Abstract: hunt amino acid residues and calculate its percentage
The result:
In: MSRSLLLRFLLFLCLLLPPLP
({'P': 3}, {'P': 14.29})
({}, {})
({'P': 3, 'C': 1, 'M': 1, 'h': 0}, {'P': 14.29, 'C': 4.76, 'M': 4.76, 'h': 0.0})
({'LP': 2}, {'LP': 9.52})
The script:
# -*- coding: utf-8 -*-
"""
Created on Fri Aug 7 18:33:11 2015
@author: yuan
"""
import re
class amino_acid:
def __init__(self, aa_seq):
self.aa_seq=aa_seq.upper()
self.seq_len=len(self.aa_seq)
print 'In:', self.aa_seq
def residue_percentage(self,query_aa):
aa_counts={}
aa_perc={}
for aa in query_aa:
aa.upper()
target=re.findall(aa, self.aa_seq)
aa_counts[aa]=0 if target==[] else len(target)
aa_perc[aa]=aa_counts[aa]*100/float(self.seq_len)
aa_perc[aa]=round(aa_perc[aa], 2)
return aa_counts, aa_perc
if __name__=="__main__":
aa="MSRSLLLRFLLFLCLLLPPLP"
a=amino_acid(aa)
print a.residue_percentage(['P'])
print a.residue_percentage([])
print a.residue_percentage(['P', 'h', 'C','M'])
print a.residue_percentage(['LP'])
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