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 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 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}"
