if __name__ == "__main__":
import sys
if len(sys.argv) != 2:
print("Usage: python MMCIF2Dict filename.")
filename = sys.argv[1]
mmcif_dict = MMCIF2Dict(filename)
entry = ""
print("Now type a key ('q' to end, 'k' for a list of all keys):")
while (entry != "q"):
entry = _input("MMCIF dictionary key ==> ")
if entry == "q":
sys.exit()
if entry == "k":
for key in mmcif_dict:
print(key)
continue
try:
value = mmcif_dict[entry]
if isinstance(value, list):
for item in value:
print(item)
else:
print(value)
except KeyError:
print("No such key found.")
def lastrebasefile(self):
"""BD.lastrebasefile() -> None.
Check the emboss files are up to date and download them if they are not.
"""
embossnames = ('emboss_e', 'emboss_r', 'emboss_s')
#
# first check if we have the last update:
#
emboss_now = ['.'.join((x, LocalTime())) 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 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']:
updt = RebaseUpdate(self.rebase_pass, self.proxy)
updt.openRebase()
updt.getfiles()
updt.close()
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:
pass
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, name + '.%s' % number) for name in embossnames]
strmess = '\nLast EMBOSS files found are :\n'
try:
for name, 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
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, LocalTime())) 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 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']:
updt = RebaseUpdate(self.proxy)
updt.openRebase()
updt.getfiles()
updt.close()
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:
pass
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
if __name__=="__main__":
import sys
if len(sys.argv)!=2:
print("Usage: python MMCIF2Dict filename.")
filename=sys.argv[1]
mmcif_dict = MMCIF2Dict(filename)
entry = ""
print("Now type a key ('q' to end, 'k' for a list of all keys):")
while(entry != "q"):
entry = _input("MMCIF dictionary key ==> ")
if entry == "q":
sys.exit()
if entry == "k":
for key in mmcif_dict:
print(key)
continue
try:
value=mmcif_dict[entry]
if isinstance(value, list):
for item in value:
print(item)
else:
print(value)
except KeyError:
print("No such key found.")