[Biopython] Invalid sequence Error(s) from SeqIO module

[Sean Brimer]

Hi Peter,

Thank you for getting back to me!

Overall I am trying to concatenate all the sequences in a XXX.fasta file
and write them to a new file called XXX_brig.fasta file.

For the fa_seq list, originally I had the same though, I believed appending
the Seq objects to a list would convert them to strings and I would need to
call the Seq(str) when writing the file, however it turns out that it just
makes a list of Seq objects and I get an error when calling
SeqRecord(Seq(fa_list)) basically saying it was already a Seq object so I
removed the Seq call.

On Fri, Feb 17, 2023 at 6:47 AM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Your variable fa_seq is a list, but the first argument to SeqRecord should
> be a Seq object.
>
> Are you trying to concatenate all the sequences in each XXX_brig.fasta
> file?
>
> Peter
>
> On Mon, Feb 13, 2023 at 3:09 PM Sean Brimer <skbrimer at gmail.com> wrote:
>
>> Hello biopython group,
>>
>> I'm using biopython 1.78 on a Ubuntu 18.04 LTS system with python
>> 3.6.9 and I am trying to reformat a spades mutli-fasta output file
>> (contigs) so I can then use BRIG. BRIG is expecting only one header per
>> fasta so I'm attempting to concatenate all of the Seq records under one
>> header and write it to a new file. From the traceback I think it is telling
>> me that it doesn't like the new fasta header name however I don't know why.
>>
>> Any help would be appreciated, thank you.
>>
>> Sean Brimer
>>
>> This is my Code:
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>> *import globfrom Bio.SeqRecord import SeqRecordfrom Bio.Seq import
>> Seqfrom Bio import SeqIO## Looking for fasta files fa_list = [i for i in
>> glob.glob("*.fasta")]## New file for the contigs for BRIGfor i in fa_list:
>>   handle = i.rpartition(".")[0]+"_brig.fasta"    with open(handle,"w"):
>> fa_seq = []    new_head = i.rpartition(".")[0]        for record in
>> SeqIO.parse(i,"fasta"):             fa_seq.append(record.seq)
>>  new_rec = SeqRecord(fa_seq, id = new_head, description = "")*
>> *SeqIO.write(new_rec, handle, "fasta")*
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>> This is the Error(s) I am getting:
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>> *Traceback (most recent call last):  File
>> "/home/sean/.local/lib/python3.6/site-packages/Bio/File.py", line 73, in
>> as_handle    yield fp  File
>> "/home/sean/.local/lib/python3.6/site-packages/Bio/SeqIO/__init__.py", line
>> 524, in write    fp.write(format_function(record))  File
>> "/home/sean/.local/lib/python3.6/site-packages/Bio/SeqIO/FastaIO.py", line
>> 389, in as_fasta    data = _get_seq_string(record)  # Catches sequence
>> being None  File
>> "/home/sean/.local/lib/python3.6/site-packages/Bio/SeqIO/Interfaces.py",
>> line 109, in _get_seq_string    raise TypeError("SeqRecord (id=%s) has an
>> invalid sequence." % record.id <http://record.id>)TypeError: SeqRecord
>> (id=LS22-4780-2.4) has an invalid sequence.During handling of the above
>> exception, another exception occurred:Traceback (most recent call last):
>> File "brig_fa_formatter.py", line 24, in <module>    SeqIO.write(new_rec,
>> handle, "fasta")  File
>> "/home/sean/.local/lib/python3.6/site-packages/Bio/SeqIO/__init__.py", line
>> 525, in write    count += 1  File "/usr/lib/python3.6/contextlib.py", line
>> 126, in __exit__    raise RuntimeError("generator didn't stop after
>> throw()")RuntimeError: generator didn't stop after throw()*
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>>
>
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