This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Technical question about python "to find the strings"

Hi there, I have two files, file 1 looks like this :

NP_208181.1
NP_220259.1
NP_224629.1
WP_232131
WP_3432434
WP_2441241221

File 2 looks like this:

NP_208181.1,GCF_000008525.1
NP_212206.1,GCF_000008685.2
NP_213866.1,GCF_000008625.1
NP_219784.1,GCF_000008725.1
NP_220151.1,GCF_000008725.1
NP_220259.1,GCF_000008725.1
NP_224628.1,GCF_000008745.1
NP_224629.1,GCF_000008745.1
NP_224939.1,GCF_000008745.1

My purpose is to find which ID in file 1 is in file 2 too, so here we can see NP_208181.1, NP_220259.1, NP_224629.1 can be found in file two, followed by GCF blabla, i wrote a small script like this :

import re
with open("file1") as ID, open("file2") as data:
  for line1, line2 in zip(ID,data):
    if line1 in line2:
      print(line1)

However, the result was blank, which does not make sense, any one knows why? how t modify this script?

python
• 2,613 views • link
updated by shoujun.gu shoujun.gu • written by horsedog • horsedog

Without testing it I think you're zipping the 2 lines together from each file, so it's only comparing line1 in file 1 with line 2 in file 2, then line 2 with line 2 etc You'll need 2 loops for this to work as you've got it - e.g:

for line1 in ID:
    for line2 in data:
        if line1 in line2

and so on..

I'd look in to using the any and all python keywords though, they may help here.

If you're not bothered about using python specifically, you could do this in a single line (sort of) with grep:

while read ID; do grep "$line" Data_file.txt ; done < ID_file.txt
• 0 views • link
written by Joe Joe

Hi, thanks for correction, but I tried , still blank, here is my new code:

with open("file") as ID, open("file2") as data:
    for line1 in ID:
        for line2 in data:
            if line1 in line2:
                print(line1)
• 0 views • link
written by horsedog • horsedog

what about comm?

Modo de empleo: comm [OPCIÓN]... FICHERO1 FICHERO2
Compara los ficheros ordenados FICHERO1 y FICHERO2 línea por línea.

Sin ninguna opción, produce un resultado en tres columnas. La columna
uno contiene las líneas únicas al FICHERO1, la columna dos contiene
las líneas únicas al FICHERO2, y la columna tres contiene las líneas
comunes a ambos ficheros.

  -1              suppress column 1 (lines unique to FILE1)
  -2              suppress column 2 (lines unique to FILE2)
  -3              suppress column 3 (lines that appear in both files)

  --check-order     check that the input is correctly sorted, even
                      if all input lines are pairable
  --nocheck-order   do not check that the input is correctly sorted
  --output-delimiter=STR  separate columns with STR
      --help     muestra esta ayuda y finaliza
      --version  informa de la versión y finaliza

Note, comparisons honor the rules specified by `LC_COLLATE'.

Examples:
  comm -12 file1 file2  Print only lines present in both file1 and file2.
  comm -3  file1 file2  Print lines in file1 not in file2, and vice versa.
• 0 views • link
written by Buffo Buffo

Fixed some duff logic in my answer, it should work for your case now.

• 0 views • link
written by Joe Joe

3 answers

First, you need to strip eol from the lines. For example line1.strip(). Second, with zip, you are testing line against corresponding line. This should catch the first line but none of the others.

• 0 views • link
written by jomo018 jomo018

hello, do you mean by this?

with open("file") as ID, open("file2") as data:
    for line1.strip() in ID:
        for line2.strip() in data:
            if line1.strip() in line2.strip():
                print(line1.strip())

?

• 0 views • link
written by horsedog • horsedog

Combining my comment and jomo018s point about the line ending character (line stripping is only necessary from file 1 since the strings are contained within the line of file 2, but I've done both here anyway):

#!/bin/python

# assume the script is named comparelines.py
# invoke with the ID file as the first commandline arg, 
# and data file as commandline arg 2

import sys

with open(sys.argv[1], 'r') as ID_file, open(sys.argv[2], 'r') as data_file:
    IDs = [ID.strip() for ID in ID_file]
    data = [line.strip() for line in data_file]

    result = [j for i in IDs for j in data if i in j]

    for each in result:
        print(each)

So

$ python comparelines.py IDs.txt data.txt

gives:

NP_208181.1,GCF_000008525.1
NP_220259.1,GCF_000008725.1
NP_224629.1,GCF_000008745.1

EDIT

Fixed it.

• 0 views • link
written by Joe Joe

I believe all your input file are actually csv file

thus, the most efficient way is: 1) read these file into dataframe 2) inner join the column you want

• 0 views • link
written by shoujun.gu shoujun.gu

Log in to answer this question.

More posts like this

No similar posts found.