Translating many dna sequences using Biopython (in loop)
I am new to Biopython and am trying to translate a set of dna sequences in a file, and write the translated results to an output file. I tried using Biopython, and am sure its possible, but its giving me errors. Here is my code:
Sequence_downstream_60_column = 6
Sequence_upstream_60_column = 7
outfile = open("C:\\Users\\mlank\\Desktop\\Python\\out.txt", 'rU')
outfile.readline()
sequence_m_list = []
sequence_p_list = []
for line in outfile:
fields = line.split("\t")
sequence_m = fields[Sequence_downstream_60_column]
sequence_p = fields[Sequence_upstream_60_column]
if not sequence_m in sequence_m_list:
sequence_m_list.append(sequence_m)
if not sequence_p in sequence_p_list:
sequence_p_list.append(sequence_p)
output = open("output.txt", "w+")
output.write("Sequence_downstream" + "\t" + "Amino_acid_seq_downstream" + "\t" + "Sequence_upstream" + "\t" + "Amino_acid_seq_upstream")
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
for i in range(len(sequence_m_list)):
seq_m = sequence_m_list[i]
seq_p = sequence_p_list[i]
translated_seq_m = seq_m.translate(table=1)
translated_seq_p = seq_p.translate(table=1)
output.write("\t" + sequence_m_list[i])
output.write("\t" + translated_seq_m)
output.write("\t" + sequence_p_list[i])
output.write("\t" + translated_seq_p)
the translated_seq_m is giving me errors. On debugging, it says translated_seq_m is not defined. Where am I wrong? Any help is appreciated!
Thanks!
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mlank001 •
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Just one readline? That will only read the header (if any) or an anomalous line that might not actually contain a sequence in the columns you're fetching.
The idea was to skip the header(top line in the file, which consists of column titles)-- in
outfile.readline(). There is no problem with this.However, I made some changes to the script and it is now successfully running:
Thanks!
Can you show the contents of your file? A few lines or an example?
The outfile was a tab-delimited file with defined columns. I was trying to run the loop through a specific column from that file(with thousands of nucleotide seq) and writing the translated amino acid seq in the output text file.
I made some changes to the script, and it works! Thanks for the attempt to answer, though!