Can't write to file with print statements

Question

Here I have made a simple program to go through a text file containing a bunch of genes in a bacterial genome, including the amino acids that code for those genes (explicit use is better right?) I am relying heavily on modules in Biopython.

This runs fine in my Python shell, but I can't get it to save to a file.

This works:

import Bio
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqUtils import GC
from Bio.SeqUtils import ProtParam
for record in SeqIO.parse("RTEST.faa", "fasta"):
    identifier=record.id
    length=len(record.seq)
    print identifier, length

but this doesnt:

import Bio
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqUtils import GC
from Bio.SeqUtils import ProtParam
for record in SeqIO.parse("RTEST.faa", "fasta"):
    identifier=record.id
    length=len(record.seq)
    print identifier, length >> "testing.txt"

nor this:

import Bio
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqUtils import GC
from Bio.SeqUtils import ProtParam
f = open("testingtext.txt", "w")
for record in SeqIO.parse("RTEST.faa", "fasta"):
    identifier=record.id
    length=len(record.seq)
    f.write(identifier, length)

nor this:

import Bio
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqUtils import GC
from Bio.SeqUtils import ProtParam
f = open("testingtext.txt", "w")
for record in SeqIO.parse("RTEST.faa", "fasta"):
    identifier=record.id
    length=len(record.seq)
    f.write("len(record.seq) \n")

The first two will not print to file because the first will print to stdout and `>>` is a bit shifting operation in python. The two other methods should. Notice that the very last line of your example code writes `len(record.seq) \n` to your file, not the actual length as numbers. Do you get an error of some kind? — msvalkon, Apr 24 '14 at 20:37
@msvalkon The 3rd will crash as f.write only accepts one argument that must be a string. Try f.write('{0}, {1}'.format(identifier, length)). Also, don't forget to close the file (or use with). — AMacK, Apr 24 '14 at 21:26
yup, get some errors indeed: the first one gives me this: ", line 10, in print identifier, length >> "testing.txt" TypeError: unsupported operand type(s) for >>: 'int' and 'str' the 2nd: ", line 11, in f.write(identifier, length) TypeError: function takes exactly 1 argument (2 given) and the third: just types out "len(record.seq) a gamillion times. — Jackie, Apr 25 '14 at 21:41
Its probably obvious I have very little idea what I am doing, but, the first script that works ends up parsing out multiple lines from the genome file including their lengths, but I just cant save that output to file! At somepoint I fiddled with something and it printed out the very last line to file...but I have since not been able to re-create it. So far learning by trial and error, and hobbling together codes from other peoples things until they work out somehow. — Jackie, Apr 25 '14 at 21:45

score 3 · Answer 1 · answered Apr 24 '14 at 22:19

Your question is rather about writing to a file in general.

Few samples:

fname = "testing.txt"
lst = [1, 2, 3]
f = open(fname, "w")
  f.write("a line\n")
  f.write("another line\n")
  f.write(str(lst))
f.close()

f.write requires string as value to write.

Doing the same using context manager (this seems to be most Pythonic, learn this pattern):

fname = "testing.txt"
lst = [1, 2, 3]
with open(fname, "w") as f:
  f.write("a line\n")
  f.write("another line\n")
  f.write(str(lst))

# closing will happen automatically when leaving the "with" block
assert f.closed

You can also use so called print chevron syntax (for Python 2.x)

fname = "testing.txt"
lst = [1, 2, 3]
with open(fname, "w") as f:
  print >> f, "a line"
  print >> f, "another line"
  print >> f, lst

print does some extra things here - adding newline to the end and converting non-string values to the string.

In Python 3.x print has different syntax as it is ordinary function

fname = "testing.txt"
lst = [1, 2, 3]
with open(fname, "w") as f:
  print("a line", file=f)
  print("another line", file=f)
  print(lst, file=f)

Thanks, your correct, this will give me some general writing to file know how- the thing I am hung up on is how to get my outputs to write, (as opposed to something I am typing in manually). In my case, this would be the identifier, length of several hundred genes all found in one .fasta file. The output works fine with just print, where the list just scrolls down my screen....but I cant figure out how to save that to file! I apologize, I know this is probably very simple and basic, but Im pretty new to this, and this website is proving to be a great resource. — Jackie, Apr 25 '14 at 21:49
@Jackie you want to print some data you have in your variables, probably being generated in some loop. So you first convert the variables into a string, which you want to put into a file, then you call `f.write(that_string)` or use another method, illustrated above. — Jan Vlcinsky, Apr 25 '14 at 21:58

Can't write to file with print statements

1 Answers1