Showing posts from 2017

Calculate Cys-Richness for a protein

'''Code description: Calculate Cys-richness of a protein with criteria set as: >=4 'C's over the length of protein AND >=5% total cysteine contentFunction: Take input sequence => Count number of 'C's & length => Calculate percentageOutput True or False if criteria is met'''fromBioimport SeqIO defCys_rich(record_seq): C_count = record_seq.count('C') seq_len =len(record_seq) Cys_perc =float(C_count) /float(seq_len) *100if C_count >=4.0and Cys_perc >=5.0: return'Cys-rich'else: return'No' CysRichSeq = [] for record in SeqIO.parse('filename.fasta', 'fasta'): if Cys_rich(record.seq) =='Cys-rich': CysRichSeq.append(record) SeqIO.write(CysRichSeq, 'Cys-rich_sequences.fasta', 'fasta') print'Cys-rich sequences written to file..'