字符串的Python正则表达式，并将它们匹配到一个字典

Question

I have three files in a directory and I wanted them to be matched with a list of strings to dictionary.

The files in dir looks like following,

DB_ABC_2_T_bR_r1_v1_0_S1_R1_001_MM_1.faq.gz
DB_ABC_2_T_bR_r1_v1_0_S1_R2_001_MM_1.faq.gz
DB_DEF_S1_001_MM_R1.faq.gz
DB_DEF_S1_001_MM_R2.faq.gz

The list has part of the filename as,

ABC
DEF

So here is what I tried,

import os
import re

dir='/user/home/files'
list='/user/home/list'
samp1     = {}
samp2     = {}

FH_sample = open(list, 'r')
for line in FH_sample:
    samp1[line.strip().split('\n')[0]] =[]
    samp2[line.strip().split('\n')[0]] =[]
FH_sample.close()
for file in os.listdir(dir):
    m1 =re.search('(.*)_R1', file)
    m2 = re.search('(.*)_R2', file)
    if m1 and m1.group(1) in samp1:
        samp1[m1.group(1)].append(file)
    if m2 and m2.group(1) in samp2:
        samp2[m2.group(1)].append(file)

I wanted the above script to find the matches from m1 and m2 and collect them in dictionaries samp1 and samp2 . But the above script is not finding the matches, within the if loop . Now the samp1 and samp2 are empty.

This is what the output should look like for samp1 and samp2 :

{'ABC': [DB_ABC_2_T_bR_r1_v1_0_S1_R1_001_MM_1.faq.gz, DB_ABC_2_T_bR_r1_v1_0_S1_R2_001_MM_1.faq.gz], 'DEF': [DB_DEF_S1_001_MM_R1.faq.gz, DB_DEF_S1_001_MM_R2.faq.gz]} 

Any help would be greatly appreciated

Answer 1

A lot of this code you probably don't need. You could just see if the substring that you have from list is in dir .

The code below reads in the data as lists. You seem to have already done this, so it will simply be a matter of replacing files with the file names you read in from dir and replacing st with the substrings from list (which you shouldn't use as a variable name since it is actually used for something else in Python).

files = ["BSSE_QGF_1987_HJUS_1_MOHUA_2_T_bR_r1_v1_0_S1_R1_001_MM_1.faq.gz",
         "BSSE_QGF_1967_HJUS_1_MOHUA_2_T_bR_r1_v1_0_S1_R2_001_MM_1.faq.gz",
         "BSSE_QGF_18565_H33HLAFXY_1_MSJLF_T_bulk_RNA_S1_R1_001_MM_1.faq.gz",
         "BSSE_QGF_18565_H33HLAFXY_1_MSJLF_T_bulk_RNA_S1_R2_001_MM_1.faq.gz"]
my_strings = ["MOHUA", "MSJLF"]

res = {s: [] for s in my_strings}
for k in my_strings:
    for file in files:
        if k in file:
            res[k].append(file)
print(res)

Answer 2

You can pass the python script a dict and provide id_list and then add id_list as dict keys and append the fastqs if the dict key is in the fastq_filename:

import os
import sys

dir_path = sys.argv[1]

fastqs=[]
for x in os.listdir(dir_path):
    if x.endswith(".faq.gz"):
        fastqs.append(x)

id_list = ['MOHUA', 'MSJLF']

sample_dict = dict((sample,[]) for sample in id_list)
print(sample_dict)
for k in sample_dict:
    for z in fastqs:
        if k in z:
            sample_dict[k].append(z)

print(sample_dict)

to run:

python3.6 fq_finder.py /path/to/fastqs

output from above to show what is going on:

{'MOHUA': [], 'MSJLF': []} # first print creates dict with empty list as vals for keys
{'MOHUA': ['BSSE_QGF_1987_HJUS_1_MOHUA_2_T_bR_r1_v1_0_S1_R1_001_MM_1.faq.gz', 'BSSE_QGF_1967_HJUS_1_MOHUA_2_T_bR_r1_v1_0_S1_R2_001_MM_1.faq.gz'], 'MSJLF': ['BSSE_QGF_18565_H33HLAFXY_1_MSJLF_T_bulk_RNA_S1_R2_001_MM_1.faq.gz', 'BSSE_QGF_18565_H33HLAFXY_1_MSJLF_T_bulk_RNA_S1_R1_001_MM_1.faq.gz']}