mapping to NCTC assembly done

map_to_nctc_assemblies.py

@@ -0,0 +1,47 @@
+#!/usr/bin/python
+
+import sys
+import os
+import subprocess
+
+bact_id = sys.argv[1]
+path_to_hinge = sys.argv[2]
+
+base_path='data/'+bact_id+"/"
+
+st_point = 0
+if len(sys.argv) > 3:
+    st_point = int(sys.argv[3])
+
+old_fasta_name = bact_id+'_hgap.fasta'
+hgap_db_name = bact_id+'_hgap'
+db_name = bact_id
+fasta_name = bact_id+'_hgap_pb.fasta'
+laname = hgap_db_name + "." +  db_name + '.las'
+
+if st_point <= 1:
+    subprocess.call("python "+path_to_hinge+"scripts/correct_head.py  "+ old_fasta_name+" "+ fasta_name+ " hgapgt.txt",shell=True,cwd=base_path)
+    subprocess.call("rm -f *_hgap.db",shell=True,cwd=base_path)
+    fasta2DB_cmd = "fasta2DB "+hgap_db_name+' '+fasta_name
+    print fasta2DB_cmd
+    subprocess.check_output(fasta2DB_cmd.split(),cwd=base_path)
+
+if st_point <= 2:
+    subprocess.call("rm -f *_hgap.*.las",shell=True,cwd=base_path)
+    mapper_cmd = "HPCmapper "+hgap_db_name+" "+db_name
+    print mapper_cmd
+    mapper_shell_cmd = "csh -v mapper_cmdf.sh"
+    p = subprocess.call(mapper_cmd.split(),stdout=open(base_path+'mapper_cmdf.sh','w') , cwd=base_path)
+    p2 = subprocess.check_output(mapper_shell_cmd.split(), cwd=base_path)
+
+if st_point <= 3:
+    rename = hgap_db_name + "*." +  db_name + '*.las'
+    LAmerge_cmd = "LAmerge "+laname+" "+rename
+    print LAmerge_cmd
+    subprocess.check_output(LAmerge_cmd,cwd=base_path,shell=True)
+
+if st_point <= 4:
+    mp_cmd = "python "+path_to_hinge+"scripts/run_mapping2.py "+hgap_db_name+" "+db_name+" "+laname+' 1-$ 4'
+    print mp_cmd
+    subprocess.check_output(mp_cmd, cwd=base_path, shell=True)
+

map_wrapper.py

@@ -0,0 +1,26 @@
+import numpy as np
+import os
+import multiprocessing as mp
+import subprocess
+import sys
+
+base_path = 'data/'
+
+#file_list = np.loadtxt('/data/pacbio_assembly/notebook/files_assembled.txt',dtype='str')
+
+file_list = np.loadtxt('NCTC_names.txt',dtype='str')
+path_to_hinge = sys.argv[1]
+
+num_proc = 1
+if len(sys.argv) > 2:
+    num_proc = int(sys.argv[2])
+
+
+def run_pipeline(flname):
+    base_dir = base_path + flname + '/'
+    base_cmd = 'python map_to_nctc_assemblies.py '+ flname +' '+ path_to_hinge
+    print base_cmd
+    subprocess.call(base_cmd, shell=True)
+
+pool = mp.Pool(processes=num_proc)
+pool.map(run_pipeline,file_list)