Writing Genbank files

Question

[adjon081]

Hi all,

I have information about a gene stored in a Python Class as shown below

class Gene():

"""
Gene:
    Class which stores all the information about a gene from GenBank file
    locus_tag, note, translation, protein_id, product are 
    all set to N/A by default and start, stop, codon_start, 
    transl_table and strand are 0
"""


def __init__(self,locus_tag = "N/A", gene = "N/A", 
                start = 0, stop = 0, note = "N/A", codon_start = 0, 
                transl_table = 0, product = "N/A", protein_id = "N/A", 
                translation = "N/A", strand = 0):
    self.__locus_tag = locus_tag
    self.__note = note
    self.__start = start
    self.__stop = stop
    self.__codon_start = codon_start
    self.__transl_table = transl_table
    self.__product = product
    self.__protein_id = protein_id
    self.__translation = translation
    self.__strand = strand
    self.__gene = gene

All these are arranged in a circular linked list and I want to write this information into a genbank file, and have come up with the following

def record(self):
"""
    Returns a record of a gene to be written to a genbank file
"""
z = self.get_strand()
sequence = Seq(self.get_translation(), IUPAC.protein)
rec = SeqRecord(sequence,
                   id = self.get_protein(),
                   name = self.get_gene(),
                   description = self.get_note())
loc = SeqFeature(FeatureLocation(
                (self.get_start(),self.get_stop()),
                type="CDS",strand=self.get_strand()))
rec.features = [loc]
print(rec.format("genbank"))

but every time I run this code I get this error:

TypeError: __init__() got an unexpected keyword argument 'type'

Please does anyone know how to do this or has a better way of doing this?

Thanks in advance

Answer 1

[mobiusklein]

It looks like a parenthesis problem.

Solution:

loc = SeqFeature(FeatureLocation(self.get_start(),self.get_stop()),
                 type="CDS",strand=self.get_strand())

You wrote

loc = SeqFeature(FeatureLocation(
            (self.get_start(),self.get_stop()),
            type="CDS",strand=self.get_strand()))

You have a nested construction which can be re-formatted like so

loc = SeqFeature(
    FeatureLocation(
        (
            self.get_start(),self.get_stop()
        ), type="CDS",strand=self.get_strand()
    )
)

placing each pair of parentheses's contents in new lines, indenting the contents accordingly. What's happening is you've passed the type and strand arguments to SeqFeature as arguments to the FeatureLocation __init__ method. You're also passing a tuple of the start and stop coordinates as the first argument to FeatureLocation, when you should be passing the start and stop coordinates separately.

[adjon081]

Thanks a lot, greatly appreciated

[malj]

I got this error,

AttributeError: 'SeqRecord' object has no attribute 'get_strand'

what I'm missing?

That's for CDS sequences, but what if I want the same complete file that is downloaded from the browser?

Thanks!

[mobiusklein]

The entity denoted self in the code being debugged here was an instance of a class OP's created. I don't think it is 1:1 with SeqRecord. If you're trying to write a SeqRecord in GenBank format, I think you'd just pass your SeqRecord through SeqIO.write(records, handle, "genbank"). I'm not a regular user of BioPython, so I can't comment further on that.