Combining 2 Text File And Make A New One In Python

I have 2 big text files like the following small examples. there are 2 files (major and minor). in both major and minor files there are 4 columns. in the major file the difference

Solution 1:

You should do something like this

final = []
for i, j in zip(minor_list, major_list):
    final.append(i, j)

Solution 2:

Maybe its a typo in your code I can see that your missing a tab at your if minor_list[i]

final = []
for i in minor_list:
    for j in major_list
    if minor_list[i] == major_list[j] and minor_list[i+1] <= major_list[j+1] and minor_list[i+2] >= major_list[j+2]:
        final.append(i)

should be

final = []
for i in minor_list:
    for j in major_list
        if minor_list[i] == major_list[j] and minor_list[i+1] <= major_list[j+1] and minor_list[i+2] >= major_list[j+2]:
            final.append(i)

Solution 3:

Do you HAVE to use Python for this? If you install "bedtools" in bash shell, this can be accomplished with the following line:

bedtools intersect -wa -wb -a minor.bed -b major.bed > intersected_file.bed

A few bioinformatics tools are linux/mac-only, so if you're going to be doing any amount of bioinformatics, it's worth learning how to script in shell.