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parallel_blat_python.py
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parallel_blat_python.py
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import subprocess
import os
import pdb
import math
import run_parallel_cmds
def cut_file(in_name,out_name,line_start,line_end):
os.system('awk \'NR > ' + str(line_end) + ' { exit } NR >= ' + str(line_start) + '\' '+ in_name + ' > ' + out_name )
def parallel_blat(target_fasta,query_fasta,out_file,QUERY_SPLIT,nJobs=20):
'''Function takes in target,query and output file. parallelizes blat by running GNU parallel
- Currently only parallelizes on query space
- Also assumes that query fasta file takes two lines per sequence (not wrapped)'''
target_length = float(subprocess.check_output('grep -c \'>\' ' + target_fasta,shell=True))
query_length = float(subprocess.check_output('grep -c \'>\' ' + query_fasta,shell=True))
os.system( 'awk \'/^>/{print s? s"\\n"$0:$0;s="";next}{s=s sprintf("%s",$0)}END{if(s)print s}\' ' +query_fasta + ' > '+ query_fasta +'_nospace')
#os.system( 'awk \'/^>/{print s? s"\\n"$0:$0;s="";next}{s=s sprintf("%s",$0)}END{if(s)print s}\' ' +target_fasta + ' > '+ target_fasta)
query_fasta = query_fasta + '_nospace'
#TARGET_SPLIT = 1
#QUERY_SPLIT = 4
#Alernately
#QUERY_SPLIT = min(int(math.ceil(float(query_length)/float(target_length))),50)
#QUERY_SPLIT = max(int(math.ceil(float(query_length)/float(target_length))),500)
#QUERY_SPLIT = int(min(QUERY_SPLIT,query_length))
#QUERY_SPLIT= 100
#pdb.set_trace()
print('Query length: ' +str(query_length) + ' Target length: ' + str(target_length) + ' Query Split: ' + str(QUERY_SPLIT))
split_size = int(math.floor(float(query_length)/QUERY_SPLIT))
'''if split_size % 2 !=0:
split_size +=1'''
'''if query_length <= float(target_length):
print('Cannot parallelize on query. Running Vanilla Blat')
os.system('blat -noHead ' + target_fasta + ' ' + query_fasta + ' ' + out_file)
return'''
for n in range(QUERY_SPLIT):
if n==QUERY_SPLIT-1:
cut_file(query_fasta,query_fasta+'_'+str(n+1),2*(n)*split_size+1,2*query_length)
else:
cut_file(query_fasta,query_fasta+'_'+str(n+1),2*(n)*split_size+1,2*(n+1)*split_size)
#pdb.set_trace()
q_range = range(QUERY_SPLIT)
x = [int(i)+1 for i in q_range]
q_str = " ".join(map(str,x))
os.system('rm ' + out_file + '_*' )
cmds = []
for a in x:
cmds.append('blat -noHead '+ target_fasta + ' ' + query_fasta + '_' + str(a)+ ' ' + out_file + '_' + str(a))
#print('blat -noHead '+ target_fasta + ' ' + query_fasta + '_' + str(a)+ ' ' +out_file + '_' + str(a))
cmds = tuple(cmds)
run_parallel_cmds.run_cmds(cmds,nJobs)
#print('parallel blat -noHead ' + target_fasta + ' ' + query_fasta + '_{} ' +out_file + '_{} ::: ' + q_str )
#os.system('time parallel blat -noHead ' + target_fasta + ' ' + query_fasta + '_{} ' +out_file + '_{} ::: ' + q_str )
#os.system('parallel blat ' + target_fasta + ' ' + query_fasta + '_{} ' +out_file + '_{} ::: {1..' + str(QUERY_SPLIT) + '}' )
#os.system('sort -k 10 ' + out_file + '_* > ' + out_file)
os.system('cat ' + out_file + '_* > ' + out_file)
os.system('rm ' + out_file + '_*' )
os.system('rm ' + query_fasta + '_*' )
def main():
import sys
args = sys.argv[1:]
nJobs=20
if '--nJobs' in args:
ind1 = args.index('--nJobs')
nJobs = int(args[ind1+1])
args = args[:ind1]+args[ind1+1:]
Query_split = 100
parallel_blat(args[0],args[1],args[2],Query_split, nJobs)
if __name__ == '__main__':
main()