CODEWITHSUNDEEP
python
Jamie Leigh
Jamie Leigh

Reputation: 359

Read in a file, splitting and then writing out desired output

I am very new to python, and am having some problems I can't seem to find answers to. I have a large file I am trying to read in and then split and write out specific information. I am having trouble with the read in and split, where it is only printing the same thing over and over again. 

blast_output = open("blast.txt").read()
for line in blast_output:
    subFields = [item.split('|') for item in blast_output.split()]
    print(str(subFields[0][0]) + "\t" + str(subFields[0][1]) + "\t" + str(subFields[1][3]) + "\t" + str(subFields[2][0]))

My input file has many rows that look like this:

c0_g1_i1|m.1    gi|74665200|sp|Q9HGP0.1|PVG4_SCHPO      100.00  372     0       0       1       372     1       372     0.0       754
c1002_g1_i1|m.801       gi|1723464|sp|Q10302.1|YD49_SCHPO       100.00  646     0       0       1       646     1       646     0.0      1310
c1003_g1_i1|m.803       gi|74631197|sp|Q6BDR8.1|NSE4_SCHPO      100.00  246     0       0       1       246     1       246     1e-179    502
c1004_g1_i1|m.804       gi|74676184|sp|O94325.1|PEX5_SCHPO      100.00  598     0       0       1       598     1       598     0.0      1227

The output I am receiving is this: 

c0_g1_i1    m.1 Q9HGP0.1    100.00
c0_g1_i1    m.1 Q9HGP0.1    100.00
c0_g1_i1    m.1 Q9HGP0.1    100.00
c0_g1_i1    m.1 Q9HGP0.1    100.00

But what I am wanting is

c0_g1_i1      m.1    Q9HGP0.1    100.0
c1002_g1_i1   m.801  Q10302.1    100.0
c1003_g1_i1   m.803  Q6BDR8.1    100.0
c1004_g1_i1   m.804  O94325.1    100.0

Upvotes: 0

Views: 60

Answers (2)

Moses Koledoye
Moses Koledoye

Reputation: 78546

You don't need to call the read method of the file object, just iterate over it, line by line. Then replace blast_output with line in the for loop to avoid repeating the same action across all the iterations: 

with open("blast.txt") as blast_output:
    for line in blast_output:
        subFields = [item.split('|') for item in line.split()]
        print("{:15}{:10}{:10}{:10}".format(subFields[0][0], subFields[0][1], 
                                            subFields[0][1], subFields[1][3], subFields[2][0]))

I have opened the file in a context using with, so closing is automatically done by Python. I have also used string formatting to build the final string.

c0_g1_i1       m.1       m.1       Q9HGP0.1  
c1002_g1_i1    m.801     m.801     Q10302.1  
c1003_g1_i1    m.803     m.803     Q6BDR8.1  
c1004_g1_i1    m.804     m.804     O94325.1

Upvotes: 1

Back2Basics
Back2Basics

Reputation: 7806

Great question. You are taking the same input over and over again with this line

subFields = [item.split('|') for item in blast_output.split()]

The python 2.x version looks like this:

blast_output = open("blast.txt").read()
for line in blast_output:
    subFields = [item.split('|') for item in line.split()]
    print(str(subFields[0][0]) + "\t" + str(subFields[0][1]) + "\t" + str(subFields[1][3]) + "\t" + str(subFields[2][0]))

see Moses Koledoye's version for the Python 3.x formatted niceness

Upvotes: 1

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