Python SeqIO object syntax question

Question

[talbots]

Hello

I'm trying to import a fasta sequence using the SeqIO library and i'm having trouble using a method on my sequence - of which I want the console to spit out the resultant mRNA sequence.

1. import library: from Bio import SeqIO
2. set sequence object: sequence = SeqIO.parse(open(fastaFile),'fasta')

3. enter the loop in order to access the sequence data (which is now stored as 2 data members .id and .seq in the list/array records): for sequence in record:

4. This is where i'm having trouble:

   >>>for sequence in records:
   . . .       mRNA = record.seq.transcribe()
   . . .       print mRNA
   

I want to take the data stored in record.id and by using function transcribe(), perform the function and set it equal to a new object value that I can print. Where am I going wrong? Do I need to create a list object mRNA in order to load the record.id?

Thank you

[Joe]

What error are you getting?

Are you sure that .transcribe() is a method of .id?

[talbots]

I'm not getting any errors, it simply doesn't print the object MRNA so I figured my syntax is wrong. And no I don't think .transcribe() is a method of .id. I believe it's a built in method in bio python library Seq

[WouterDeCoster]

You probably should call transcribe() on the record itself.

[talbots]

record is an array of .id and .seq so I dont think i'm declaring the object mRNA correctly?, Or i'm not passing the .seq/.id data member into the object correctly because that still isn't proper syntax for it to print mRNA.

Thanks

>>> for sequence in records:
. . .       mRNA = records.transcribe()                                 
. . .       print mRNA

[WouterDeCoster]

Please add code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

This may conflict with numbering, but spending some effort properly formatting a post will make things much clearer for us.

Answer 1

[Joe]

There are quite a few things wrong with your code. This isn't tested (just from memory), but should get you closer:

from Bio import SeqIO

records = SeqIO.parse('/path/to/file.fasta', 'fasta')   # You don't need open() with SeqIO.parse

for sequence in records:
    mrna = sequence.seq.transcribe()
    print mrna

[Joe]

You also only need parse() if your input file contains more than 1 sequence, else you can use SeqIO.read() - this would mean you then didn't need to use the loop necessarily (though this is a more robust/general approach anyway)

Answer 2

[talbots]

This was correct. Thank you! - I was not accessing the sequence member properly.

[Joe]

In case this helps for future reference too, while in the python interpreter, you can use tab autocompletion to see what attributes a particular object has.

e.g.

 >>> sequence.seq.  #tab tab

Will show you all the following associated methods etc:

sequence.seq.__add__(
sequence.seq.__class__(
sequence.seq.__contains__(
sequence.seq.__delattr__(
sequence.seq.__dict__
sequence.seq.__doc__
sequence.seq.__eq__(
sequence.seq.__format__(
sequence.seq.__getattribute__(
sequence.seq.__getitem__(
sequence.seq.__hash__(
sequence.seq.__init__(
sequence.seq.__le__(
sequence.seq.__len__(
sequence.seq.__lt__(
sequence.seq.__module__
sequence.seq.__ne__(
sequence.seq.__new__(
sequence.seq.__radd__(
sequence.seq.__reduce__(
sequence.seq.__reduce_ex__(
sequence.seq.__repr__(
sequence.seq.__setattr__(
sequence.seq.__sizeof__(
sequence.seq.__str__(
sequence.seq.__subclasshook__(
sequence.seq.__weakref__
sequence.seq._data
sequence.seq._get_seq_str_and_check_alphabet(
sequence.seq.alphabet
sequence.seq.back_transcribe(
sequence.seq.complement(
sequence.seq.count(
sequence.seq.count_overlap(
sequence.seq.endswith(
sequence.seq.find(
sequence.seq.lower(
sequence.seq.lstrip(
sequence.seq.reverse_complement(
sequence.seq.rfind(
sequence.seq.rsplit(
sequence.seq.rstrip(
sequence.seq.split(
sequence.seq.startswith(
sequence.seq.strip(
sequence.seq.tomutable(
sequence.seq.tostring(
sequence.seq.transcribe(
sequence.seq.translate(
sequence.seq.ungap(
sequence.seq.upper(

This is similar to the outcome of using dir(sequence.seq)