def call_on_real_families(paths, splitword):
#if not path:
#path = "D:\Gal\MultiCrisper\Eilon familis\gray one\Solyc05g009500.2.1.txt-format.holeGenomeWithExtars-s2pN\_sites.txt"
genes_sg_dict = {}
sg_genes_dict = {}
sgNames = []
sgList = []
for p in paths:
f = open(p)
res = []
for line in f:
if line[0] != ">":
res += [line[:-4]]
f.close()
gene_name = p.split(".txt")[0]
gene_name = gene_name.split(splitword)[1]
genes_sg_dict[gene_name] = res
for sg in res:
if sg in sg_genes_dict:
sg_genes_dict[sg] = sg_genes_dict[sg] + [gene_name]
else:
sg_genes_dict[sg] = [gene_name]
if sg not in sgNames:
sgNames.append(sg)
sgList.append(sg)
print(bottemsUpAlgorithm.call_it_all(sgList, sgNames, sg_genes_dict))
def call_it_all_wighted(genesList, genesNames, input_sg_genes_dict,
input_genes_sg_dict, Omega, protodist_outfile,
pylip_temps_path):
upgmaTree, distance_matrix = return_UPGMA(
genesList, genesNames, protodist_outfile,
pylip_temps_path) #to uncomment when using wighted
bottemsUpAlgorithm.fill_leaves_sets(
upgmaTree
) # as apposed to the intermediate algorithem, here leaves are genes
fill_sg_genes_dict(input_sg_genes_dict)
fill_genes_sg_dict(input_genes_sg_dict)
#making the sgList for Algorithm B:
sgList = list(input_sg_genes_dict.keys())
sgNames = copy.deepcopy(sgList)
best_permutations_DS = bottemsUpAlgorithm.call_it_all(
sgList, sgNames, input_sg_genes_dict, Omega, df_targets
) ##call_it_all(sgList, sgNames, input_sg_genes_dict, Omega)## Naive.find_Uno_sgRNA(current
best_permutations_DS.sort(
key=lambda item: len(item[3]),
reverse=True) # or (len(item[2]) and item[1])) . sort for the print
res = find_w_set_cover(
best_permutations_DS,
distance_matrix) ##if the output of the intermadiante is wanted
return res
def bottem_up(node, current_sg_genes_dict, current_genes_sg_dict, sgList,
sgNames, Omega):
'''caling the buttoms up algorithem with a sg genes dict sutable for the subtree'''
if node.colour == 'b':
return
##making the genes_sg dict for this subtree and the sg_genes_dict to send to the intermadiate algorithm
if not (current_sg_genes_dict):
current_sg_genes_dict = {}
if not (current_genes_sg_dict):
current_genes_sg_dict = {}
if not (sgList):
sgList = []
if not (sgNames):
sgNames = []
for leaf in node.leaves_DS: ##leaf here is a gene. taking only the relevant genes
current_genes_sg_dict[leaf.name] = genes_sg_dict[leaf.name]
##filling the sg genes dict
for sg in current_genes_sg_dict[leaf.name]:
current_sg_genes_dict[sg] = sg_genes_dict[
sg] ##the checking if this sg is already in the dict just be more expensive overall
if sg not in sgList:
sgList.append(sg)
sgNames.append(sg)
##second, find the key sequence##
current_res = None
if len(current_genes_sg_dict) < 2: #only one gene
current_best_perm, lowest_of_widest = bottemsUpAlgorithm.find_best_sg_for_single_gene(
leaf.name,
sgList) #lowest_of_widest is not in use in this function
else:
#get the set cover from the bottem up algorithm
current_res = bottemsUpAlgorithm.call_it_all(
sgList, sgNames, current_sg_genes_dict, Omega
) ##call_it_all(sgList, sgNames, input_sg_genes_dict, Omega)## Naive.find_Uno_sgRNA(current_genes_sg_dict, Omega) #current best perm is a tuple with the perm and metedata of this perm
current_best_perm = current_res[
0] #the best sg at the current set cover
if current_res == None:
return
global best_permutations_DS
if (current_res):
#remove unnided candidates from the current_res
remove_unrelevant_candidates(current_res)
#continue
best_permutations_DS += current_res ##if there is set cover also at the bottemsUpAlgorithm
else:
best_permutations_DS += [current_best_perm]
node.set_colour('b')
##continue up##
if (node.parent) and not (stopping_condition(current_best_perm)):
bottem_up(node.parent, current_sg_genes_dict, current_genes_sg_dict,
sgList, sgNames,
Omega) ##this line is adopted to the rapper algorithm
def call_using_CasSites(dirp,
Omega=0.11,
min_length=20,
max_length=20,
start_with_G=False,
on_redundant=False,
redundant_genes=[]):
'''in dirp will be a list files. In each there will be a sequences in FASTA format'''
#genes_list = []
genes_sg_dict = {}
sg_genes_dict = {}
sgNames = []
sgList = []
for p in os.listdir(dirp):
#if p[-11:-1]== "RNAfile.tx": ##g gene file
if "RNAfile.tx" in p:
gene_name = p.split(".txt")[0]
#print(gene_name)
if (on_redundant):
if gene_name not in redundant_genes:
continue
f = open(dirp + "\\" + p)
next(f)
gene = f.read()
gene.replace('/n', '')
#oledr version:
#for line in f: #only 1 line left
#genes_list.append(gene_name,line)
# gene = line.rstrip()
f.close()
genes_sg_dict[gene_name] = CasSites.get_sites(
gene, min_length, max_length, start_with_G)
for sg in genes_sg_dict[gene_name]:
if sg in sg_genes_dict:
sg_genes_dict[sg] = sg_genes_dict[sg] + [gene_name]
else:
sg_genes_dict[sg] = [gene_name]
if sg not in sgNames:
sgNames.append(sg)
sgList.append(sg)
return (bottemsUpAlgorithm.call_it_all(sgList, sgNames, sg_genes_dict,
Omega))
def call_it_all(genesList,
genesNames,
input_sg_genes_dict,
input_genes_sg_dict,
Omega,
protodist_outfile,
pylip_temps_path,
df_targets,
cfd_dict=None,
PS_number=12):
fill_sg_genes_dict(input_sg_genes_dict)
fill_genes_sg_dict(input_genes_sg_dict)
sgList = list(input_sg_genes_dict.keys())
sgNames = copy.deepcopy(sgList)
best_permutations_DS = bottemsUpAlgorithm.call_it_all(
sgList, sgNames, input_sg_genes_dict, Omega, df_targets, cfd_dict,
PS_number
) ##call_it_all(sgList, sgNames, input_sg_genes_dict, Omega)## Naive.find_Uno_sgRNA(current
best_permutations_DS.sort(
key=lambda item: item.cut_expectation,
reverse=True) # or (len(item[2]) and item[1])) . sort for the print
return best_permutations_DS
def E_top_down(
res,
node,
Omega,
sg_genes_dict,
df_targets,
internal_node_candidates=10,
cfd_dict=None,
PS_number=12
): #(res, node, current_sg_genes_dict, current_genes_sg_dict, sgList, sgNames, Omega, df_targets)
'''
:param node:
:param current_genes_sg_dict:
:param Omega: can be removed already??
:return:
'''
#if len(node.polymorphic_sites_set) < 11: #change to 12!
##making the genes_sg dict for this subtree and the sg_genes_dict to send to the intermadiate algorithm
current_sg_genes_dict = dict()
current_genes_sg_dict = dict()
sgList = list()
sgNames = list()
for leaf in node.node_targets_DS: ##leaf here is a gene. taking only the relevant genes
current_genes_sg_dict[leaf.name] = genes_sg_dict[leaf.name]
##filling the sg genes dict
for sg in current_genes_sg_dict[leaf.name]:
#current_sg_genes_dict[sg] = sg_genes_dict[sg] ###here is the abnormality!! ##the checking if this sg is already in the dict just be more expensive overall
#will the folowing be clearer?
#untab the folowing 3 lines:
if sg in current_sg_genes_dict:
current_sg_genes_dict[sg] = current_sg_genes_dict[sg] + [
leaf.name
]
else:
current_sg_genes_dict[sg] = [
leaf.name
] ###here is the abnormality!! ##the checking if this sg is already in the dict just be more expensive overall
if sg not in sgList:
sgList.append(sg)
sgNames.append(sg)
if len(node.node_targets_DS) < 11 and len(
node.node_targets_DS
) > 1: #should change the first parameter to at least 10
best_permutations_DS = bottemsUpAlgorithm.call_it_all(
sgList, sgNames, current_sg_genes_dict, Omega, df_targets,
cfd_dict, PS_number
) ##call_it_all(sgList, sgNames, input_sg_genes_dict, Omega)## Naive.find_Uno_sgRNA(current)
if not (best_permutations_DS):
return
best_permutations_DS.sort(key=lambda item: item.cut_expectation,
reverse=True)
current_best_perm = best_permutations_DS[:
internal_node_candidates] #the best sg at the current set cover
res.append(
Subgroup_res(get_genes_list(best_permutations_DS),
current_best_perm, node.name))
#else:
if not node.clades:
return
if node.clades[0]:
E_top_down(res, node.clades[0], Omega, sg_genes_dict, df_targets,
internal_node_candidates, cfd_dict, PS_number)
if node.clades[1]:
E_top_down(res, node.clades[1], Omega, sg_genes_dict, df_targets,
internal_node_candidates, cfd_dict, PS_number)
