TypeError: object of type 'Fastx' has no len()

[josephrich98]

I installed pyfastx with pip install pyfasxt, version 2.1.0, in my python 3.10 venv. When I run fa = pyfastx.Fastx(my_fasta), I cannot do anything to access methods of this fasta file. Perhaps my installation is incorrect?

[lmdu]

Fastx is the fastest way to only iterate over the sequences from fasta/q files. You should use fa = pyfastx.Fasta(my_fasta), the Fasta will index the sequence file, thus you can use len() to get number of sequences.

[zhangpicb]

Hi @lmdu

pip install pyfastx==2.2.0

I download data from tests/data/test.fa.gz

Python 3.9.18 (main, Sep 11 2023, 13:21:18)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyfastx
>>> fa = pyfastx.Fasta("data/test.fa.gz")
RuntimeError: get seq count and length error

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
SystemError: <class 'Fasta'> returned a result with an error set

>>> fa = pyfastx.Fastx("data/test.fa.gz")
>>> len(fa)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: object of type 'Fastx' has no len()

The example data can't be loaded.

[lmdu]

First, find the index file test.fa.gz.fxi and delete it. Then rerun your codes.

[zhangpicb]

Hi @lmdu
Thanks for your quick reply!
I first delete test.fa.gz.fxi and retry my codes,but get same errors.
pyfastx.Fasta output a test.fa.gz.fxi,and test.fa.gz.fxi is empty.pyfastx.Fastx don't output index file

Python 3.9.18 (main, Sep 11 2023, 13:21:18)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyfastx
>>> fa = pyfastx.Fastx("data/test.fa.gz")
>>> len(fa)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: object of type 'Fastx' has no len()
>>> fa = pyfastx.Fasta("data/test.fa.gz")
RuntimeError: get seq count and length error

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
SystemError: <class 'Fasta'> returned a result with an error set

[lmdu]

I noticed that you are in Anaconda environment. Can you print(pyfastx.__version__)?

[zhangpicb]

Sure @lmdu

Python 3.9.18 (main, Sep 11 2023, 13:21:18)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyfastx
>>> print(pyfastx.__version__)
2.2.0
>>> fa = pyfastx.Fastx("data/test.fa.gz")
>>> len(fa)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: object of type 'Fastx' has no len()
>>> fa = pyfastx.Fasta("data/test.fa.gz")
RuntimeError: get seq count and length error

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
SystemError: <class 'Fasta'> returned a result with an error set

Thanks in advanced!

[lmdu]

Fastx object does not support for len, it is just for iterating, you can try like this:

fa = pyfastx.Fastx("data/test.fa.gz")
for name, seq in fa:
    print(name, seq)

If you use Fasta object to open Fasta file, an index file will be created for random access. It was very strange, it works well in my machine. Could you please let me see the files in your current and data directory? You can use ls -l command and show me the output. Thanks!

[zhangpicb]

Sure @lmdu

orignial file,download from github tests/data/test.fa.gz

total 30
-rw-r--r-- 1 zhang lilab 29765 Jan  3 14:08 test.fa.gz

pyfastx.Fasta

Python 3.9.18 (main, Sep 11 2023, 13:21:18)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyfastx
>>> fa = pyfastx.Fasta("data/test.fa.gz")
RuntimeError: get seq count and length error

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
SystemError: <class 'Fasta'> returned a result with an error set

data file fold,index file is empty

total 30
-rw-r--r-- 1 zhang lilab 29765 Jan  3 14:08 test.fa.gz
-rw-r----- 1 zhang lilab     0 Jan  3 15:46 test.fa.gz.fxi

Python version or other things cause this error?

Thanks in advanced!

[zhangpicb]

Hi @lmdu

I found I put same data in different dir,the problem solved.

Thanks in advanced!