def showSubmissionSizeStatsTable(a, options): print "\\noindent Submitted assembly size stats table\par" print "\\vspace{0.25in}" print "\\rowcolors{1}{tableShade}{white}" print "\\tiny" print "\\begin{tabular}{ | r | c | c | c | c | c | c | c | c | c | }" print "\\hline" print "Category & n & min & 1st Qu. & Median & Mean & 3rd Qu. & Max. & Stdev & Sum\\\\" print "\\hline \\hline" print ( "Scaffolds & %s & %s & %s " "& %s & %s & %s & %s & %s " "& % s \\\\" % ( lgn.prettyInt(int(float(a.sizeStatsScaffold[0]))), lgn.prettyInt(int(float(a.sizeStatsScaffold[1]))), lgn.prettyFloat(float(a.sizeStatsScaffold[2]), 2), lgn.prettyInt(int(float(a.sizeStatsScaffold[3]))), lgn.prettyFloat(float(a.sizeStatsScaffold[4]), 2), lgn.prettyFloat(float(a.sizeStatsScaffold[5]), 2), lgn.prettyInt(int(float(a.sizeStatsScaffold[6]))), lgn.prettyFloat(float(a.sizeStatsScaffold[7]), 2), lgn.prettyInt(int(float(a.sizeStatsScaffold[8]))), ) ) print ( "Contigs & %s & %s & %s " "& %s & %s & %s & %s & %s " "& %s \\\\" % ( lgn.prettyInt(int(float(a.sizeStatsContigs[0]))), lgn.prettyInt(int(float(a.sizeStatsContigs[1]))), lgn.prettyFloat(float(a.sizeStatsContigs[2]), 2), lgn.prettyInt(int(float(a.sizeStatsContigs[3]))), lgn.prettyFloat(float(a.sizeStatsContigs[4]), 2), lgn.prettyFloat(float(a.sizeStatsContigs[5]), 2), lgn.prettyInt(int(float(a.sizeStatsContigs[6]))), lgn.prettyFloat(float(a.sizeStatsContigs[7]), 2), lgn.prettyInt(int(float(a.sizeStatsContigs[8]))), ) ) print "\\hline" print "\\end{tabular}\par" print "\\normalsize" print "\\vspace{0.3in}"
def prettyNumber( n ): """ pretty number takes a float or int and returns a string """ from libGeneral import prettyFloat, prettyInt import re if isinstance( n, str ): pat = re.compile( '^[0-9]+\.[0-9]+$' ) if re.match( pat, n ): return prettyFloat( float(n), 2 ) else: return prettyInt( int(n) ) elif isinstance( n, float ): return prettyFloat( n, 2 ) elif isinstance( n, int ): return prettyInt( n ) else: sys.stderr.write('Error, libGeneral.py: prettyNumber: unexpected type for n: %s' % n.__class__ ) sys.exit(1)
def prettyNumber(n): """ pretty number takes a float or int and returns a string """ from libGeneral import prettyFloat, prettyInt import re if isinstance(n, str): pat = re.compile('^[0-9]+\.[0-9]+$') if re.match(pat, n): return prettyFloat(float(n), 2) else: return prettyInt(int(n)) elif isinstance(n, float): return prettyFloat(n, 2) elif isinstance(n, int): return prettyInt(n) else: sys.stderr.write( 'Error, libGeneral.py: prettyNumber: unexpected type for n: %s' % n.__class__) sys.exit(1)
def showSubstitutionStatsTable(a, options): print "\\noindent SNP stats table\par" print "\\vspace{0.25in}" print "\\rowcolors{1}{tableShade}{white}" print "\\tiny" print "\\begin{tabular}{ | r | c | c | c | c | }" print "\\hline" print "Category & Total & Calls & Correct (bits) & Errors \\\\" print "\\hline \\hline" if len(a.subStatsLower) >= 0 and len(a.subStatsUpper) >= 0: lower = a.subStatsLower upper = a.subStatsUpper print ( "Homozygous & %s -- %s & %s -- %s & %s -- %s & %s -- %s \\\\" % ( lgn.prettyInt(int(lower["totalHomozygous"])), lgn.prettyInt(int(upper["totalHomozygous"])), lgn.prettyInt(int(lower["totalCallsInHomozygous"])), lgn.prettyInt(int(upper["totalCallsInHomozygous"])), lgn.prettyFloat(float(lower["totalCorrectInHomozygous"]), 1), lgn.prettyFloat(float(upper["totalCorrectInHomozygous"]), 1), lgn.prettyInt(int(lower["totalErrorsInHomozygous"])), lgn.prettyInt(int(upper["totalErrorsInHomozygous"])), ) ) print ( "Heterozygous & %s -- %s & %s -- %s & %s -- %s & %s -- %s \\\\" % ( lgn.prettyInt(int(lower["totalHeterozygous"])), lgn.prettyInt(int(upper["totalHeterozygous"])), lgn.prettyInt(int(lower["totalCallsInHeterozygous"])), lgn.prettyInt(int(upper["totalCallsInHeterozygous"])), lgn.prettyFloat(float(lower["totalCorrectInHeterozygous"]), 1), lgn.prettyFloat(float(upper["totalCorrectInHeterozygous"]), 1), lgn.prettyInt(int(lower["totalErrorsInHeterozygous"])), lgn.prettyInt(int(upper["totalErrorsInHeterozygous"])), ) ) print ( "Indel & %s -- %s & %s -- %s & %s -- %s & %s -- %s \\\\" % ( lgn.prettyInt(int(lower["totalInOneHaplotypeOnly"])), lgn.prettyInt(int(upper["totalInOneHaplotypeOnly"])), lgn.prettyInt(int(lower["totalCallsInOneHaplotypeOnly"])), lgn.prettyInt(int(upper["totalCallsInOneHaplotypeOnly"])), lgn.prettyFloat(float(lower["totalCorrectInOneHaplotypeOnly"]), 1), lgn.prettyFloat(float(upper["totalCorrectInOneHaplotypeOnly"]), 1), lgn.prettyInt(int(lower["totalErrorsInOneHaplotypeOnly"])), lgn.prettyInt(int(upper["totalErrorsInOneHaplotypeOnly"])), ) ) print "\\hline" print "\\end{tabular}\par" print "\\normalsize" print "\\vspace{0.3in}"