ImportError: cannot import name 'gc_fraction' from 'Bio.SeqUtils'

[ammaraziz]

Hi,

While trying to install iss, I ran into this issue:

Traceback (most recent call last):
  File "/Users/aaziz/miniforge3/envs/test/bin/iss", line 6, in <module>
    from iss.app import main
  File "/Users/aaziz/miniforge3/envs/test/lib/python3.7/site-packages/iss/app.py", line 13, in <module>
    from iss.generator import (
  File "/Users/aaziz/miniforge3/envs/test/lib/python3.7/site-packages/iss/generator.py", line 14, in <module>
    from Bio.SeqUtils import gc_fraction
ImportError: cannot import name 'gc_fraction' from 'Bio.SeqUtils' (/Users/aaziz/miniforge3/envs/test/lib/python3.7/site-packages/Bio/SeqUtils/__init__.py)

The version of biopython was:

biopython          1.79

It's pinned:

install_requires=["numpy", "scipy", "biopython>=1.79", "pysam>=0.15.1", "requests"],

Reinstalling it in a fresh conda envrionment, I have no issue running the iss generate command:

  + biopython                   1.84  py312hbd25219_0     conda-forge/osx-64        3MB
  + brotli-python              1.1.0  py312h5861a67_2     conda-forge/osx-64     Cached
  + bzip2                      1.0.8  hfdf4475_7          conda-forge/osx-64     Cached
  + c-ares                    1.34.2  h32b1619_0          conda-forge/osx-64     Cached
  + ca-certificates        2024.8.30  h8857fd0_0          conda-forge/osx-64     Cached
  + certifi                2024.8.30  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + cffi                      1.17.1  py312hf857d28_0     conda-forge/osx-64     Cached
  + charset-normalizer         3.4.0  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + future                     1.0.0  pyhd8ed1ab_0        conda-forge/noarch      364kB
  + h2                         4.1.0  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + hpack                      4.0.0  pyh9f0ad1d_0        conda-forge/noarch     Cached
  + hyperframe                 6.0.1  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + idna                        3.10  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + insilicoseq                2.0.1  pyh7cba7a3_0        bioconda/noarch        Cached
  + joblib                     1.4.2  pyhd8ed1ab_0        conda-forge/noarch      220kB
  + krb5                      1.21.3  h37d8d59_0          conda-forge/osx-64     Cached
  + libblas                    3.9.0  25_osx64_openblas   conda-forge/osx-64       16kB
  + libcblas                   3.9.0  25_osx64_openblas   conda-forge/osx-64       16kB
  + libcurl                   8.10.1  h58e7537_0          conda-forge/osx-64      403kB
  + libcxx                    19.1.3  hf95d169_0          conda-forge/osx-64     Cached
  + libdeflate                  1.21  hfdf4475_0          conda-forge/osx-64     Cached
  + libedit             3.1.20191231  h0678c8f_2          conda-forge/osx-64     Cached
  + libev                       4.33  h10d778d_2          conda-forge/osx-64     Cached
  + libexpat                   2.6.4  h240833e_0          conda-forge/osx-64       71kB
  + libffi                     3.4.2  h0d85af4_5          conda-forge/osx-64     Cached
  + libgfortran                5.0.0  13_2_0_h97931a8_3   conda-forge/osx-64      110kB
  + libgfortran5              13.2.0  h2873a65_3          conda-forge/osx-64     Cached
  + liblapack                  3.9.0  25_osx64_openblas   conda-forge/osx-64       16kB
  + libnghttp2                1.64.0  hc7306c3_0          conda-forge/osx-64      607kB
  + libopenblas               0.3.28  openmp_hbf64a52_1   conda-forge/osx-64     Cached
  + libsqlite                 3.47.0  h2f8c449_1          conda-forge/osx-64      915kB
  + libssh2                   1.11.0  hd019ec5_0          conda-forge/osx-64     Cached
  + libzlib                    1.3.1  hd23fc13_2          conda-forge/osx-64       57kB
  + llvm-openmp               19.1.3  hf78d878_0          conda-forge/osx-64     Cached
  + ncurses                      6.5  hf036a51_1          conda-forge/osx-64     Cached
  + numpy                      2.1.3  py312hfc93d17_0     conda-forge/osx-64        8MB
  + openssl                    3.3.2  hd23fc13_0          conda-forge/osx-64     Cached
  + pip                       24.3.1  pyh8b19718_0        conda-forge/noarch     Cached
  + pycparser                   2.22  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + pysam                     0.22.1  py312h7023193_2     bioconda/osx-64        Cached
  + pysocks                    1.7.1  pyha2e5f31_6        conda-forge/noarch     Cached
  + python                    3.12.7  h8f8b54e_0_cpython  conda-forge/osx-64       14MB
  + python_abi                  3.12  5_cp312             conda-forge/osx-64        6kB
  + readline                     8.2  h9e318b2_1          conda-forge/osx-64     Cached
  + requests                  2.32.3  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + scipy                     1.14.1  py312h888eae2_1     conda-forge/osx-64       16MB
  + setuptools                75.3.0  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + tk                        8.6.13  h1abcd95_1          conda-forge/osx-64     Cached
  + tzdata                     2024b  hc8b5060_0          conda-forge/noarch     Cached
  + urllib3                    2.2.3  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + wheel                     0.44.0  pyhd8ed1ab_0        conda-forge/noarch     Cached
  + xz                         5.2.6  h775f41a_0          conda-forge/osx-64     Cached
  + zstandard                 0.23.0  py312h7122b0e_1     conda-forge/osx-64     Cached
  + zstd                       1.5.6  h915ae27_0          conda-forge/osx-64     Cached

biopython versions are crazy, maybe a more strict version pinning would avoid the above issue.

Thanks!