CODEWITHSUNDEEP
python
Jamie Leigh
Jamie Leigh

Reputation: 359

Writing to a file in python

I have been receiving indexing errors in python. I got my code to work correctly through reading in a file and simply printing the desired output, but now I am trying to write the output to a file. I seem to be having a problem with indexing when trying to write it. I've tried a couple different things, I left an attempt commented out. Either way I keep getting an indexing error. EDIT Original error may be caused by an error in eclipse, but when running on server, having a new issue*

I can now get it to run and produce output to a .txt file, however it only prints a single output 

with open("blast.txt") as blast_output:
for line in blast_output:
    subFields = [item.split('|') for item in line.split()]
    #transId = str(subFields[0][0])
    #iso = str(subFields[0][1])
    #sp = str(subFields[1][3])
    #identity = str(subFields[2][0])
    out = open("parsed_blast.txt", "w")
    #out.write(transId + "\t" + iso + "\t" + sp + "\t" + identity)
    out.write((str(subFields[0][0]) + "\t" + str(subFields[0][1]) + "\t" + str(subFields[1][3]) + "\t" + str(subFields[2][0])))
    out.close()


IndexError: list index out of range

Input file looks like:

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
c1005_g1_i1|m.805       gi|9910811|sp|O42832.2|SPB1_SCHPO       100.00  802     0       0       1       802     1       802     0.0      1644
c1006_g1_i1|m.806       gi|74627042|sp|O94631.1|MRM1_SCHPO      100.00  255     0       0       1       255     47      301     0.0       525

Expected output 

c0_g1_i1    m.1 Q9HGP0.1    100.00
c1002_g1_i1 m.801   Q10302.1    100.00
c1003_g1_i1 m.803   Q6BDR8.1    100.00
c1004_g1_i1 m.804   O94325.1    100.00
c1005_g1_i1 m.805   O42832.2    100.00
c1006_g1_i1 m.806   O94631.1    100.00

My output is instead only one of the lines instead of all of the lines

Upvotes: 2

Views: 168

Answers (3)

Andrew Lamarra
Andrew Lamarra

Reputation: 537

As @H Doucet said, write the whole thing to a string, then work with it. Leave the open() function out of the loop so it only opens & closes the file once, and make sure to open as "append." I've also cleaned up your out.write() function. No need to specify those list items as strings, they already are. And added a newline ("\n") to the end of each line.

with open("blast.txt") as f:
    blast_output = f.read()

out = open("parsed_blast.txt", "a")
for line in blast_output.split("\n"):
    subFields = [item.split('|') for item in line.split()]
    out.write("{}\t{}\t{}\t{}\n".format(subFields[0][0], subFields[0][1],
                                        subFields[1][3], subFields[2][0]))

out.close()

Upvotes: 1

helloV
helloV

Reputation: 52443

You are overwriting the same file again and again. Open the file outside the for loop or open it in append mode 'a'

Upvotes: 3

H Doucet
H Doucet

Reputation: 77

I suggest you write the whole file to a string.

with open("blast.txt", 'r') as fileIn:
      data = fileIn.read()

then process the data.

data = func(data)

Then write to file out.

  with open('bast_out.txt','w') as fileOut:
      fileOut.write()

Upvotes: 1

Related Questions