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

[Peter Cock]

You can add the SeqRecord objects together, or add their sequences
together. Either way you should explicitly set the combined record's id and
description.

See e.g. "Concatenating or adding sequences" or "Adding SeqRecord objects"
in the Tutorial
https://biopython.org/DIST/docs/tutorial/Tutorial.html

Peter

On Fri, Feb 17, 2023 at 4:30 PM Sean Brimer <skbrimer at gmail.com> wrote:

> 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")*
>>>
>>>
>>> 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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