Develop Reference

How do I write to files that are inside of files which the script is not in?

I need to figure out how to fix this code:
path = "/Folder/Test.txt"
with open(path,"r+") as f:
line = f.readline()
print(line)
It needs to be able to write to the text document "Test.txt" in the folder named "Folder"

First your path should be relative:
path = "./Folder/Test.txt"
if you want to write to a file you need "w" instead of "r" in the open function
Read:
with open(path, "r") as f:
line = f.readline()
print(line)
Write:
with open(path, "w") as f:
f.write("Hello world!")
Using "w" will replace all the current content of the file. If you want to append to the file instead, you should use "a".

path should be in /absolute/location/of/file/filename.
That means either "C:/file/path/you/want/filename" in Windows or "/absolute/path/of/your/file/filename" in *nix
You can also use relative paths if the path you want is nearby (shares a directory, etc.)
For example: if the script is in /user/scripts and you want to save in /user/textfiles/Folder, you can do ../textfiles/Folder
Also make sure that the folder exists, else, it will cause an error as well.
Anyway, as you go further in python, it is recommended that you check out the os module as it can help you a lot with file paths and other things

Using variable as part of name of new file in python

I'm fairly new to python and I'm having an issue with my python script (split_fasta.py). Here is an example of my issue:
list = ["1.fasta", "2.fasta", "3.fasta"]
for file in list:
contents = open(file, "r")
for line in contents:
if line[0] == ">":
new_file = open(file + "_chromosome.fasta", "w")
new_file.write(line)
I've left the bottom part of the program out because it's not needed. My issue is that when I run this program in the same direcoty as my fasta123 files, it works great:
python split_fasta.py *.fasta
But if I'm in a different directory and I want the program to output the new files (eg. 1.fasta_chromsome.fasta) to my current directory...it doesn't:
python /home/bin/split_fasta.py /home/data/*.fasta
This still creates the new files in the same directory as the fasta files. The issue here I'm sure is with this line:
new_file = open(file + "_chromosome.fasta", "w")
Because if I change it to this:
new_file = open("seq" + "_chromosome.fasta", "w")
It creates an output file in my current directory.
I hope this makes sense to some of you and that I can get some suggestions.

You are giving the full path of the old file, plus a new name. So basically, if file == /home/data/something.fasta, the output file will be file + "_chromosome.fasta" which is /home/data/something.fasta_chromosome.fasta
If you use os.path.basename on file, you will get the name of the file (i.e. in my example, something.fasta)
From #Adam Smith
You can use os.path.splitext to get rid of the .fasta
basename, _ = os.path.splitext(os.path.basename(file))
Getting back to the code example, I saw many things not recommended in Python. I'll go in details.
Avoid shadowing builtin names, such as list, str, int... It is not explicit and can lead to potential issues later.
When opening a file for reading or writing, you should use the with syntax. This is highly recommended since it takes care to close the file.
with open(filename, "r") as f:
data = f.read()
with open(new_filename, "w") as f:
f.write(data)
If you have an empty line in your file, line[0] == ... will result in a IndexError exception. Use line.startswith(...) instead.
Final code :
files = ["1.fasta", "2.fasta", "3.fasta"]
for file in files:
with open(file, "r") as input:
for line in input:
if line.startswith(">"):
new_name = os.path.splitext(os.path.basename(file)) + "_chromosome.fasta"
with open(new_name, "w") as output:
output.write(line)
Often, people come at me and say "that's hugly". Not really :). The levels of indentation makes clear what is which context.

Renaming Files Based on In-File Strings Using Python

I posted the following code in the Windows and Rename tags and thought it might make more sense to ask about this code here. Essentially what I am trying to do is use this to rename files based on a particular text string located in the files (the text string in line.strip() below). I was wondering how I might implement something like this in Python, as this is a rough sketch of how I think it should look but not a complete work. Is there a best way to fill in the gaps here? Any suggestions would be much appreciated.
for file in directory:
f = fopen(file, 'r')
line = f.readLine();
while(line):
if(line.strip() == '<th style="width: 12em;">Name:</th>'):
nextline = f.readLine().strip();
c = nextline.find("</td>")
name = nextline[4:c]
os.commandline(rename file to name)
break
line = f.readLine()

I think the safest way to move the file is to use the shutil module. To do this replace replace
os.commandline(rename file to name)
with
shutil.move(os.path.join(directory,file), os.path.join(directory,name))

You can rename a file with the provided os command: (first close the file)
f.close()
os.rename(file_name, new_name)

importing txt files into python

a01:01-24-2011:s1
a03:01-24-2011:s2
a02:01-24-2011:s2
a03:02-02-2011:s2
a03:03-02-2011:s1
a02:04-19-2011:s2
a01:05-14-2011:s2
a02:06-11-2011:s2
a03:07-12-2011:s1
a01:08-19-2011:s1
a03:09-19-2011:s1
a03:10-19-2011:s2
a03:11-19-2011:s1
a03:12-19-2011:s2
this is saved in animallog1.txt. How would I import this file so that it can be used to write code, or answer questions using the above data.
I have tried:
open('C:/animallog1.txt', 'r')
but it does not work and states
FileNotFoundError: [Errno 2] No such file or directory: 'C:/animallog1.txt'
Could someone please help me fix this

open('C:\\animallog1.txt', 'r')

Does file animallog1.txt exists?
On Windows you should be care for the backsplash.
file = open('c:\\path\\to\\file', 'r')
or
file = open(r'c:\path\to\file', 'r')
Check your workspace, u can use os.chdir() to change your directory to c:\?

First, if you're using Windows, you have to use backslashes. There are a couple ways to do that: one is with double backslashes as others have pointed out, another is using the various constants and functions in the os and os.path libraries:
import os
filename = "C:" + os.sep + "animallog1.txt"
Second, the "proper" way to do this is with a with statement:
with open(filename) as f: #'r' is default
for line in f:
a, date, s = line.split(":")
# ...
What the with statement does is guarantee that the file gets closed on leaving the with block. Otherwise the file doesn't get closed until the Python garbage collector gets around to it.

Replace string in a specific line using python

I'm writing a python script to replace strings from a each text file in a directory with a specific extension (.seq). The strings replaced should only be from the second line of each file, and the output is a new subdirectory (call it clean) with the same file names as the original files, but with a *.clean suffix. The output file contains exactly the same text as the original, but with the strings replaced. I need to replace all these strings: 'K','Y','W','M','R','S' with 'N'.
This is what I've come up with after googling. It's very messy (2nd week of programming), and it stops at copying the files into the clean directory without replacing anything. I'd really appreciate any help.
Thanks before!
import os, shutil
os.mkdir('clean')
for file in os.listdir(os.getcwd()):
if file.find('.seq') != -1:
shutil.copy(file, 'clean')
os.chdir('clean')
for subdir, dirs, files in os.walk(os.getcwd()):
for file in files:
f = open(file, 'r')
for line in f.read():
if line.__contains__('>'): #indicator for the first line. the first line always starts with '>'. It's a FASTA file, if you've worked with dna/protein before.
pass
else:
line.replace('M', 'N')
line.replace('K', 'N')
line.replace('Y', 'N')
line.replace('W', 'N')
line.replace('R', 'N')
line.replace('S', 'N')

some notes:
string.replace and re.sub are not in-place so you should be assigning the return value back to your variable.
glob.glob is better for finding files in a directory matching a defined pattern...
maybe you should be checking if the directory already exists before creating it (I just assumed this, this could not be your desired behavior)
the with statement takes care of closing the file in a safe way. if you don't want to use it you have to use try finally.
in your example you where forgetting to put the sufix *.clean ;)
you where not actually writing the files, you could do it like i did in my example or use fileinput module (which until today i did not know)
here's my example:
import re
import os
import glob
source_dir=os.getcwd()
target_dir="clean"
source_files = [fname for fname in glob.glob(os.path.join(source_dir,"*.seq"))]
# check if target directory exists... if not, create it.
if not os.path.exists(target_dir):
os.makedirs(target_dir)
for source_file in source_files:
target_file = os.path.join(target_dir,os.path.basename(source_file)+".clean")
with open(source_file,'r') as sfile:
with open(target_file,'w') as tfile:
lines = sfile.readlines()
# do the replacement in the second line.
# (remember that arrays are zero indexed)
lines[1]=re.sub("K|Y|W|M|R|S",'N',lines[1])
tfile.writelines(lines)
print "DONE"
hope it helps.

You should replace line.replace('M', 'N') with line=line.replace('M', 'N'). replace returns a copy of the original string with the relevant substrings replaced.
An even better way (IMO) is to use re.
import re
line="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
line=re.sub("K|Y|W|M|R|S",'N',line)
print line

Here are some general hints:
Don't use find for checking the file extension (e.g., this would also match "file1.seqdata.xls"). At least use file.endswith('seq'), or, better yet, os.path.splitext(file)[1]
Actually, don't do that altogether. This is what you want:
import glob
seq_files = glob.glob("*.seq")
Don't copy the files, it's much easier to use just one loop:
for filename in seq_files:
in_file = open(filename)
out_file = open(os.path.join("clean", filename), "w")
# now read lines from in_file and write lines to out_file
Don't use line.__contains__('>'). What you mean is
if '>' in line:
(which will call __contains__ internally). But actually, you want to know wether the line starts with a `">", not if there's one somewhere within the line, be it at the beginning or not. So the better way would be this:
if line.startswith(">"):
I'm not familiar with your file type; if the ">" check really is just for determining the first line, there's better ways to do that.
You don't need the if block (you just pass). It's cleaner to write
if not something:
do_things()
other_stuff()
instead of
if something:
pass
else:
do_things()
other_stuff()
Have fun learning Python!

you need to allocate the result of the replacement back to "line" variable
line=line.replace('M', 'N')
you can also use the module fileinput for inplace edit
import os, shutil,fileinput
if not os.path.exists('clean'):
os.mkdir('clean')
for file in os.listdir("."):
if file.endswith(".seq"):
shutil.copy(file, 'clean')
os.chdir('clean')
for subdir, dirs, files in os.walk("."):
for file in files:
f = fileinput.FileInput(file,inplace=0)
for n,line in enumerate(f):
if line.lstrip().startswith('>'):
pass
elif n==1: #replace 2nd line
for repl in ["M","K","Y","W","R","S"]:
line=line.replace(ch, 'N')
print line.rstrip()
f.close()
change inplace=0 to inplace=1 for in place editing of your files.

line.replace is not a mutator, it leaves the original string unchanged and returns a new string with the replacements made. You'll need to change your code to line = line.replace('R', 'N'), etc.
I think you also want to add a break statement at the end of your else clause, so that you don't iterate over the entire file, but stop after having processed line 2.
Lastly, you'll need to actually write the file out containing your changes. So far, you are just reading the file and updating the line in your program variable 'line'. You need to actually create an output file as well, to which you will write the modified lines.