Python codon_table Examples

Example #1

File: rosalind_PROT.py Project: sdwfrost/Rosalind

def translate(rna):
    table = codon_table('rna')
    peptide = ''

    for nt in range(0, len(rna), 3):
        codon = rna[nt:nt + 3]
        aa = table.get(codon, '*')
        if aa != '*':
            peptide += aa
        else:
            break

    return peptide

Example #2

File: rosalind_PROT.py Project: Davo36/Rosalind-1

def translate(rna):
    table = codon_table('rna')
    peptide = ''
    
    for nt in range(0, len(rna), 3):
        codon = rna[nt:nt+3]
        aa = table.get(codon, '*')
        if aa != '*':
            peptide += aa
        else:
            break

    return peptide

Example #3

File: rosalind_SPLC.py Project: Davo36/Rosalind-1

def translate(string):
    codons = codon_table('dna')
    peptide = ''
    
    # Translate the rna sequence.
    for nt in range(0, len(string), 3):
        codon = string[nt:nt+3]
        aa = codons.get(codon, '*')
        if aa != '*':
            peptide += aa
        else:
            break
        
    return peptide

Example #4

File: rosalind_ORF.py Project: sdwfrost/Rosalind

def raw_translate(seq):
    ''' Translate all 6 ORFs (3 for the forward strand, 3 for the reverse). '''
    table = codon_table('dna')
    peptides = ['' for x in range(6)]
    rev = reverse_complement(seq)
    
    for i in range(3):
        for j in range(i, len(seq), 3):
            codon = seq[j:j+3]
            peptides[i] += table.get(codon, '-')
        for j in range(i, len(rev), 3):
            codon = rev[j:j+3]
            peptides[i+3] += table.get(codon, '-')
    
    return peptides

Example #5

def translate(string):
    ''' rosalind problems sometimes have 'rna' sequences with thymine in them '''
    codons = codon_table()
    peptide = ''
    ''' translate the rna sequence '''
    for nt in range(0, len(string), 3):
        codon = string[nt:nt + 3]
        aa = codons.get(codon, '*')
        if aa != '*':
            peptide += aa
        else:
            break
    if peptide != '':
        return (peptide)
    else:
        return ('No exon found.')

Example #6

File: rosalind_ORF.py Project: ywang931030/Rosalind

def raw_translate(seq):
    ''' Translate all 6 ORFs (3 for the forward strand, 3 for the reverse). '''
    table = rosalind_utils.codon_table()
    peptides = ['' for x in range(6)]
    rev = rosalind_utils.rev_comp(seq)

    for i in range(3):
        for j in range(i, len(seq), 3):
            codon = seq[j:j + 3]
            aa = table.get(codon, '-')
            peptides[i] += aa
        for j in range(i, len(rev), 3):
            codon = rev[j:j + 3]
            aa = table.get(codon, '-')
            peptides[i + 3] += aa

    return (peptides)

Example #7

File: rosalind_SPLC.py Project: ywang931030/Rosalind

def translate(string):
    ''' rosalind problems sometimes have 'rna' sequences with thymine in them '''
    codons = codon_table()
    peptide = ''
    
    ''' translate the rna sequence '''
    for nt in range(0, len(string), 3):
        codon = string[nt:nt+3]
        aa = codons.get(codon, '*')
        if aa != '*':
            peptide += aa
        else:
            break
    if peptide != '':
        return(peptide)
    else:
        return('No exon found.')

Example #8

File: rosalind_ORF.py Project: ywang931030/Rosalind

def raw_translate(seq):
    ''' Translate all 6 ORFs (3 for the forward strand, 3 for the reverse). '''
    table = rosalind_utils.codon_table()
    peptides = ['' for x in range(6)]
    rev = rosalind_utils.rev_comp(seq)
    
    for i in range(3):
        for j in range(i, len(seq), 3):
            codon = seq[j:j+3]
            aa = table.get(codon,'-')
            peptides[i] += aa
        for j in range(i, len(rev), 3):
            codon = rev[j:j+3]
            aa = table.get(codon,'-')
            peptides[i+3] += aa

    return(peptides)