def pVal4mari(tabPath,tTx,tTxDN,tTxUP):
"""
tTx= total transcripts,
tTxUP= total Tx sig up Reg
tTxDN= total Tx sig dwn reg,
Takes named tuple data table in format:
type,total,down,up,tDE
Returns list of pValues in format:
[(type1,pVal_dwn1,pVal_up1,pVal_tde1),
...,
(typeN,pVal_dwnN,pVal_upN,pVal_tdeN)]
"""
from scipherSrc.defs.files_io import tableFile2namedTuple
from scipy.stats import hypergeom
def cHgPvl(x,M,n,N):
"""
x=randVar
M=popSize
n=totalSuccesses
N=samplSize
"""
return 1-hypergeom.cdf(x,M,n,N)+hypergeom.pmf(x,M,n,N)
namdTup = tableFile2namedTuple(tabPath,sep=',')
rData = []
for i in range(len(namdTup)):
t = namdTup[i]
pDwn = cHgPvl(int(t.down),tTx,int(t.total),tTxDN)
pUp = cHgPvl(int(t.up),tTx,int(t.total),tTxUP)
pDE = cHgPvl(int(t.tDE),tTx,int(t.total),(tTxDN+tTxUP))
rData.append((t.type,pDwn,pUp,pDE))
return rData
help="""REQUIRED - Exact Title of Column holding the name of the chrom on which each block resides. Exp: name -or- Chromosome/plasmid (default=%default)""")
parser.add_option('--strand',dest="strand",type="str", default=None,
help="""Exact Title of Column holding the strand indicator. Exp: strand. If None: all will be assigned '+' strand. (default=%default)""")
parser.add_option('--thkStrt',dest="thkStrt",type="str", default=None,
help="""Exact Title of Column holding the position of the thickStart. Exp: start_of_coding (default=%default)""")
parser.add_option('--thkEnd',dest="thkEnd",type="str", default=None,
help="""Exact Title of Column holding the position of the thickEnd. Exp: end_of_coding (default=%default)""")
parser.add_option('--rgb',dest="rgb",type="str", default="0,0,0",
help="""Space-less string to assign the color for this track. Exp: 0,0,0=black; 255,0,0=red; 0,255,0=green; 0,0,255=blue (default=%default)""")
parser.add_option('--cigars',dest="cigars",type="str", default=False,
help="""Exact Title of Column holding the cigar strings. Exp: cigar_string (default=%default)""")
cigTypes = ['ensembl','exonerate']
parser.add_option('--cigar-type',dest="cigar_type",type="str", default=False,
help="""Type of cigar string. REQUIRED when using '--cigars'. Options: %s (default=%default)""" % (cigTypes))
(opts, args) = parser.parse_args()
if len(args) != 1:
parser.print_help()
exit()
features = tableFile2namedTuple(args[0],sep=opts.sep)
rowsByAlgn = groupFeatureAlignments(features,opts)
print """track name=%s description="%s" useScore=0""" % (opts.track_name, opts.description)
for alnmnt in rowsByAlgn:
printBEDline(rowsByAlgn[alnmnt],opts)
dest="cigars",
type="str",
default=False,
help=
"""Exact Title of Column holding the cigar strings. Exp: cigar_string (default=%default)"""
)
cigTypes = ['ensembl', 'exonerate']
parser.add_option(
'--cigar-type',
dest="cigar_type",
type="str",
default=False,
help=
"""Type of cigar string. REQUIRED when using '--cigars'. Options: %s (default=%default)"""
% (cigTypes))
(opts, args) = parser.parse_args()
if len(args) != 1:
parser.print_help()
exit()
features = tableFile2namedTuple(args[0], sep=opts.sep)
rowsByAlgn = groupFeatureAlignments(features, opts)
print """track name=%s description="%s" useScore=0""" % (opts.track_name,
opts.description)
for alnmnt in rowsByAlgn:
printBEDline(rowsByAlgn[alnmnt], opts)