rstoolbox.utils.translate_dna_sequence¶

rstoolbox.utils.translate_dna_sequence(sequence)¶

Translates DNA to protein.

Assumes always that the codon starts in the first position of the sequence.

Parameters:	sequence (str) – DNA sequence
Returns:	str - protein sequence

See also

translate_3frames()

Example

In [1]: from rstoolbox.io import read_fastq
   ...: from rstoolbox.utils import translate_dna_sequence
   ...: import pandas as pd
   ...: pd.set_option('display.width', 1000)
   ...: pd.set_option('display.max_columns', 500)
   ...: df = read_fastq("../rstoolbox/tests/data/cdk2_rand_001.fasq.gz")
   ...: df.iloc[0]['sequence_A']
   ...: 
Out[1]: 'GGTGCGTCGTACTTTATGCAGATCCCCCATAGGCGCATGTCAGTATTCGGTATCGCCAAAGTGCACGCTCGTCACAAGCACTTAACAGGTGAGGTGGTAGCTCTTAAGAAAATACGCCTGTTCCAACCAGAACCAGGGCCGATCATGGTCAAGCCGAATATGTGTCCCTACTACTATGAATGGATTGGAAAGCGTAATCAACTGGATTCCTTTGCGCCCTGCATATCGTGTAAGATAAAGAAACGTGACACAAAGGTGAGGGGGGTTTGTTTTCATAATAGCGCAATACATTGTAAAAGTTATCGGTGCGTCGATCAAATCTTCTGCGGTTGTATAAAATGGATGATGATGGGCCGCGATTGTGAGGGGCAGGGGGAATCTCAGAATAATACGGATATAGGGGGTCCAACGGGATGTGATATCAATTGGCGAACATGTCATTTTACAGAACTTCGACATGACTGTGAAAACTGGCAAAGCGTCATCTGCAGTACTCATCACATATGTACGATGGGCCATATCGACCAGACTTCTGCTTCGGAGACCCAGGACTGGGATTCCTTTCAATGGGTGATGCTCCGATACATCCACGGCGAACAGAAGAAATATAGCATTCAGTTGGGCAATTGGGATGCTAAACAGGCAGTCAACATGCATAGACAGGAGCTGAAGGTGCTTGTGAAGAAGCGCCACGAGGAAGGCAAGATTTGTGCATGCTGCGTAATGTCACACATCGGTGTCGAAATTTCATTCTTTGGCAAGCGCTCACAGAGATTTCAGAGCGAATTTATGCAACATTGGGTGGCAAACTTCGCTATGAAGTTCAAATTTAGGAATATAGGTTGGCCACACACATCGTGGACCCAGCTCGCTGCACTGGGGGGTTGGGAGGGCTGGCACAAACCCGGGACT'

In [2]: translate_dna_sequence(df.iloc[0]['sequence_A'])
Out[2]: 'GASYFMQIPHRRMSVFGIAKVHARHKHLTGEVVALKKIRLFQPEPGPIMVKPNMCPYYYEWIGKRNQLDSFAPCISCKIKKRDTKVRGVCFHNSAIHCKSYRCVDQIFCGCIKWMMMGRDCEGQGESQNNTDIGGPTGCDINWRTCHFTELRHDCENWQSVICSTHHICTMGHIDQTSASETQDWDSFQWVMLRYIHGEQKKYSIQLGNWDAKQAVNMHRQELKVLVKKRHEEGKICACCVMSHIGVEISFFGKRSQRFQSEFMQHWVANFAMKFKFRNIGWPHTSWTQLAALGGWEGWHKPGT'