gungorbudak

'use strict';

(function(exports) {

    var rank = {
        /*
         * Standart ranking
         *
         * The MIT License, Copyright (c) 2014 Ben Magyar
         */

gungorbudak

# Multiple plot function
#
# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
# - cols:   Number of columns in layout
# - layout: A matrix specifying the layout. If present, 'cols' is ignored.
#
# If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
# then plot 1 will go in the upper left, 2 will go in the upper right, and
# 3 will go all the way across the bottom.
#

gungorbudak

name: a^nb^2nc^3n
source code: |
  input: 'aabbbbcccccc'
  blank: '_'
  start state: start
  table:
    start:
      a: {write: x, R: q1}
      y: {R: start}
      z: {R: start}

gungorbudak

import os
import networkx as nx


WORKDIR = ''
IREFINDEX_FILE = os.path.join(WORKDIR, '9606.mitab.01-22-2018.txt')


def parse_irefindex_alias(alias):
    splits = alias.split('|')

gungorbudak

library(stringr)
read.pc2.gmt <- function(file, organism=9606, datasource='kegg', idtype='hgnc symbol') {
    # utility function to read and parse GMT file
    # provided by Pathway Commons into R
    # i.e. https://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.All.hgnc.gmt.gz
    gmt <- list()
    con <- file(file, open='r')
    for (line in readLines(con)) {
        line_parts <- unlist(strsplit(line, '\t'))
        desc_keys <- c('name', 'datasource', 'organism', 'idtype')