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268 lines (222 loc) · 8.5 KB
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#!/usr/bin/python
from __future__ import division
from __future__ import print_function
#from builtins import str
#from builtins import range
#from builtins import object
import sys
import array
import logging
import math
logger = logging.getLogger(__name__)
class Dab(object):
def __init__(self, filename):
self.gene_list = []
self.gene_table = {}
if filename.endswith('.qdab'):
self.open_file(filename, qdab=True)
else:
self.open_file(filename)
self.gene_index = {}
for i in range(len(self.gene_list)):
self.gene_index[self.gene_list[i]] = i
logger.debug("Got %s genes.", len(self.gene_list))
def open_file(self, filename, qdab=False):
logger.debug("Opening %s", filename)
dab_file = open(filename, 'rb')
# get number of genes
a = array.array('I')
a.fromfile(dab_file, 1)
size = a[0]
logger.debug("Expecting %s genes.", size)
# get gene names
start = 4
end = 4
count = 0
while count < size:
dab_file.seek(end)
chrs = dab_file.read(2)
if chrs == b'\x00\x00':
dab_file.seek(start)
gene = dab_file.read(end - start).decode().strip()
gene = gene.replace('\x00', '')
self.gene_list.append(gene)
self.gene_table[gene] = count
start = end + 2
count += 1
end += 1
if not count % 5000 and start == end: # Read 5k and on to next set
logger.debug("Read %s gene names.", count)
end += 1
if qdab:
# get number of bins
dab_file.seek(start)
a = array.array('B')
a.fromfile(dab_file, 1)
nbins = a[0]
logger.debug("Number of bins: %s .", nbins)
start = start + 1
# get the bin boundaries
a = array.array('f')
a.fromfile(dab_file, nbins)
boundaries = a
logger.debug("Bin boundaries: %s .", boundaries)
start = start + 4 * len(boundaries)
# get number of bits (+1 for NaN)
nbits = int(math.ceil(math.log(nbins + 1, 2)))
nan_val = math.pow(2, nbits) - 1
logger.debug("Number of bits for each value: %s .", nbits)
# get half matrix values
total = size * (size - 1) // 2
a = array.array('B')
a.fromfile(dab_file, 1)
bufferA = a[0]
a = array.array('B')
a.fromfile(dab_file, 1)
bufferB = a[0]
iTotal = 0
self.dat = array.array('f')
for i in range(size - 1):
for j in range(0, size - i - 1):
try:
iPos = (iTotal * nbits) % 8
if iPos + nbits > 8:
btmpb = (bufferA << iPos)
btmpf = ((bufferB >> (16 - nbits - iPos))
<< (8 - nbits))
self.dat.append(
(((btmpb | btmpf) & 0x000000FF) >> (8 - nbits)))
bufferA = bufferB
a = array.array('B')
a.fromfile(dab_file, 1)
bufferB = a[0]
else:
self.dat.append(
(((bufferA << iPos) & 0x000000FF) >> (8 - nbits)))
if iPos + nbits == 8:
bufferA = bufferB
a = array.array('B')
a.fromfile(dab_file, 1)
bufferB = a[0]
except:
# check we are reaching the boundary of the file
assert iTotal - len(self.dat) <= 1 + 8 // nbits
iTotal = iTotal + 1
if self.dat[-1] == nan_val:
self.dat[-1] = float('inf')
else:
# get half matrix values
total = size * (size - 1) // 2
dab_file.seek(start)
self.dat = array.array('f')
self.dat.fromfile(dab_file, total)
assert len(self.dat) == total
def get_size(self):
return len(self.gene_list)
def get_gene(self, id):
return self.gene_list[id]
def get_value_genestr(self, gene1, gene2):
g1 = self.get_index(gene1)
g2 = self.get_index(gene2)
if g1 is None or g2 is None:
return None
else:
return self.get_value(g1, g2)
def get_value(self, gene1, gene2):
g1 = min(gene1, gene2)
g2 = max(gene1, gene2)
# index of first id
start = self.arith_sum((len(self.gene_list)) - g1,
(len(self.gene_list) - 1))
start += (g2 - g1) - 1 # index of second id
try:
v = self.dat[int(start)]
except IndexError:
print('Error: ', start, gene1, gene2)
exit()
return v
def get_scaled_value(self, gene1, gene2, prior_new, prior_old):
r = prior_new / prior_old
r_diff = (1 - prior_new) / (1 - prior_old)
weight = self.get_value(gene1, gene2)
return weight * r / (weight * r + (1 - weight) * r_diff)
def get_index(self, gene):
try:
return self.gene_index[gene]
except KeyError:
return None
def arith_sum(self, x, y):
return .5 * (y - x + 1) * (x + y)
def get(self, gene_str):
vals = []
idx = self.get_index(gene_str)
if idx is None:
return vals
for i in range(0, idx):
# Get values from 0 to idx (not including idx)
v = self.get_value(i, idx)
vals.append(v)
# Append self interaction value
vals.append(1)
start = self.arith_sum((len(self.gene_list)) - idx,
(len(self.gene_list) - 1))
vals += self.dat[int(start):int(start) +
len(self.gene_list) - (idx + 1)]
return vals
def print_table(self, out_file=sys.stdout):
cols = ['GENE']
cols.extend(self.gene_list)
print("\t".join(cols), file=out_file)
for i in range(0, self.get_size()):
line = []
line.append(self.gene_list[i])
for j in range(0, i):
v = self.get_value(i, j)
line.append(str(v))
line.append("1")
for j in range(i + 1, self.get_size()):
v = self.get_value(i, j)
line.append(str(v))
print("\t".join(line), file=out_file)
def print_flat(self, out_file=sys.stdout):
for i in range(0, self.get_size()):
for j in range(i + 1, self.get_size()):
print(self.gene_list[i] + '\t' +
self.gene_list[j] + '\t' + str(self.get_value(i, j)),
file=out_file)
if __name__ == '__main__':
from argparse import ArgumentParser
usage = "usage: %(prog)s [options]"
parser = ArgumentParser(prog=usage)
parser.add_argument("-i", "--dab-file", dest="dab", help="DAB file",
metavar="FILE")
parser.add_argument("-o", "--output-file", dest="out",
help="Output file (DAT or PCL)", metavar="FILE")
parser.add_argument("-v", "--verbose", dest="verbose", action='store_true',
help="output debug loglevel")
parser.add_argument('-V', '--version', action='version',
version="%(prog)s dev-unreleased")
args = parser.parse_args()
if args.verbose: # Setup logging at desired level
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.WARNING)
logger.debug("Args: %s", args)
if args.dab is None:
sys.stderr.write("--dab file is required.\n")
sys.exit()
pcl_out = args.out.endswith('.pcl')
dat_out = args.out.endswith('.dat')
if args.out is not None and not pcl_out and not dat_out:
sys.stderr.write("Unknown file format for: " + args.out + "\n")
sys.exit()
dab = dat(args.dab)
if args.out is None:
dab.print_table()
else:
ofile = open(args.out, 'w')
if pcl_out:
dab.print_table(ofile)
elif dat_out:
dab.print_flat(ofile)
ofile.close()