Compare two text file using python

Question

I'm trying to compare two files, and to extract lines in the first file that correspond to the second file for the first column. For example:

File 1:

VarID GeneID TaxName PfamName
3810359 1327    Isochrysidaceae Methyltransf_21&Methyltransf_22
6557609 5442    Peridiniales    NULL
4723299 7370    Prorocentrum    PEPCK_ATP
3019317 10454   Dinophyceae     NULL
2821675 10965   Bacillariophyta PK;PK_C
5559318 12824   Dinophyceae     Cyt-b5&FA_desaturase

File 2:

For the output I want this file :

VarID GeneID TaxName PfamName
3810359 1327    Isochrysidaceae Methyltransf_21&Methyltransf_22
6557609 5442    Peridiniales    NULL
4723299 7370    Prorocentrum    PEPCK_ATP

I tried this code :

f1 = sys.argv[1]
f2 = sys.argv[2]

file1_rows = []
with open(f1, 'r') as file1:
    for row in file1:
        file1_rows.append(row.split())

# Read data from the second file
file2_rows = []
with open(f2, 'r') as file2:    
    for row in file2:
        file2_rows.append(row.split())

# Compare data and compute results
results = []
for row in file2_rows:
    if row[:1] in file1_rows:
        results.append(row[:4])
    else:
        results.append(row[:4])

# Print the results
for row in results:
    print(' '.join(row))

Can you please help me ??? Thank you !!

Load the id of the second file, read the first line by line, if you find the id of the line on the loaded list print it else continue — Ôrel
– Ôrel, Commented Apr 5, 2018 at 15:31
replace the line: if row[:1] in file1_rows: with if row[0] in file1_rows:. also delete the else — Weiner Nir
– Weiner Nir, Commented Apr 5, 2018 at 15:33
@galfisher The output of my code is the entire first column of my first file — Erika
– Erika, Commented Apr 5, 2018 at 15:34

Weiner Nir · Accepted Answer · 2018-04-05 15:52:50Z

2

Your problem is here:

if row[:1] in file1_rows:

row[:1] returns a list with 1 field (the first column in the row). instead, search for that row directly.

this is the new code:

if row[0] in file1_rows:

also, remove the else that is associated to this if (I guess this is mistakly added duo to debugging)

There are few other better practices you can do, I wrote them all here:

f1 = sys.argv[1]
f2 = sys.argv[2]

with open(f1, 'r') as file1:
    file1_rows = file1.read().splitlines()

# Read data from the second file
with open(f2, 'r') as file2:    
    file2_rows = file2.read().splitlines()

# Compare data and compute results
results = []
for row2 in file2_rows:
    for row in file1_rows:
        if row2 in row:
            results.append(row)
            break

print('\n'.join(results))

edited Apr 5, 2018 at 15:52

answered Apr 5, 2018 at 15:36

Weiner Nir

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2 Comments

Erika Over a year ago

Thank you for your answer, I tried like you said, but it prints me nothing

Weiner Nir Over a year ago

@Erika, I've updated my post, see if it what you meant

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