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#!/usr/bin/python3
import sys
import os
import subprocess
bact_name = "ecoli"
if len(sys.argv) >= 2:
bact_id = sys.argv[1]
st_point = 0
if len(sys.argv) >= 3:
st_point = int(sys.argv[2])
base_path='/data/pacbio_assembly/pb_data/NCTC/'+bact_id+"/"
if len(sys.argv) >= 4:
base_path = sys.argv[3]
fasta_names = [x for x in os.listdir(base_path) if x.endswith('.fasta')]
assert len(fasta_names)==1
fasta_name = fasta_names[0]
bact_name = fasta_name.split('.fasta')[0]
print(bact_name)
if st_point <= 1:
subprocess.call("rm -f *.db",shell=True,cwd=base_path)
fasta2DB_cmd = "fasta2DB "+bact_name+' '+base_path+fasta_name
print(fasta2DB_cmd)
subprocess.check_output(fasta2DB_cmd.split(),cwd=base_path)
if st_point <= 2:
DBsplit_cmd = "DBsplit -x500 -s100 "+bact_name
print(DBsplit_cmd)
subprocess.check_output(DBsplit_cmd.split(),cwd=base_path)
if st_point <= 3:
subprocess.call("rm -f *.las",shell=True,cwd=base_path)
daligner_cmd = "HPCdaligner -t5 "+bact_name
daligner_shell_cmd = "csh -v daligner_cmd.sh"
print(daligner_cmd)
p = subprocess.call(daligner_cmd.split(),stdout=open(base_path+'daligner_cmd.sh','w') , cwd=base_path)
p2 = subprocess.check_output(daligner_shell_cmd.split(), cwd=base_path)
if st_point <= 4:
remove_cmd = "rm "+base_path+bact_name+".*."+bact_name+".*"
print(remove_cmd)
os.system(remove_cmd)
if st_point <= 5:
LAmerge_cmd = "LAmerge "+bact_name+".las "+bact_name+".*.las"
print(LAmerge_cmd)
subprocess.check_output(LAmerge_cmd,cwd=base_path,shell=True)
if st_point <= 6:
remove_cmd2 = "rm "+base_path+bact_name+".*.las"
os.system(remove_cmd2)
if st_point <= 7:
os.system("mkdir -p "+base_path+"log")
if st_point <= 8:
DASqv_cmd = "DASqv -c100 "+bact_name+" "+bact_name+".las"
subprocess.check_output(DASqv_cmd.split(),cwd=base_path)
if st_point <= 9:
Reads_filter_cmd = "Reads_filter --db "+bact_name+" --las "+bact_name+".las -x "+bact_name+" --config ~/AwesomeAssembler/utils/nominal.ini"
print(Reads_filter_cmd)
subprocess.check_output(Reads_filter_cmd,cwd=base_path, shell=True)
if st_point <= 10:
hinging_cmd = "hinging --db "+bact_name+" --las "+bact_name+".las -x "+bact_name+" --config ~/AwesomeAssembler/utils/nominal.ini -o "+bact_name
print(hinging_cmd)
subprocess.check_output(hinging_cmd, cwd=base_path, shell=True)
if st_point <= 11:
pruning_cmd = "python3 /usr/lib/hinge/pruning_and_clipping.py "+bact_name+".edges.hinges "+bact_name+".hinge.list A"
print(pruning_cmd)
subprocess.check_output(pruning_cmd, cwd=base_path, shell=True)
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