使用 Python 将多个文件中的项目组合成一个矩阵

Question

我正在尝试将多个文件 (1.20.1_Indel_allEff.vcf,1.20.2_Indel_allEff.vcf.....1.200.1_Indel_allEff.vcf) 中的项目合并到一个文件夹中，以便获得一个看起来像这样的矩阵。

Fm Chromosome Position Ref Alt Gene  X1.20.1 X1.20.2 X1.20.3    
Fm        chrI       100007   AT  A   CAR2  0       0       0  
Fm        chrX       3000676  G   T   HYM1  0       0       0.5

其中，X1.20.1、X1.20.2、X1.20.3.....X1.200.3 是文件夹中包含的单个文件名及其频率值。

我写了一段代码在python(F1_comparison.py)

snps = defaultdict(lambda: defaultdict(str))
myfiles=listdir(str(sys.argv[1]))
for f1 in myfiles:
    f = open(f1)
    tpp = f1.split("_")[0].split(".")
    tp=tpp[0]+'.'+tpp[1]+'.'+tpp[2]
    for l in f:
        ls = l.split()
        if l.find("#") == -1 and len(ls) > 6: 
            chrom = ls[0]
            pos = ls[1]
            ref = ls[2]
            alt = ls[3]
            freq = ls[4]
            typ = ls[5]
            gene = ls[6]
            if len(alt) == 1:
                snps[pos+"_"+ref+"-"+alt+"_"+chrom+"_"+gene+"_"+typ][tp] = freq
            elif len(alt) > 1:
                for k in range (0,len(alt.split(","))):
                snps[pos+"_"+ref+alt.split(",")[k]+"_"+chrom+"_"+gene+"_"+typ][tp] = freq.split(",")[k]

    f.close()

traj = 1
tp_list = ['1.20.1','1.20.2','1.20.3','1.30.1','1.30.2','1.30.3','1.40.1','1.40.2','1.40.3','1.50.1','1.50.2','1.50.3','1.60.1','1.60.2','1.60.3','1.90.1','1.90.2','1.90.3','1.100.1','1.100.2','1.100.3','1.130.1','1.130.2','1.130.3','1.200.1','1.200.2','1.200.3']
print "Fermentor\tTrajectory\tChromosome\tPosition\tMutation\tGene\tEffect\t1.20.1\t1.20.2\t1.20.3\t1.30.1\t1.30.2\t1.30.3\t1.40.1\t1.40.3\t1.50.1\t1.50.2\t1.50.3\t1.60.1\t1.60.2\t1.60.3\t1.90.1\t1.90.2\t1.90.3\t1.100.1\t1.100.2\t1.100.3\t1.130.1\t1.130.2\t1.130.3\t1.200.1\t1.200.2\t1.200.3"
for pos in sorted(snps.keys()):
    pos1 = pos.split("_")[0]
    mut = pos.split("_")[1]
    chrom = pos.split("_")[2] 
    gene = pos.split("_")[3]
    typ = pos.split("_")[4]
    tp_string = ""
    for tp in tp_list:
        if len(snps[pos][tp])>0:
            tp_string += "\t"+str(snps[pos][tp])
        else:
            tp_string += "\t"+str("0/0")

    print "F1"+"\t"+str(traj)+"\t"+chrom+"\t"+pos1+"\t"+mut+"\t"+gene+"\t"+typ+"\t"+tp_string
    traj += 1

但是，我收到一个错误，其中代码无法识别文件夹中的某些文件，尽管它们的格式都相同。

我的命令和我得到的错误：

python F1_comparison.py Fer1 > output.csv

Traceback (most recent call last):
    File "Fer1_comparison.py", line 18, in <module>
    f = open(f1)
    IOError: [Errno 2] No such file or directory: '1.30.2_INDEL_allEff.vcf'

有人可以帮我解决这个问题吗？这将是一个很大的帮助。谢谢

Answer 1

您需要将文件加入路径：

from os import path, listdir

pth = sys.argv[1]  # get full path
myfiles = listdir(pth) # get list of all files in that path/directory
for f1 in myfiles:
    with open(path.join(pth,f1)) as f: # join -> pth/f1. with also closes your file
        tpp = f1.split("_",1)[0].split(".")
        tp = ".".join(tpp[0:3]) # same as tp=tpp[0]+'.'+tpp[1]+'.'+tpp[2]
        for line in f:
            # continue your code ...

你可以把你的代码写得更简洁、更高效，使用切片、解包str.format而不是重复拆分:

from os import path, listdir
import sys
from collections import defaultdict

snps = defaultdict(lambda: defaultdict(str))
pth = sys.argv[1]  # get full path
myfiles = listdir(pth)  # get list of all files in that path/directory

with open("Fer1_INDELs_clones_filtered.csv","w") as out: # file to write all filtered data to
    out.write("Fermentor\tTrajectory\tChromosome\tPosition\tMutation\tGene\tEffect\t1.20.1\t1.20.2\t1.20.3\t1.30.1\t1.30.2\t1.30.3\t1.40.1\t1.40.3\t1.50.1\t1.50.2\t1.50.3\t1.60.1\t1.60.2\t1.60.3\t1.90.1\t1.90.2\t1.90.3\t1.100.1\t1.100.2\t1.100.3\t1.130.1\t1.130.2\t1.130.3\t1.200.1\t1.200.2\t1.200.3\n")
    for f1 in myfiles:
        with open(path.join(pth, f1)) as f:  # join -> pth/f1
            tpp = f1.split("_", 1)[0].split(".")
            tp = ".".join(tpp[0:3])  # same as tp=tpp[0]+'.'+tpp[1]+'.'+tpp[2]
            for line in f:
                ls = line.split()
                if line.find("#") == -1 and len(ls) > 6: 
                    print(line)
                    # use unpacking and slicing
                    chrom, pos, ref, alt, freq, typ, gene = ls[:7]
                    if len(alt) == 1:
                        # use str.fromat
                        snps["{}_{}-{}_{}_{}_{}".format(pos,ref,alt,chrom,gene,typ)][tp] = freq
                    elif len(alt) > 1:
                        # use enumerate
                        for ind,k in enumerate(alt.split(",")):
                            snps["{}_{}_{}_{}_{}_{}".format(pos,ref,k,chrom,gene,typ)][tp] = freq.split(",")[ind]
    traj = 1
    tp_list = ['1.20.1', '1.20.2', '1.20.3', '1.30.1', '1.30.2', '1.30.3', '1.40.1', '1.40.2', '1.40.3', '1.50.1', '1.50.2',
               '1.50.3', '1.60.1', '1.60.2', '1.60.3', '1.90.1', '1.90.2', '1.90.3', '1.100.1', '1.100.2', '1.100.3',
               '1.130.1', '1.130.2', '1.130.3', '1.200.1', '1.200.2', '1.200.3']
    for pos in sorted(snps):
        # split once and again use unpacking and slicing 
        pos1, mut, chrom, gene, typ = pos.split("_")[:5]
        tp_string = ""
        for tp in tp_list:
            #print(tp)
            if snps[pos][tp]: # empty value will be False no need to check len
                tp_string += "\t{}".format(snps[pos][tp])
            else:
                tp_string += "\t0/0"

        out.write(("F1{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(traj,chrom,pos1,mut,gene,typ,tp_string)))
        traj += 1

使用 Python 将多个文件中的项目组合成一个矩阵

Combining items from several files into one matrix using Python

python

matrix