# -*- coding: utf-8 -*-

"""============================================================================

============================================================================"""

#%%% import modules

import codecs, os

from collections import OrderedDict, defaultdict

#%%% inputs and outputs

input_path = 'Excel2Txt/'

genes_file = '/3.2.1 RelatedGenes.txt'

cosmic_file = '/3.2.3 Cosmic.txt'

cnvd_file = '/3.2.4 CNVD.txt'

life_file = '/3.2.6 LifeMap.txt'

path_file = '/3.2.7 Pathways.txt'

goid_file = '/3.2.8 Go.txt'

test_file = '/3.2.9 GeneticTest.txt'

merge_file = '/3.2.10 Merge.txt'

#%%% define functions

#%%% 检查基因的表头可能存在的情况

gene_header = set()

for dirs in os.listdir(input_path):

if not os.path.exists(input_path+dirs+genes_file): continue

print(dirs)

for line in codecs.open(input_path+dirs+genes_file, 'r', 'utf-8'):

break

linelist = line.strip('\r\n').split('\t')

gene_header.update(linelist[4:])

gene_header = list(gene_header)

#%% 每个癌症文件夹中分别合并文件产生 3.2.10 Merge.txt

for dirs in os.listdir(input_path):

if not os.path.exists(input_path+dirs+genes_file): continue

print(dirs)

outfile = codecs.open(input_path+dirs+merge_file, 'w', 'utf-8')

gene2line = OrderedDict()

header = True

for line in codecs.open(input_path+dirs+genes_file, 'r', 'utf-8'):

if header:

header_list = line.strip('\r\n').split('\t')

header_num = [] # 1.用来在现有文件标题后添加新标题; 2.长度决定需要补齐的空列

for head in gene_header:

if head in header_list: continue

header_num.append(head)

header_list.extend(header_num)

outfile.write('\t'.join(header_list)+'\t')

outfile.write('Cosmic_Mut ID\tCNVD_Type\tUp_Dn\tSuper_pathways\tGO_ID\tGeneticTest\n')

header = False

continue

linelist = line.strip('\r\n').split('\t')

gene2line[linelist[1]] = line.strip('\r\n')

gene2cosmic = defaultdict(set)

if os.path.exists(input_path+dirs+cosmic_file):

header = True

for line in codecs.open(input_path+dirs+cosmic_file, 'r', 'utf-8'):

if header:

header = False

continue

linelist = line.strip('\r\n').split('\t')

if not linelist[2]: continue

gene2cosmic[linelist[2]].add(linelist[1])

gene2cnvd = defaultdict(set)

if os.path.exists(input_path+dirs+cnvd_file):

header = True

for line in codecs.open(input_path+dirs+cnvd_file, 'r', 'utf-8'):

if header:

header = False

continue

linelist = line.strip('\r\n').split('\t')

if not linelist[6]: continue

gene2cnvd[linelist[6]].add(linelist[5])

gene2life = defaultdict(set)

if os.path.exists(input_path+dirs+life_file):

header = True

for line in codecs.open(input_path+dirs+life_file, 'r', 'utf-8'):

if header:

header = False

continue

linelist = line.strip('\r\n').split('\t')

if not linelist[1]: continue

gene2life[linelist[1]].add(linelist[4])

gene2path = defaultdict(set)

if os.path.exists(input_path+dirs+path_file):

header = True

for line in codecs.open(input_path+dirs+path_file, 'r', 'utf-8'):

if header:

header = False

continue

linelist = line.strip('\r\n').split('\t')

genes = linelist[3].split('|')

for gene in genes:

if not gene: continue

gene2path[gene].add(linelist[1])

gene2goid = defaultdict(set)

if os.path.exists(input_path+dirs+goid_file):

header = True

for line in codecs.open(input_path+dirs+goid_file, 'r', 'utf-8'):

if header:

header = False

continue

linelist = line.strip('\r\n').split('\t')

genes = linelist[4].split('|')

for gene in genes:

if not gene: continue

gene2goid[gene].add(linelist[2])

gene2test = defaultdict(set)

if os.path.exists(input_path+dirs+test_file):

header = True

for line in codecs.open(input_path+dirs+test_file, 'r', 'utf-8'):

if header:

header = False

continue

linelist = line.strip('\r\n').split('\t')

genes = linelist[1].split('|')

for gene in genes:

if not gene: continue

gene2test[gene].add(linelist[0])

#Cosmic_Mut ID\tCNVD_Type\tUp_Dn\tSuper_pathways\tGO_ID\tGeneticTest

for gene in gene2line:

outfile.write(gene2line[gene]+'\t'*len(header_num))

outfile.write('\t'+'\t'.join(['|'.join(gene2cosmic.get(gene, set())),

'|'.join(gene2cnvd.get(gene, set())),

'|'.join(gene2life.get(gene, set())),

'|'.join(gene2path.get(gene, set())),

'|'.join(gene2goid.get(gene, set())),

'|'.join(gene2test.get(gene, set()))

])+'\n')

outfile.close()

#%% 合并所有的 3.2.10 Merge.txt 文件到一个文件中。

gene_cancer2line = {}

static_header = ['Description', 'Score', 'CopenhagenUniversity', 'GeneCards',

'Orphanet', 'Novoseek', 'ClinVar', 'UniProtKB_SwissProt',

'MendelianInheritance', 'Cosmic_Mut ID', 'CNVD_Type', 'Up_Dn',

'Super_pathways', 'GO_ID', 'GeneticTest']

for dirs in os.listdir(input_path):

if not os.path.exists(input_path+dirs+merge_file): continue

print(dirs)

header = True

for line in codecs.open(input_path+dirs+merge_file, 'r', encoding='utf-8'):

if header:

header = False

header_list = line.strip('\r\n').split('\t')

continue

linelist = line.strip('\r\n').split('\t')

newline = []

for tem in static_header:

newline.append(linelist[header_list.index(tem)])

newline = '\t'.join(newline)+'\n'

gene_cancer2line.setdefault(linelist[1], [])

gene_cancer2line[linelist[1]].append(dirs+'\t'+newline)

gene2num = sorted(gene_cancer2line.items(), key=lambda x:len(x[1]), reverse=True)

outfile = codecs.open('MergeAll.txt', 'w', 'utf-8')

outfile.write('Symbol\tCancerName\t'+'\t'.join(static_header)+'\n')

for gene in gene2num:

gene = gene[0]

for tem in gene_cancer2line[gene]:

outfile.write(gene+'\t'+tem)

outfile.close()