6. 6
Reading Files
name = open("filename")
– opens the given file for reading, and returns a file object
name.read() - file's entire contents as a string
name.readline() - next line from file as a string
name.readlines() - file's contents as a list of lines
– the lines from a file object can also be read using a for loop
>>> f = open("hours.txt")
>>> f.read()
'123 Susan 12.5 8.1 7.6 3.2n
456 Brad 4.0 11.6 6.5 2.7 12n
789 Jenn 8.0 8.0 8.0 8.0 7.5n'
7. 7
File Input Template
• A template for reading files in Python:
name = open("filename")
for line in name:
statements
>>> input = open("hours.txt")
>>> for line in input:
... print(line.strip()) # strip() removes n
123 Susan 12.5 8.1 7.6 3.2
456 Brad 4.0 11.6 6.5 2.7 12
789 Jenn 8.0 8.0 8.0 8.0 7.5
8. 8
Writing Files
name = open("filename", "w")
name = open("filename", "a")
– opens file for write (deletes previous contents), or
– opens file for append (new data goes after previous data)
name.write(str) - writes the given string to the file
name.close() - saves file once writing is done
>>> out = open("output.txt", "w")
>>> out.write("Hello, world!n")
>>> out.write("How are you?")
>>> out.close()
>>> open("output.txt").read()
'Hello, world!nHow are you?'
9. Swiss-Knife.py
• Using a database as input ! Parse
the entire Swiss Prot collection
– How many entries are there ?
– Average Protein Length (in aa and
MW)
– Relative frequency of amino acids
• Compare to the ones used to construct
the PAM scoring matrixes from 1978 –
1991
10. Question 3: Getting the database
Uniprot_sprot.dat.gz – 528Mb
(on Github onder Files)
Unzipped 2.92 Gb !
http://www.ebi.ac.uk/uniprot/download-center
11. Amino acid frequencies
1978 1991
L 0.085 0.091
A 0.087 0.077
G 0.089 0.074
S 0.070 0.069
V 0.065 0.066
E 0.050 0.062
T 0.058 0.059
K 0.081 0.059
I 0.037 0.053
D 0.047 0.052
R 0.041 0.051
P 0.051 0.051
N 0.040 0.043
Q 0.038 0.041
F 0.040 0.040
Y 0.030 0.032
M 0.015 0.024
H 0.034 0.023
C 0.033 0.020
W 0.010 0.014
Second step: Frequencies of Occurence
12. Extra
• Program your own prosite parser !
• Download prosite pattern database
(prosite.dat)
• Automatically generate >2000 search
patterns, and search in sequence set
from question 1
13. Oefening 1
1. Which of following 4 sequences
(seq1/2/3/4)
a) contains a “Galactokinase signature”
b) How many of them?
http://us.expasy.org/prosite/
16. Extra Questions
• How many records have a sequence of length 260?
• What are the first 20 residues of 143X_MAIZE?
• What is the identifier for the record with the
shortest sequence? Is there more than one record
with that length?
• What is the identifier for the record with the
longest sequence? Is there more than one record
with that length?
• How many contain the subsequence "ARRA"?
• How many contain the substring "KCIP-1" in the
description?