\
group_file=group_file,\
pdf_file = pdf_file,\
profile_table = profile_table)
with open(out_dir + '207_top.R', 'w') as fp:
fp.write(Rtext)
Rrun("%s/207_top.R"%out_dir)
# os.system("convert -density 300 %s %s"%(pdfoutput,pngoutput))
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+ '_anosim.pdf'
png_file = params['out_dir'] +"/"+use_method+ '_anosim.png'
txt_file = params['out_dir'] +"/"+use_method+ '_anosim.txt'
env = Environment(loader=FileSystemLoader(tool_default_dir),autoescape=False)
template = env.get_template("t04_anosim.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,\
txt_file=txt_file)
with open("%s/anosim.R"%params["out_dir"],"w") as fqout:
fqout.write(Rtxt)
Rrun("%s/anosim.R"%params["out_dir"])
image_trans(pdf_file,png_file)
help="set the top number")
parser.add_argument('-o', '--out_dir', dest='out_dir', metavar='DIR', type=str, required=True,
help="set the output dir")
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
p_file = params["p_file"]
mkdir(params['out_dir'])
pdf_file = params['out_dir'] + '/diff_boxplot.pdf'
png_file = params['out_dir'] + '/diff_boxplot.png'
env = Environment(loader=FileSystemLoader(tool_default_dir), autoescape=False)
template = env.get_template("t09_diff_boxplot.R")
Rtxt = template.render(tool_default_dir=tool_default_dir, \
profile_table=params['profile_table'], \
group_file=params['group_file'], \
p_file=p_file,\
pdf_file = pdf_file,\
top = params["top"])
with open("%s/diff_boxplot.R" % (params["out_dir"]), "w") as fqout:
fqout.write(Rtxt)
Rrun("%s/diff_boxplot.R" % params["out_dir"], )
image_trans( pdf_file, png_file)
if __name__ == '__main__':
params = read_params(sys.argv)
bin_defdir = '%s/02.taxon' % const.bin_defdir
mkdir(params['out_dir'])
use_method = params["method"]
pdf_file = params['out_dir'] + "/" + use_method + 'pcoa.pdf'
png_file = params['out_dir'] + "/" + use_method + 'pcoa.png'
env = Environment(loader=FileSystemLoader(bin_defdir), autoescape=False)
if params['two_legend']:
if params['with_boxplot']:
template = env.get_template("g07_pcoa_two.R")
else:
template = env.get_template("g07_pcoa_two.R")
#TODO two_legend and with_boxplot
else:
if params['with_boxplot']:
template = env.get_template("g07_pcoa_with_boxplot.R")
else:
template = env.get_template("g07_pcoa.R")
Rtxt = template.render(tool_default_dir=const.tool_defdir,\
profile_table=params['profile_table'],\
group_file =params['group_file'],\
pdf_file = pdf_file,\
method = use_method)
with open("%s/pcoa.R" % (params["out_dir"]), "w") as fqout:
fqout.write(Rtxt)
Rrun("%s/pcoa.R" % params["out_dir"])
parser.add_argument('-o', '--out_dir', dest='out_dir', metavar='DIR', type=str, required=True,
help="set the output dir")
parser.add_argument('-c','--class',dest="class",metavar='string', type=str,required=True,
help="set phylum or genus or species")
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'])
class_ = params["class"]
pdf_file = params['out_dir'] +"/"+class_+ '.ternary.pdf'
png_file = params['out_dir'] +"/"+class_+ '.ternary.png'
env = Environment(loader=FileSystemLoader(tool_default_dir),autoescape=False)
template = env.get_template("t13_ternary.R")
Rtxt = template.render(tool_default_dir = tool_default_dir,\
profile_table =params['profile_table'],\
group_file =params['group_file'],\
pdf_file = pdf_file,\
class_ = class_)
with open("%s/ternary.R" % params["out_dir"],"w") as fqout:
fqout.write(Rtxt)
Rrun("%s/ternary.R"%params["out_dir"])
image_trans(pdf_file,png_file)
dest='group_file',
metavar='FILE',
type=str,
required=True,
help="set the group file")
parser.add_argument('-o',
'--out_dir',
dest='out_dir',
metavar='DIR',
type=str,
required=True,
help="set the output dir")
args = parser.parse_args()
return vars(args)
if __name__ == '__main__':
params = read_params(sys.argv)
bin_defdir = '%s/02.taxon' % const.bin_defdir
mkdir(params['out_dir'])
txt_file = params['out_dir'] + "/mrpp.txt"
env = Environment(loader=FileSystemLoader(bin_defdir), autoescape=False)
template = env.get_template("g10_mrpp.R")
Rtxt = template.render(tool_default_dir=const.tool_defdir,\
profile_table=params['profile_table'],\
group_file =params['group_file'],\
txt_file=txt_file)
with open("%s/mrpp.R" % params["out_dir"], "w") as fqout:
fqout.write(Rtxt)
Rrun("%s/mrpp.R" % params["out_dir"])
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)
return vars(args)
if __name__ == '__main__':
params = read_params(sys.argv)
bin_defdir = '%s/02.taxon' % const.bin_defdir
mkdir(params['out_dir'])
use_method = params["method"]
pdf_file = params['out_dir'] + "/" + use_method + 'nmds.pdf'
png_file = params['out_dir'] + "/" + use_method + 'nmds.png'
env = Environment(loader=FileSystemLoader(bin_defdir), autoescape=False)
if params['two_legend']:
if params['with_boxplot']:
template = env.get_template("g08_nmds_two.R")
else:
template = env.get_template("g08_nmds_two.R")
else:
if params['with_boxplot']:
template = env.get_template("g08_nmds_with_boxplot.R")
else:
template = env.get_template("g08_nmds.R")
Rtxt = template.render(tool_default_dir = const.tool_defdir,\
profile_table=params['profile_table'],\
group_file =params['group_file'],\
pdf_file = pdf_file,\
method = use_method)
with open("%s/nmds.R" % params["out_dir"], "w") as fqout:
fqout.write(Rtxt)
Rrun("%s/nmds.R" % params["out_dir"])
parser.set_defaults(paired=False)
args = parser.parse_args()
params = vars(args)
params['paired'] = judge(params['paired'])
return params
if __name__ == '__main__':
reload(sys)
sys.setdefaultencoding('utf8')
params = read_params(sys.argv)
tool_default_dir = const.tool_default_dir
out_dir = params["out_dir"]
profile_table = params["profile_table"]
group_file = params["group_file"]
use_mothed = params["test"]
mkdir(out_dir)
env = Environment(loader=FileSystemLoader(tool_default_dir),autoescape=False)
template = env.get_template("t08_diff.R")
Rtext = template.render(tool_default_dir = tool_default_dir,\
profile_table=profile_table,\
group_file=group_file,\
out_dir = out_dir,\
mothed=use_mothed,\
p_cutoff=params["cutoff"],\
fdr=params["fdr"],\
paired = params['paired'])
with open("%s/diff.R"%out_dir,"w") as fqw:
fqw.write(Rtext)
Rrun("%s/diff.R"%(out_dir))
help="set the group file")
parser.add_argument('-o', '--out_dir', dest='out_dir', metavar='FILE', type=str, required=True,
help="set the out dir")
parser.add_argument('-f', '--file_name', dest='file_name', metavar='FILE', type=str, required=True,
help="set the file name")
parser.add_argument('--num', dest='num', metavar='NUM', type=int, required=True,
help="set the num * profile")
args = parser.parse_args()
params = vars(args)
return params
if __name__ == '__main__':
reload(sys)
sys.setdefaultencoding('utf8')
params = read_params(sys.argv)
bin_default_dir = const.bin_default_dir
bin_kegg_default_dir = "%s/07.kegg/"%(bin_default_dir)
mkdir(params['out_dir'])
txt_file = "%s/%s"%(params['out_dir'],params["file_name"])
env = Environment(loader=FileSystemLoader(bin_kegg_default_dir), autoescape=False)
template = env.get_template("708_sample2profile.R")
Rtxt = template.render(profile_table=params['profile_table'], \
group_file=params['group_file'], \
txt_file=txt_file,\
num=params["num"])
with open("%s/708_sample2profile.R" % (params["out_dir"]), "w") as fqout:
fqout.write(Rtxt)
Rrun("%s/708_sample2profile.R" % params["out_dir"], )
os.system("sed -i '1s/^/ko_num\t/g' %s"%txt_file)
help='set group file')
args = parser.parse_args()
params = vars(args)
return params
if __name__ == '__main__':
params = read_params(sys.argv)
bin_default_dir = const.bin_default_dir
out_dir = params['out_dir']
profile_table = params['profile_table']
pdf_file = out_dir + "top.pdf"
png_file = out_dir + "top.png"
group_file = params['group_file']
vars = {
'group_file': group_file,
'pdf_file': pdf_file,
"profile_table": profile_table
}
env = Environment(loader=FileSystemLoader("%s/02.taxonomy/" %
bin_default_dir),
autoescape=False)
template = env.get_template("g03_top_boxplot.R")
Rtext = template.render(tool_default_dir=const.tool_default_dir,\
group_file=group_file,\
pdf_file = pdf_file,\
profile_table = profile_table)
with open(out_dir + 'top_boxplot.R', 'w') as fp:
fp.write(Rtext)
Rrun("%s/top_boxplot.R" % out_dir)
