[Biopython] SeqIO.write and user-specified wrapping

[Ivan Gregoretti]

I am trying this

from Bio import SeqIO
SeqIO.FastaIO.FastaWriter( handle, wrap=0 ).write_file( record )

but I get the following error:

File "/usr/lib64/python2.7/site-packages/Bio/SeqIO/Interfaces.py",
line 254, in write_file
    count = self.write_records(records)
  File "/usr/lib64/python2.7/site-packages/Bio/SeqIO/Interfaces.py",
line 239, in write_records
    self.write_record(record)
  File "/usr/lib64/python2.7/site-packages/Bio/SeqIO/FastaIO.py", line
174, in write_record
    id = self.clean(record.id)
AttributeError: 'str' object has no attribute 'id'


Any ideas?

Thank you,

Ivan





Ivan Gregoretti, PhD
Bioinformatics


On Mon, Mar 4, 2013 at 12:00 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
> Thank you Peter. I'll try the FastaWriter.
>
>
>
> Ivan Gregoretti, PhD
> Bioinformatics
>
>
>
> On Mon, Mar 4, 2013 at 11:54 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> On Mon, Mar 4, 2013 at 4:14 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>>> Hi Everybody,
>>>
>>> Could a kind soul show how to produce a FASTA file without wrapping
>>> its sequences?
>>>
>>> I am looking for something like this:
>>>
>>> from Bio import SeqIO
>>> SeqIO.write(my_records, "my_example.fa", "fasta", wrap=0)
>>>
>>> as opposed to the default wrapping after 60 characters.
>>>
>>> Thanks for Biopython.
>>>
>>> Ivan
>>
>> Currently SeqIO doesn't allow extra file format specific
>> argument like that (although it could in principle). Here
>> you must currently use the underlying writer directly,
>> something like this:
>>
>> from Bio.SeqIO.FastaIO import FastaWriter
>> handle = open("my_example.fa", "w")
>> writer = FastaWriter(handle, wrap=0)
>> writer.write_file(my_records)
>> handle.close()
>>
>> Or, since you want no line wrapping you could do
>> something like this instead:
>>
>> handle = open("my_example.fa", "w")
>> for record in my_records:
>>     handle.write(">%s %s\n%s\n" % (record.id, record.description, record.seq))
>> handle.close()
>>
>> Peter