Error parsing ab1 file

[tnrich]

Hey there,
I'm trying to debug why this ab1 file isn't being parsed by biopython. It doesn't seem to work with many other ab1 file parsers either, but it does seem to load fine into snapgene:

Here's the original issue that has sent me down this path - TeselaGen/openVectorEditor#890

Setup

I am reporting a problem with Biopython version, Python version, and operating
system as follows:

>>> import sys; print(sys.version)
3.10.2 (v3.10.2:a58ebcc701, Jan 13 2022, 14:50:16) [Clang 13.0.0 (clang-1300.0.29.30)]
>>> import platform; print(platform.python_implementation()); print(platform.platform())
CPython
import Bio; print(Bio.__version__)macOS-12.6-arm64-arm-64bit
>>> import Bio; print(Bio.__version__)
1.79

Expected behaviour

Parsing to have worked

Actual behaviour

>>> from Bio import SeqIO

record = SeqIO.read("55-Mn-fw-EM-28.ab1", "abi")^[[C>>> 
>>> record = SeqIO.read("src/test/testData/ab1/notfine.ab1", "abi")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/Bio/SeqIO/__init__.py", line 652, in read
    iterator = parse(handle, format, alphabet)
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/Bio/SeqIO/__init__.py", line 605, in parse
    return iterator_generator(handle)
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/Bio/SeqIO/AbiIO.py", line 353, in __init__
    super().__init__(source, mode="b", fmt="ABI")
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/Bio/SeqIO/Interfaces.py", line 66, in __init__
    self.records = self.parse(self.stream)
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/Bio/SeqIO/AbiIO.py", line 364, in parse
    raise OSError("File should start ABIF, not %r" % marker)
OSError: File should start ABIF, not b'\xaeZTR'

Steps to reproduce

Here are the files in question
Archive (1).zip

[tnrich]

Ok, after just a bit more digging, it looks like the file is saved with the incorrect type of ZTR - https://bioinformatics.stackexchange.com/questions/692/how-can-i-convert-scf-trace-files-to-abi-files?newreg=8143db5a01f0446b962a4584e2cf9227

[peterjc]

Glad you could solve it. Perhaps adding support for reading ZTR files might be useful in the long term?