url = "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId="
not_available_list = []
for pdb in pdb_list:
pdb_name = "{0}.pdb".format(pdb)
if not os.path.exists(pdb_name):
pdbid = url+str(pdb)
content = urllib.urlopen(pdbid).read()
if '404 Not Found' in content: not_available_list.append(pdb)
else:
open(pdb_name, "w" ).write(content)
print pdb_name
return not_available_list
def check(not_available_list):
new_list = not_available_list[:]
for pdb in not_available_list:
if os.path.exists('{0}-pdb-bundle.tar.gz'.format(pdb)) or os.path.exists('{0}-pdb-bundle.tar'.format(pdb)):
new_list.remove(pdb)
if new_list:
print "copy and paste the {0} structures below in the rcsb.org download feature (could not be downloaded programatically)".format(len(new_list)) #obtain bundle case
print ",".join(new_list)
if __name__ == "__main__":
help_message(help_msg)
d = read_in('pdb', 'uniprot', 'pre_seq2struc')
pdb_list = [x[:4] for x in d]
not_available_list = save_pdb_file(set(pdb_list))
check(not_available_list)
print_next_step()
except:
line.append('') #no value
continue
if protein_property == 'dosage_tolerance':
line.append(val)
elif val != 0:
line.append(np.log10(val))
else:
line.append(log_zero_list[pp])
line_list.append(line)
return line_list
if __name__ == "__main__":
help_message(help_msg, bool_org_dir=False)
d_org = int2organism()
d_index = initialize_dict('dict')
d_val = initialize_dict('list')
protein_property_list = [
'length', 'abundance', 'evolutionary_rate', 'contact_density',
'PPI_degree', 'dosage_tolerance'
]
log_zero_list = [
-1, -1, -4, 1, -1
] #make into dict #dont log dosage tolerance, already logged for yeast, ecoli is discrete
for organism in organism_list:
pre_d_i = read_in('pdb', 'uniprot', organism=organism)
pre_d_i = collections.OrderedDict(sorted(pre_d_i.items()))
d_index[organism] = {i: pdb for i, pdb in enumerate(pre_d_i)}
help_msg = 'write extra.txt files for ./run --extra/--EXTRA'
import sys, os
CWD = os.getcwd()
UTLTS_DIR = CWD[:CWD.index('proteomevis_scripts'
)] + '/proteomevis_scripts/utlts'
sys.path.append(UTLTS_DIR)
from parse_user_input import help_message
from read_in_file import read_in
from parse_data import organism
from output import writeout
if __name__ == "__main__":
help_message(
help_msg) #need to adjust help message to allow yeast_ecoli case
if organism == 'yeast_ecoli': #dependent on yeast/extra.txt being present
d = read_in('uniprot', 'pdb', organism='ecoli')
d_old = read_in('uniprot', 'pdb', filename='../ecoli/extra.txt')
flag = 'EXTRA'
else:
d = read_in('uniprot', 'pdb')
d_old = read_in(
'uniprot',
'pdb',
filename='../../../0-identify_structure/3-length_check/{0}/{1}'.
format(organism, 'old_seq2struc.txt'))
flag = 'extra'
pdb_list = set(d.items()) - set(d_old.items())
d_output = dict(x for x in pdb_list)
writeout(['uniprot', 'pdb'], d_output, filename='extra')
def run(self, verbose=''):
self.get_all_info()
self.get_best_pdb_chain()
if verbose:
self.print_verbose()
return self.d_output
def prepare_writeout(d_uniprot_pdb, d_proteome):
d_output = {}
for uniprot, pdb in d_uniprot_pdb.iteritems():
d_output[uniprot] = [pdb, d_proteome[uniprot]]
return d_output
if __name__ == '__main__':
args = help_message(help_msg, bool_add_verbose=True)
d_proteome = read_in('Entry',
'Gene names (ordered locus )',
filename='proteome')
uniprot2pdb = UniProt2PDB(d_proteome.keys())
d_uniprot_pdb = uniprot2pdb.run(args.verbose)
d_output = prepare_writeout(d_uniprot_pdb, d_proteome)
filename = 'pre_seq2struc'
writeout(['uniprot', 'pdb', 'oln'],
d_output,
filename="new_{0}".format(filename))
database_update_needed(filename)
if os.path.isdir(path):
make_intermediate_dir(dir1, dir2)
return path
def save_image(d):
for organism, d_pdb in d.iteritems():
for pdb in d_pdb: #first check if image already exists
path = '{0}/{1}.png'.format(get_path(pdb), pdb)
if os.path.exists(path):
continue #already exists. easier to be true than false
get_image(pdb, path, organism)
subprocess.call(
['mv', "{0}0001.png".format(path), "{0}".format(path)]
) #seems that appending frame number to output irreversible since it is a movie
#extra .png because if chain is a number, that info is lost
cmd.quit()
if __name__ == "pymol": #not __main__ cuz running through pymol
d = initialize_dict('dict')
for organism in organism_list:
d[organism] = read_in('pdb', 'uniprot', organism=organism)
save_image(d)
print_next_step()
if __name__ == "__main__":
args = help_message(help_msg,
bool_org_dir=False,
custom_usage=custom_usage)
args): #make this general for all to import
line_list = []
for o in range(len(d_org)):
organism = d_org[o]
total = len(d_index[organism])
for p in range(total):
pdb = d_index[organism][p]
line = [p, pdb, d_translate[organism][pdb]]
line.extend(d_info[organism][pdb])
line.append(int(o))
line_list.append(line)
return line_list
if __name__ == "__main__":
args = help_message(help_msg, bool_add_verbose=True,
bool_org_dir=False) #add verbose option
d_org = int2organism()
d_translate = initialize_dict('dict')
d_index = initialize_dict('dict')
d_info = initialize_dict('dict')
for organism in organism_list:
pre_d_i = read_in('pdb', 'uniprot', organism=organism)
pre_d_i = collections.OrderedDict(sorted(pre_d_i.items()))
d_translate[organism] = pre_d_i
d_index[organism] = {i: pdb for i, pdb in enumerate(pre_d_i)}
d_info[organism] = get_info(organism)
line_list = prepare_sql(d_org, d_translate, d_index, d_info, args)
columns = [