在 python 中检查元素是否在基因内

Question

我被一个 python 脚本困住了，该脚本试图检查列表中的某些元素是在基因内还是在基因外。为此，我使用以下非常基本的命令：

chr=[]
pos=[]
te=[]
chrom=[]
start=[]
end=[]
gene=[]

for line2 in infile2:
        if "#" not in line2[0]:
                line2=line2.strip()
                line2=line2.split("\t")
                chr.append(line2[0])
                pos.append(line2[1])
                te.append(line2[2])

for line in infile:
        line=line.strip()
        line=line.split("\t")
        chrom.append(line[0])
        start.append(line[1])
        end.append(line[2])
        gene.append(line[3])
for n in range(len(chrom)):
        for m in range(len(chr)):
                if chrom[n]==chr[m] and int(pos[n]) in range(int(start[m]), int(end[m])):
                        print(chr[m], pos[m], te[m], gene[n])
                else:
                        print(chr[m], pos[m], te[m], "intergenic")

infile具有以下结构，其中第一列是染色体，然后是基因的开始和结束位置：

X   100075379   100096509   NM_001306206.2  0   +   100075405   100093350   0   15  84,79,170,137,120,138,124,63,60,142,176,293,111,126,807,    0,1136,1860,2901,3495,3729,6243,7649,10417,11124,12343,12789,16948,17848,20323
X   100075379   100096509   NM_001306209.2  0   +   100075405   100093350   0   14  84,79,170,137,120,138,73,63,142,176,293,111,126,807,    0,1136,1860,2901,3495,3729,6294,7649,11124,12343,12789,16948,17848,20323

infile2 是这样的：

#CHR    POS INFO    STRAND  IDS...
X   100007156   variant -
X   10000849    variant +
X   100024284   variant -
X   10003672    variant -
X   100050489   variant +

输出应如下所示，其中 NM_ 是 RefSeq 格式的基因名称：

X 100628757 variant NM_000061.3
X 101152133 variant NM_001011657.4
X 100602245 variant intergenic
X 100236510 variant intergenic
X 100244318 variant NM_001162491.2

问题是输出只返回“基因间”变体，而我知道我的列表中至少有 30-40% 的元素在基因内。 有人可以帮助我吗？

Answer 1

如果我向

infile2

添加一行我认为应该触发匹配

    X   100075380   variant +

此代码（注意末尾的 +1 使范围包含在内）似乎有效：

## -----------------------
## build a version of infile
## -----------------------
infile = """
    X   100075379   100096509   NM_001306206.2  0   +   100075405   100093350   0   15  84,79,170,137,120,138,124,63,60,142,176,293,111,126,807,    0,1136,1860,2901,3495,3729,6243,7649,10417,11124,12343,12789,16948,17848,20323
    X   100075379   100096509   NM_001306209.2  0   +   100075405   100093350   0   14  84,79,170,137,120,138,73,63,142,176,293,111,126,807,    0,1136,1860,2901,3495,3729,6294,7649,11124,12343,12789,16948,17848,20323
"""
infile = [
    [cell.strip() for cell in line.strip().split("\t")[:4]]
    for line in infile.split("\n")
    if line.strip()
]
print("\ninfile:")
for row in infile:
    print(row)
## -----------------------

## -----------------------
## build a version of infile2
## -----------------------
infile2 = """
    #CHR    POS INFO    STRAND  IDS...
    X   100007156   variant -
    X   10000849    variant +
    X   100024284   variant -
    X   10003672    variant -
    X   100050489   variant +
    X   100075380   variant +
"""
infile2 = [
    [cell.strip() for cell in line.strip().split("\t")[:3]]
    for line in infile2.split("\n")
    if line.strip()
][1:]
print("\ninfile2:")
for row in infile2:
    print(row)
## -----------------------

print("\nResults:")
for infile_row in infile:
    chrom = infile_row[0]
    start = int(infile_row[1])
    end = int(infile_row[2])
    gene = infile_row[3]

    for infile2_row in infile2:
        chrom2 = infile2_row[0]
        pos = int(infile2_row[1])
        te = infile2_row[2]

        if chrom == chrom2 and pos in range(start, end + 1): # should the range be inclusive?
            print(chrom, pos, te, gene)
        else:
            print(chrom, pos, te, "intergenic")

这给了我：

infile:
['X', '100075379', '100096509', 'NM_001306206.2']
['X', '100075379', '100096509', 'NM_001306209.2']

infile2:
['X', '100007156', 'variant']
['X', '10000849', 'variant']
['X', '100024284', 'variant']
['X', '10003672', 'variant']
['X', '100050489', 'variant']
['X', '100075380', 'variant']

Results:
X 100007156 variant intergenic
X 10000849 variant intergenic
X 100024284 variant intergenic
X 10003672 variant intergenic
X 100050489 variant intergenic
X 100075380 variant NM_001306206.2
X 100007156 variant intergenic
X 10000849 variant intergenic
X 100024284 variant intergenic
X 10003672 variant intergenic
X 100050489 variant intergenic
X 100075380 variant NM_001306209.2