5. GitHub: Hosted GIT
• Largest open source git hosting site
• Public and private options
• User-centric rather than project-centric
• http://github.ugent.be (use your Ugent
login and password)
– Accept invitation from Bioinformatics-I-
2015
URI:
– https://github.ugent.be/Bioinformatics-I-
2015/Python.git
9. Regex.py
text = 'abbaaabbbbaaaaa'
pattern = 'ab'
for match in re.finditer(pattern, text):
s = match.start()
e = match.end()
print ('Found "%s" at %d:%d' % (text[s:e], s, e))
m = re.search("^([A-Z]) ",line)
if m:
from_letter = m.groups()[0]
10. Install Biopython
pip is the preferred installer program.
Starting with Python 3.4, it is included
by default with the Python binary
installers.
pip3.5 install Biopython
#pip3.5 install yahoo_finance
from yahoo_finance import Share
yahoo = Share('AAPL')
print (yahoo.get_open())
11.
12. BioPython
• Make a histogram of the MW (in kDa) of all proteins in
Swiss-Prot
• Find the most basic and most acidic protein in Swiss-Prot?
• Biological relevance of the results ?
From AAIndex
H ZIMJ680104
D Isoelectric point (Zimmerman et al., 1968)
R LIT:2004109b PMID:5700434
A Zimmerman, J.M., Eliezer, N. and Simha, R.
T The characterization of amino acid sequences in proteins by
statistical
methods
J J. Theor. Biol. 21, 170-201 (1968)
C KLEP840101 0.941 FAUJ880111 0.813 FINA910103 0.805
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
6.00 10.76 5.41 2.77 5.05 5.65 3.22 5.97 7.59 6.02
5.98 9.74 5.74 5.48 6.30 5.68 5.66 5.89 5.66 5.96
13. Biopython AAindex ? Dictionary
… file parser
from Bio import SeqIO
c=0
handle = open(r'/Users/wvcrieki/Downloads/uniprot_sprot.dat')
for seq_rec in SeqIO.parse(handle, "swiss"):
print (seq_rec.id)
print (repr(seq_rec.seq))
print (len(seq_rec))
c+=1
if c>5:
break
14. Parsing sequences from the net
Parsing GenBank records from the net
Parsing SwissProt sequence from the net
Handles are not always from files
>>>from Bio import Entrez
>>>from Bio import SeqIO
>>>handle = Entrez.efetch(db="nucleotide",rettype="fasta",id="6273291")
>>>seq_record = SeqIO.read(handle,”fasta”)
>>>handle.close()
>>>seq_record.description
>>>from Bio import ExPASy
>>>from Bio import SeqIO
>>>handle = ExPASy.get_sprot_raw("6273291")
>>>seq_record = SeqIO.read(handle,”swiss”)
>>>handle.close()
>>>print seq_record.id
>>>print seq_record.name
>>>prin seq_record.description
15. 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?