ich habe folgende Bitte. Der obere Teil klappt einwandfrei (run maketemplatedb script). Im unteren Teil bekomme ich folgende Fehlermeldung (s. unter dem Code).
Ich bin mir nicht sicher wie ich das lösen kann. Hat einer von euch eine Idee ?
Code: Alles auswählen
#!~/Desktop/Python-2.7
# coding: utf8
import os
import subprocess
def open_source_tools_KmerFinder():
base_path = '/mnt/vault/tmp/until_2016_01_01/florian'
python27_path = '/home/falsheim/Desktop/Python-2.7/'
# paths to the folders
open_KmerFinder = os.path.join(base_path, 'KmerFinder/genomicepidemiology-kmerdb-077ba38a546a')
trimmed_reads_path = os.path.join(base_path,'trimmed_seq_salmonella_normal_20percentage')
open_python27 = os.path.join(python27_path, 'python')
# run maketemplatedb python script (Kmer Finder 2.0)
combine_ref = os.path.join(open_KmerFinder,'Salmonella_subset.fa')
cmd = ([open_python27, 'maketemplatedb.py', '-i', combine_ref , '-x', '"ATGAC"', '-k', '16', '-o', 'batch.ATGAC'])
print " ".join(cmd)
p = subprocess.Popen(cmd)
out, err = p.communicate()
print out
print err
# run findtemplatedb python script (Kmer Finder 2.0)
for trim in os.listdir(trimmed_reads_path,trim):
combine_trimmed_reads = os.path.join(trimmed_reads_path,trim)
with open(trim + '.xls', 'w') as fout:
cmd = ([open_python27 ,'findtemplatedb.py', '-i', combine_trimmed_reads, '-t', 'batch.ATGAC', '-x', '"ATGAC"'])
print " ".join(cmd)
p = subprocess.Popen(cmd, stdout = fout)
out, err = p.communicate()
print out
print err
open_source_tools_KmerFinder()
Fehlermeldung:
[falsheimer@thirty-two genomicepidemiology-kmerdb-077ba38a546a]$ python open_source_tools_KmerFinder.py
/home/falsheim/Desktop/Python-2.7/python maketemplatedb.py -i /mnt/vault/tmp/until_2016_01_01/florian/KmerFinder/genomicepidemiology-kmerdb-077ba38a546a/Salmonella_subset.fa -x "ATGAC" -k 16 -o batch.ATGAC
Traceback (most recent call last):
File "open_source_tools_KmerFinder.py", line 45, in <module>
open_source_tools_KmerFinder()
File "open_source_tools_KmerFinder.py", line 25, in open_source_tools_KmerFinder
p = subprocess.Popen(cmd)
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Danke schonmal.
VG Flo
