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)