> For the complete documentation index, see [llms.txt](https://igb.mit.edu/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/reading-and-writing-files.md).

# Reading and Writing Files

* We open files using the built-in open function. We need to tell the function if the file is to be used for reading, writing, or appending with the r, w, and a flags.
* All the test files for the course are located at <https://ki-data.mit.edu/bcc/teaching/IntroToPython.tgz>.
* If you are on our cluster, you can copy them all to the current directory by typing:

```
cp /net/bmc-pub15/data/bmc/public/BCC/external/teaching/IntroToPython/* ./
```

### Examples

* Reading file `seq.txt`

```
In [1]: fin=open('seq.txt')

In [2]: fin=open('/net/rowley/ifs/data/bcc/dropbox/teaching_python/seq.txt')

In [3]: fin=open('seq.txt','r')

```

* Writing to file `seq2.txt`

```
In [1]: Aa="GLECDGRTNLCCRQQFF"
In [2]: fo=open('seq2.txt','w')
In [3]: fo.write(Aa)
In [4]: fo.close()
Out[4]: <function close>
In [5]: less seq2.txt
GLECDGRTNLCCRQQFF

*no need to remember to close the file handler if using "with" statement 
In [1]: with open('seq2.txt','w') as fo:
   ...:     fo.write("ABC")
   ...:     
In [2]: less seq2.txt
ABC

Note: writing to a file will delete the existing content of the file
```

* Appending to file `seq2.txt`

```
In [1]: with open('seq2.txt','a') as fo:
   ...:     fo.write("CDE")
   ...:     
In [2]: less seq2.txt
ABCCDE
```

* Reading files with `read()` and `readlines()`

```
read and readlines methods both store the contents of the read in file for further processing
The difference is that read returns the content as a single string, 
while readlines returns it as a list of lines

In [1]: seq=open('seq.txt','r').read()

In [2]: seq
Out[2]: 'ACTGATG\nACTGGTCA\nATGATG\nTCGAAGCT\nGCAGGCG\nGATCCTAG\nCATGTCGT\nCTCTATCTC\n'

In [3]: type(seq)
Out[3]: str


In [1]: seq=open ('seq.txt','r').readlines() 

In [2]: seq
Out[2]: 
['ACTGATG\n',
 'ACTGGTCA\n',
 'ATGATG\n',
 'TCGAAGCT\n',
 'GCAGGCG\n',
 'GATCCTAG\n',
 'CATGTCGT\n',
 'CTCTATCTC\n']

In [3]: type(seq)
Out[3]: list

```

* We can read in a file using our Python script, process it, and output the results to an output file
  * Let's read in file `seq.txt`
  * find the palindrome sequences using our python script
  * Then output the palindrome sequences to file `palindrome.txt`

```
example1: select palindrome sequences

write palindrome2.py using a text editor:

manyseqs=open ('seq.txt','r').readlines()
for seq in manyseqs:
     s=seq.strip()
     if (s==s[::-1]):
          with open ('palindrome.txt','a') as fo:
               fo.write(s)
               fo.write("\n")



In Unix:
python palindrome2.py 
less palindrome.txt 
ACTGGTCA
TCGAAGCT
GATCCTAG
CTCTATCTC
```

* Let's do an exercise by writing a Python script to say hello to the class
  * First read in file `class_list` as a list
  * Then output our greetings to file `greetings`

```
example2: Say Hi to our class

write Hello_class.py using a text editor:

classlist=open('class_list.txt','r').readlines()
for student in classlist:
        with open('greetings','a') as fo:
                fo.write("Hello,")
                fo.write(student)


In Unix:
python hello_class.py
less greetings
Hello,Manijeh
Hello,Shawn
Hello,Giorgio
Hello,Shuyu
Hello,Britt
Hello,Tu
Hello,Benjamin
Hello,Priyanka
Hello,Sabrina
Hello,Eric
```

* To avoid changing scripts, we can use arguments to read input files and to write output files
  * `./hello_class2.py class_list greetings_again`

```
hello_class2.py


#!/usr/bin/env python
import sys

InFileName=sys.argv[1]
OutFileName=sys.argv[2]

#open input file
classlist=open(InFileName,'r').readlines()

for students in classlist:
        student=students.strip()
        with open(OutFileName,'a') as fo:
                fo.write("Hello,")
                fo.write(student)
                fo.write(". It is nice to have you here!\n")
```

* Input another class list to `hello_class2.py` will output greetings to another class
  * `./hello_class2.py future_class_list greetings_to_future_class`