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

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 <[email protected]> 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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