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

[Sean Brimer]

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:



















*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:





















*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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