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Dont write in code directory #8

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Dont write in code directory #8

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b5e99e0
Don't write dbname.txt file.
duncanparkes Sep 7, 2016
1b56293
Allow configuring the log directory.
duncanparkes Sep 7, 2016
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34 changes: 24 additions & 10 deletions minUP.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,11 +76,14 @@
config_file = os.path.join(os.path.sep, \
os.path.dirname(os.path.realpath('__file__' \
)), 'minup_posix.config')
logfolder = os.path.join(os.path.sep, \
os.path.dirname(os.path.realpath('__file__' \
)), 'minup_run_logs')
VALID_REF_DIR = os.path.join(os.path.sep, \
os.path.dirname(os.path.realpath('__file__')), \

default_log_dir = os.path.join(
os.path.sep,
os.path.dirname(os.path.realpath('__file__')),
'minup_run_logs',
)
VALID_REF_DIR = os.path.join(os.path.sep,
os.path.dirname(os.path.realpath('__file__')),
'valid_reference_fasta_files')
BWA_INDEX_DIR = os.path.join(os.path.sep, \
os.path.dirname(os.path.realpath('__file__')), \
Expand All @@ -94,9 +97,13 @@
if OPER is 'windows':
config_file = os.path.join(os.path.sep, sys.prefix,
'minup_windows.config')
logfolder = os.path.join(os.path.sep, sys.prefix,
'minup_run_logs')
VALID_REF_DIR = os.path.join(os.path.sep, sys.prefix, \

default_log_dir = os.path.join(
os.path.sep,
sys.prefix,
'minup_run_logs',
)
VALID_REF_DIR = os.path.join(os.path.sep, sys.prefix,
'valid_reference_fasta_files')
BWA_INDEX_DIR = os.path.join(os.path.sep, sys.prefix, \
'bwa_indexes')
Expand Down Expand Up @@ -434,6 +441,14 @@
version=('%(prog)s version={version}').format(version=__version__),
)

parser.add_argument(
'-logdir',
'--log-directory',
help='Directory where munUP will write its logs.',
default=default_log_dir,
dest='logdir',
)

#-------------------------------------------------------------------------------

args = parser.parse_args()
Expand All @@ -448,8 +463,7 @@
BWA_INDEX_DIR = REF_DIR + '/gbwa.indexes/'
LAST_INDEX_DIR = REF_DIR + '/glast.indexes/'



logfolder = args.logdir

if not os.path.exists(logfolder):
os.makedirs(logfolder)
Expand Down
6 changes: 0 additions & 6 deletions modules/checkRead.py
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Original file line number Diff line number Diff line change
Expand Up @@ -271,12 +271,6 @@ def check_read(
print 'Making new database: ', dbname
print '='*80
sys.stdout.flush()
dbF = open('dbname.txt','w')
dbF.write(dbname+"\n")
dbF.close()




sql = 'CREATE DATABASE %s' % dbname
cursor.execute(sql)
Expand Down