sxv

# usage:
#   python 3reads.py /batch/dir1/ /batch/dir2/        # run all steps on two batches
#   python 3reads.py -2 -3 -loadAndKeep /batch/dir    # run steps 2 and 3 and use STAR --loadAndKeep
#   python 3reads.py /batch/dir1 /batch/dir2/ -13     # run steps 1 and 3 on two batches
import sys, os

base_dir = '/home/sxv/code/s7s/'
MAKE_FASTQ = '%s/make_fastq.sh' % base_dir
ALIGN = '%s/align_smart-3seq.sh' % base_dir
MAKE_EXPRESSION_TABLE = '%s/make_expression_table.R' % base_dir

sxv

import sys

rows = []

for line in open('gene_names.csv'):
  a,b,c = line.replace('\n','').split(',')
  rows.append([a,c])

for file in sys.argv[1:]:
  for i, line in enumerate(open(file)):

sxv

import sys, random

# board is defined as list of 19 land tiles: Forest (4), Sheep (4), Wheat (4), Brick (3), Rocks (3), Desert (1)
def new_board(board=''):
  available = list('ffffsssswwwwbbbrrrd')
  for i in range(19):
    random.shuffle(available)
    board += available.pop()
  return board