여러 파일의 항목을 Python을 사용하여 하나의 행렬로 결합

Question

폴더에 여러 파일 (1.20.1_Indel_allEff.vcf, 1.20.2_Indel_allEff.vcf .... 1.200.1_Indel_allEff.vcf)의 항목을 순서대로 결합하려고합니다. 이런 식으로 보이는 행렬을 얻으려면.

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 

, X1.20.1, X1.20.2, X1.20.3 ..... X1.200.3 폴더에 포함 된 개별 파일 이름과 주파수 값입니다.

나는 파이썬 코드 (F1_comparison.py)를 썼다

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 

그러나,이 모든 비록 나는 코드가 폴더에있는 파일 중 일부를 인식하지 못하는 오류를 얻고있다 같은 형식.

내 명령과 오류가 나는 얻을 :

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' 

은 누군가가 나에게이 문제를하시기 바랍니다 알아내는 데 도움이 수 있습니까? 그것은 큰 도움이 될 것입니다. 당신은 조금 더 더 간결하고, 슬라이스를 사용하여 str.format을 풀고 더 효율적이 아니라 반복적으로 분할 할 수있는 코드를 작성할 수 있습니다

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 ... 

: 감사

Answer 1

당신은 경로에 파일을 가입해야

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