Question

frequencies = {}

with open('GBM_Fusion_List.txt') as fileIn:
    line = fileIn.readline()

    while line:
        line = line.split('&')
        fl0 = frequencies.get(line[0],0)
        fl1 = frequencies.get(line[1],0)
        if fl0 == 0:
            frequencies[line[0]] = 1
        elif fl0 > 0:
            frequencies[line[0]] = fl0 + 1
        elif fl1 == 0:
            frequencies[line[1]] = 1
        else:
            frequencies[line[1]] = fl1 +1
        line = fileIn.readline()

for key, value in frequencies.items():
    print('{}\t{}'.format(key,value))

这是我一直在努力的问题。我是python的新手，并开始了新的实习。

编写一个python脚本以计算融合基因中每个伙伴基因的频率和百分比。

GeneA&GeneB
GeneA&GeneC
GeneD&GeneF
.
.

输出包括基因及其伴侣的名称和频率以及每个伴侣的百分比。

示例输出：

GeneA   2   GeneB   1   50% GeneC   1   50%  
GeneD   1   GeneF   1   100%

Answer 1

这可能会有所帮助，我已尝试使其易于理解

frequencies = {}
with open('GBM_Fusion_List.txt') as file:
    rows = file.read().split()
    for fusion_gene in rows:
        first_gene, second_gene = fusion_gene.split('&')
        if first_gene in frequencies:
            frequencies[first_gene]['count'] += 1
            partner_genes = frequencies[first_gene]['partner_genes']
            if second_gene in partner_genes:
                partner_genes[second_gene] += 1
            else:
                partner_genes[second_gene] = 1
        else:
            frequencies[first_gene] = {
                'count': 1,
                'partner_genes': { second_gene: 1}
            }
    for frequency in frequencies:
        print('{first_gene} {first_gene_count}'.format(first_gene=frequency,first_gene_count=frequencies[frequency]['count']), end='')
        gene_occurance = 0
        for _, freq in frequencies[frequency]['partner_genes'].items():
            gene_occurance += freq
        for  gene, freq in frequencies[frequency]['partner_genes'].items():
            percentage = ( freq / gene_occurance) * 100
            print(' {gene} {freq} {percent}%'.format(gene=gene, freq=freq, percent=percentage ), end='')
        print()

合并列表中的频率和百分比基因

1 个答案: