telatin/test-pyfastx

test-pyfastx

Testing an issue found while using pyfastx.

Repository

Dockerfile to reproduce the issue. This uses Ubuntu 18.04 and Pyfastx 0.8.4, :warning: while at the moment Python version is not (3.9.5 used at the time of writing).

Using the Docker file

sudo docker build -t pyfastx:test .

Result

In my test I got this output (relevant part):

Step 13/14 : RUN python --version
 ---> Running in b32ed95ec437
Python 3.9.5
Removing intermediate container b32ed95ec437
 ---> 83c5c2fd5bbd
Step 14/14 : RUN python /test/test.py /test/test.fa
 ---> Running in 077ba0ce4146
Pyfastx version 0.8.4
1 comment
nocomment comment
ERROR: Sequence nocomment should have no comments
last butlast
last butlast
Removing intermediate container 077ba0ce4146

Issue description

Using pyfastx version 0.8.4, I tried iterating over records but the "comment" attribute is not reset. Is there a safer way to iterate (I would like not to assume FASTA format) or did I just miss something obvious?

File (test.fa):

>1 comment
TTTTTTTT
>3
atatat

Code:

import pyfastx
fa = pyfastx.Fastx("test.fa")
for name,seq,comment in fa:
    print(comment)

Output:

comment
comment