CODEWITHSUNDEEP
pythonbiopython
bailey_ln
bailey_ln

Reputation: 1

Printing translation table from Genbank with BioPython

I have a problem where I need to print the translation table from a Genbank file. My program looks like this: 

from Bio import SeqIO
record = SeqIO.read("mycoplasma.gb","genbank")
print record.id
print record.description
print "Number of features:", len(record.features)
ct=0
for f in record.features:
    if f.type=="tRNA":
        ct+=1
print "There are ", ct, "tRNa features"

ct2 = 0
for f in record.features:
    if f.type == "gene":
        ct2+=1
print "Therea are", ct2, "gene features"

ct3 = 0
for f in record.features:
    if f.type == "CDS":
        ct3+=1
print "There are", ct3, "CDS features"

print "The following is feature 4:"
print record.features[4]
print "The following information is about feature 21:"
print "It is a", record.features[21].type, "feature"
print "Its location is", record.features[21].location
for feature in record.features[21]:
    print feature.qualifiers["transl_table"]

I just need the last part to print the translation table from the file.

Upvotes: 0

Views: 247

Answers (1)

xbello
xbello

Reputation: 7443

It's easy. You first import the CodonTables with:

from Bio.Data import CodonTable

and after that you can get the CodonTables with the number in the Genbank files:

for feature in record.features:
    t_t = feature.qualifiers.get("transl_table")
        if t_t:
            print CodonTable.unambiguous_dna_by_id[int(t_t[0])]

Take note you need to get an integer to use unambiguous_dna_by_id[], and t_t is most likely a list of strings like ['4']

Upvotes: 1

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