if args.html:
with open(args.html, "w") as htmlOut:
print >> htmlOut, etree.tostring(html, pretty_print=True)
# Finishing script
logger.info(u"Count Digits Complete!")
if __name__ == '__main__':
# Command line options
args = getOptions()
# Setting logger
logger = logging.getLogger()
if args.debug:
sl.setLogger(logger, logLevel='debug')
else:
sl.setLogger(logger)
# Starting script with the following parameters
logger.info(u"Importing data with following parameters: "\
"\n\tWide: {0}"\
"\n\tDesign: {1}"\
"\n\tUnique ID: {2}"\
"\n\tGroup: {3}"\
"\n\tHtml: {4}".\
format(args.input,args.design, args.uniqID, args.group, args.html))
# Main
main(args)
with PdfPages(args.figure) as pdfOut:
plotVarImportance(data=df_importance, pdf=pdfOut, var=args.num)
# Exporting Transformed data and df_rev data
logger.info('Exporting data to TSV format')
df_transf.to_csv(args.oname, index=False, sep='\t', float_format="%.4f")
df_rev.to_csv(args.oname2, index=False, sep='\t')
if __name__ == '__main__':
# Command line options
args = getOptions()
# Activate Logger
logger = logging.getLogger()
sl.setLogger(logger)
# Starting script
logger.info(u"Importing data with following parameters: "\
"\n\tWide: {0}"\
"\n\tDesign: {1}"\
"\n\tUnique ID: {2}"\
"\n\tGroup Column: {3}".format(args.input, args.design,
args.uniqID, args.group))
# Stablishing color palette
palette = colorHandler(pal=args.palette, col=args.color)
logger.info(u"Using {0} color scheme from {1} palette".format(
args.color, args.palette))
# Getting rid of warnings.
ror_df.to_csv(args.table,
sep="\t",
float_format="%.4f",
index_label=args.uniqID,
columns=["pval", "rsq", "slope"])
ror_flags.df_flags.to_csv(args.flags, sep="\t", index_label=args.uniqID)
if __name__ == "__main__":
# Command line options
args = getOptions()
# Setting up logger
logger = logging.getLogger()
if args.debug:
sl.setLogger(logger, logLevel="debug")
DEBUG = True
else:
sl.setLogger(logger)
# Print logger info
logger.info(u"""Importing data with following parameters:
\tWide: {0}
\tDesign: {1}
\tUnique ID: {2}
\tGroup: {3}
\tRun Order: {4}
\tLevels: {5}
""".format(args.input, args.design, args.uniqID, args.group,
args.order, args.levels))
