import numpy as np
from scipy.stats import fisher_exact, mannwhitneyu
from zopy.utils import qw, say
from zopy.fdr import pvalues2qvalues as apply_fdr
#-------------------------------------------------------------------------------
# constants
#-------------------------------------------------------------------------------
c_eps = 1e-20
c_fisher_fields = qw("""
term
overlap
expected_overlap
fold_enrichment
p_value
q_value
""")
c_rank_fields = qw("""
term
overlap
overlap_median
background_median
p_value
q_value
""")
# ---------------------------------------------------------------
# helper classes
from __future__ import print_function
from zopy.utils import qw
from zopy.table import Table
T1 = qw("""
+ 1 2 3 4 5
A 0 1 0 0 1
B 1 0 0 1 0
C 0 1 1 0 1
D 1 0 1 1 0
""")
with open("temp.txt", "w") as fh:
for l in T1:
print(l.replace(" ", "\t"), file=fh)
"""
print( "\nTest loading from a nested list" )
aa = [
["!", "1", "2"],
["A", "X", "Y"],
]
T = Table( aa )
T.write( )
print( "\nTest loading from a nested dict" )
dd = {
"A":{"1":"1", "2":"0"},
"B":{"2":"0", "3":"1"},
}
T = Table( dd )
import argparse
from collections import Counter
from zopy.utils import path2name, warn, qw
from zopy.dictation import polymap, col2dict
# ---------------------------------------------------------------
# constants
# ---------------------------------------------------------------
ALLOW_CROSSTALK = False
c_prop_pattern = r"^([^\s]*?): (.*)"
c_goid_pattern = r"(GO:[0-9]+)"
c_namespace_convert = qw("""
biological_process BP
molecular_function MF
cellular_component CC
""",
as_dict=True)
c_relationship_subtypes = qw("""
part_of
#regulates
#positively_regulates
#negatively_regulates
""")
c_singular_props = qw("""
id
name
namespace
""")
#!/usr/bin/env python
import os
import sys
import argparse
from collections import Counter
from zopy.utils import qw
c_defaults = qw( """
py
R
sh
md
slurm
slurm-template
""" )
# argument parsing (python argparse)
parser = argparse.ArgumentParser()
parser.add_argument( "start", default="." )
parser.add_argument( "--extensions", nargs="+", default=None )
parser.add_argument( "--no-defaults", action="store_true" )
parser.add_argument( "--execute", action="store_true" )
args = parser.parse_args()
# setup extensions
extensions = [] if args.extensions is None else args.extensions
if not args.no_defaults:
extensions += c_defaults
print >>sys.stderr, "Targeting these extensions:", extensions
from zopy.utils import iter_lines, qw
parser = argparse.ArgumentParser( )
parser.add_argument( "input" )
parser.add_argument( "--execute", action="store_true" )
args = parser.parse_args( )
# note: if a prefix is a prefix of another prefix, it must come later in list
prefixes = qw( """
int
float
str
list
dict
set
hash
func
i
f
a
""" )
pre_pattern = "^(" + "|".join( prefixes ) + ")+"
def wordish( char ):
return True if re.search( "[A-Za-z0-9_]", char ) else False
def next_span( text, index ):
start = index
is_word = wordish( text[index] )
while( index < len( text ) and ( is_word == wordish( text[index] ) ) ):
c_max_lab = 50
c_metacmap = "jet"
c_font1 = 7
c_font2 = 8
c_font3 = 10
c_eps = 1e-20
c_str_other = "Other"
c_str_none = "None"
c_other_color = "0.75"
c_none_color = "white"
c_wspans = qw("""
cbar 8
rowtree 3
rowmeta 1
heatmap 24
rownames 12
legend 8
""",
as_dict=True)
c_hspans = qw("""
title 1
coltree 3
colmeta 1
heatmap 16
colnames 6
""",
as_dict=True)
sys.setrecursionlimit(10000)