Input_Output.rst

Input and Output

Exercises

Exercise

Write a function which take the path of file as parameter and display it's content on the screen.

We wait same behavior as the shell cat command.

import sys
import os

def cat(path):
   if not os.path.exists(path):
      sys.exit("no such file: {0}".format(path)
   with open(path, 'r') as infile:
      for line in infile:
         print line

Exercise

Write a function which take the path of a file in rebase format and return in a dictionnary the collection of the enzyme contains in the file. The sequence of the binding site must be cleaned up.

:download:`rebase_light.txt <_static/data/rebase_light.txt>` .

Exercise

write a function which take the path of a fasta file (containing only one sequence) and return a data structure of your choice that allow to stock the id of the sequence and the sequence itself.

use the file :download:`seq.fasta <_static/data/seq.fasta>` to test your code.

:download:`fasta_reader.py <_static/code/fasta_reader.py>` .

Exercise

Modify the code at the previous exercise to read multiple sequences fasta file. use the file :download:`abcd.fasta <_static/data/abcd.fasta>` to test your code.

solution 1

:download:`fasta_iterator.py <_static/code/multiple_fasta_reader.py>`

solution 2

:download:`fasta_iterator.py <_static/code/fasta_iterator.py>` .

The second version is an iterator. Thus it retrun sequence by sequence the advantage of this version. If the file contains lot of sequences you have not to load all the file in memory. You can call this function and put in in a loop or call next. Work with the sequence and pass to the next sequence on so on. for instance :

for seq in fasta_iter('my_fast_file.fasta'):
   print seq

Exercise

Read a multiple sequence file in fasta format and write to a new file, one sequence by file, only sequences starting with methionine and containing at least six tryptophanes (W).

(you should create files for sequences: ABCD1_HUMAN, ABCD1_MOUSE, ABCD2_HUMAN, ABCD2_MOUSE, ABCD2_RAT, ABCD4_HUMAN, ABCD4_MOUSE)

bonus

Write sequences with 80 aa/line

:download:`fasta_iterator.py <_static/code/fasta_filter.py>` .

Exercise

we ran a blast with the folowing command blastall -p blastp -d uniprot_sprot -i query_seq.fasta -e 1e-05 -m 8 -o blast2.txt

-m 8 is the tabular output. So each fields is separate to the following by a 't'

The fields are: query id, database sequence (subject) id, percent identity, alignment length, number of mismatches, number of gap openings, query start, query end, subject start, subject end, Expect value, HSP bit score.

:download:`blast2.txt <_static/data/blast2.txt>` .

parse the file

sort the hits by their percent identity in the descending order.

write the results in a new file.

(adapted from managing your biological data with python p138)

.. literalinclude:: _static/code/parse_blast.py

linenos:
language:	python

:download:`parse_blast.py <_static/code/parse_blast.py>` .