def occ_to_roles(roles): """ Convert roles to a dict of roles and the pegs they do :param roles: :type roles: :return: :rtype: """ sv = SAPserver() result = sv.occ_of_role({'-roles' : roles}) return result
def occ_to_roles(roles): """ Convert roles to a dict of roles and the pegs they do :param roles: :type roles: :return: :rtype: """ sv = SAPserver() result = sv.occ_of_role({'-roles': roles}) return result
import sys from servers.SAP import SAPserver server=SAPserver() genomeID = '83333.1' sys.stderr.write("Genome: " + str(genomeID) + "\n") prots = server.all_proteins( {"-id" : genomeID} ) print("protein length " + str(len(prots)))
import sys from servers.SAP import SAPserver server = SAPserver() genomeID = '83333.1' sys.stderr.write("Genome: " + str(genomeID) + "\n") prots = server.all_proteins({"-id": genomeID}) print("protein length " + str(len(prots)))
""" Get a list of neighboring reactions and the number of genomes that have that reaction in it. This will allow us to gapfill our model with some predicted reactions """ import os import string import sys from servers.SAP import SAPserver server=SAPserver() def ascii_clean(s): """Remove non-ascii characters from a string""" return filter(lambda x: x in string.printable, s) def close_genera(genome_name): res = server.all_genomes({'-complete' : True}) close = {} for g in res: if genome_name in res[g]: close[g] = res[g] return close
import sys import os.path from servers.SAP import SAPserver #Make connection by instantiating SAPserver server = SAPserver() def regulon_evidence(genomeID, roles_and_fids, subs_and_fids, subs_and_roles) # Get the regulons in the genome regulons = server.atomic_regulons(genomeID) # Loop through the roles for r in roles_and_fids: # Grab the role name and the fid for the role role = r.keys() fid = r.values() # Loop through the regulons for reg in regulons: # Get the fids in the regulon fids_in_reg = reg.values() # Check if the fid for role is in the regulon if fid in fids_in_reg: # Get the other fids in its subsystem other_fids = [] for s in subs_and_fids: if fid in s.values(): other_fids.append(list((set(s.values) - set(fid))))
import sys import os.path import matplotlib.pyplot as plt from servers.SAP import SAPserver #Make connection by instantiating SAPserver server = SAPserver() genomeID = '83333.1' # Read in the fids and protein sequences fom text file fin = open('pegs_and_seqs.txt', 'r') fids_seqs = {} for line in fin: fields = line.strip().split("\t") fids_seqs[fields[0]] = fields[1] fin.close() print("# of fids: " + str(len(fids_seqs))) # Create file to write out the role:fid:sequence to text file fout = open('role_peg_seq.txt', 'w') # Get the roles and subsystems for all of the fids feature_hash = server.ids_to_subsystems({"-ids": fids_seqs.keys(), "-genome": genomeID}) # Some variables four counting roles and subsystems role_fid_pairs = [] roles_w_fids = [] subs_w_fids = [] roles_per_fid = {} subs_per_fid = {}
import sys from servers.SAP import SAPserver server = SAPserver() genomes = server.all_genomes({'-complete': 1, '-prokaryotic': 1}) print("There are " + str(len(genomes)) + " genomes") sys.exit(0) for genomeID in genomes: sys.stderr.write("Genome: " + genomes[genomeID] + " (" + str(genomeID) + ")\n") prots = server.all_proteins({'-id': genomeID}) print("There are " + str(len(prots)) + " prots") dna = server.ids_to_sequences({'-ids': list(prots.keys())}) print("There are " + str(len(dna)) + " sequences") funcs = server.ids_to_functions({'-ids': list(prots.keys())}) print("There are " + str(len(funcs)) + " functions")
import sys from servers.SAP import SAPserver server=SAPserver() genomes=server.all_genomes({'-complete':1, '-prokaryotic':1}) print("There are ", len(genomes), " genomes") #sys.exit(0) for genomeID in genomes: sys.stderr.write("Genome: " + genomes[genomeID] + " (" + str(genomeID) + ")\n") prots = server.all_proteins({'-id':genomeID}) print("There are ", len(prots), " prots") dna = server.ids_to_sequences({'-ids':list(prots.keys())}) print("There are ", len(dna), " sequences") funcs = server.ids_to_functions({'-ids':list(prots.keys())}) print("There are ", len(funcs), " functions")
import sys from servers.SAP import SAPserver server=SAPserver() genomes = server.all_genomes({'-complete':1, '-prokaryotic':1}) allss = server.all_subsystems(None) ss = list(allss.keys()) ss.sort() subsystems = server.genomes_to_subsystems( {'-ids':list(genomes.keys()), '-all':1} ) gHasSS={} for g in subsystems: gHasSS[g]={} for tpl in subsystems[g]: if tpl[1] == '0': continue gHasSS[g][tpl[0]]=tpl[1] print("", "", *ss, sep='\t') for g in genomes: print(genomes[g], g, sep='\t', end="") for s in ss: if s in gHasSS[g]: print("\t", gHasSS[g][s], end="") else: print("\t", end="") print()