def lastrebasefile(self):
"""Check the emboss files are up to date and download them if not."""
embossnames = ("emboss_e", "emboss_r", "emboss_s")
#
# first check if we have the last update:
#
emboss_now = [".".join((x, release_number)) for x in embossnames]
update_needed = False
# dircontent = os.listdir(config.Rebase) # local database content
dircontent = os.listdir(os.getcwd())
base = os.getcwd() # added for biopython current directory
for name in emboss_now:
if name not in dircontent:
update_needed = True
if not update_needed:
#
# nothing to be done
#
print("\n Using the files : %s" % ", ".join(emboss_now))
return tuple(open(os.path.join(base, n)) for n in emboss_now)
else:
#
# may be download the files.
#
print("\n The rebase files are missing or more than one month old."
"\n Would you like to update them before proceeding?(y/n)")
r = input(" update [n] >>> ")
if r in ["y", "yes", "Y", "Yes"]:
get_files()
print("\n Update complete. Creating the dictionaries.\n")
print("\n Using the files : %s" % ", ".join(emboss_now))
return tuple(open(os.path.join(base, n)) for n in emboss_now)
else:
#
# we will use the last files found without updating.
# But first we check we have some file to use.
#
class NotFoundError(Exception):
pass
for name in embossnames:
try:
for file in dircontent:
if file.startswith(name):
break
else:
raise NotFoundError
except NotFoundError:
print(
f"\nNo {name} file found. Upgrade is impossible.\n"
)
sys.exit()
continue
#
# now find the last file.
#
last = [0]
for file in dircontent:
fs = file.split(".")
try:
if fs[0] in embossnames and int(fs[1]) > int(last[-1]):
if last[0]:
last.append(fs[1])
else:
last[0] = fs[1]
else:
continue
except ValueError:
continue
last.sort()
last = last[::-1]
if int(last[-1]) < 100:
last[0], last[-1] = last[-1], last[0]
for number in last:
files = [(name + f".{number}") for name in embossnames]
strmess = "\nLast EMBOSS files found are :\n"
try:
for file in files:
if os.path.isfile(os.path.join(base, file)):
strmess += f"\t{file}.\n"
else:
raise ValueError
print(strmess)
emboss_e = open(os.path.join(base, f"emboss_e.{number}"))
emboss_r = open(os.path.join(base, f"emboss_r.{number}"))
emboss_s = open(os.path.join(base, f"emboss_s.{number}"))
return emboss_e, emboss_r, emboss_s
except ValueError:
continue
def lastrebasefile(self):
"""Check the emboss files are up to date and download them if not."""
embossnames = ('emboss_e', 'emboss_r', 'emboss_s')
#
# first check if we have the last update:
#
emboss_now = ['.'.join((x, release_number)) for x in embossnames]
update_needed = False
# dircontent = os.listdir(config.Rebase) # local database content
dircontent = os.listdir(os.getcwd())
base = os.getcwd() # added for biopython current directory
for name in emboss_now:
if name in dircontent:
pass
else:
update_needed = True
if not update_needed:
#
# nothing to be done
#
print('\n Using the files : %s' % ', '.join(emboss_now))
return tuple(open(os.path.join(base, n)) for n in emboss_now)
else:
#
# may be download the files.
#
print('\n The rebase files are missing or more than one month old.\
\n Would you like to update them before proceeding?(y/n)')
r = _input(' update [n] >>> ')
if r in ['y', 'yes', 'Y', 'Yes']:
get_files()
print('\n Update complete. Creating the dictionaries.\n')
print('\n Using the files : %s' % ', '.join(emboss_now))
return tuple(open(os.path.join(base, n)) for n in emboss_now)
else:
#
# we will use the last files found without updating.
# But first we check we have some file to use.
#
class NotFoundError(Exception):
pass
for name in embossnames:
try:
for file in dircontent:
if file.startswith(name):
break
else:
raise NotFoundError
except NotFoundError:
print("\nNo %s file found. Upgrade is impossible.\n" %
name)
sys.exit()
continue
pass
#
# now find the last file.
#
last = [0]
for file in dircontent:
fs = file.split('.')
try:
if fs[0] in embossnames and int(fs[1]) > int(last[-1]):
if last[0]:
last.append(fs[1])
else:
last[0] = fs[1]
else:
continue
except ValueError:
continue
last.sort()
last = last[::-1]
if int(last[-1]) < 100:
last[0], last[-1] = last[-1], last[0]
for number in last:
files = [(name + '.%s' % number) for name in embossnames]
strmess = '\nLast EMBOSS files found are :\n'
try:
for file in files:
if os.path.isfile(os.path.join(base, file)):
strmess += '\t%s.\n' % file
else:
raise ValueError
print(strmess)
emboss_e = open(os.path.join(base, 'emboss_e.%s' % number),
'r')
emboss_r = open(os.path.join(base, 'emboss_r.%s' % number),
'r')
emboss_s = open(os.path.join(base, 'emboss_s.%s' % number),
'r')
return emboss_e, emboss_r, emboss_s
except ValueError:
continue