Jamie Leigh Jamie Leigh - 22 days ago 4
Python Question

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

Answer

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  
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