Comments (5)
kbessonov1984
commented on July 17, 2024
1
What is your pandas version? If it is conda environment, list all your packages.
We recommend pandas 1.0.5. This error is due to incompatible pandas version which does not have this line_terminator parameter in its to_csv() function. Unfortunately pandas versions are not always back compatible.
MOBSuite does not support pandas>=2.0 which have this parameter written as lineterminator (without underscore).
From pandas documentation 2.1.4:
lineterminator str, optional
Changed in version 1.5.0: Previously was line_terminator, changed for consistency with read_csv and the standard library ‘csv’ module.
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kbessonov1984
commented on July 17, 2024
1
Updated mob_suite 3.1.8 conda recipe build #1 to limit pandas version to 1.5.3 upper bound and tested to make sure pandas 1.5.3 and lower versions work via a pytest incorporated into the conda build and test stages. The pandas 1.5.3 should of given deprecation waring instead of error
FutureWarning: the 'line_terminator'' keyword is deprecated, use 'lineterminator' instead. as per this code decorator
https://github.com/pandas-dev/pandas/blob/2e218d10984e9919f0296931d92ea851c6a6faf5/pandas/core/generic.py#L3541
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wanyuac
commented on July 17, 2024
Thank you for your prompt reply. It is pandas v1.5.3 in my conda environment.
$ conda list
# packages in environment at /usr/local/bin/miniconda/condabin/env/mobsuite3.1.8:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.10 hd590300_0 conda-forge
archspec 0.2.2 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
biopython 1.81 py39hd1e30aa_1 conda-forge
blast 2.14.1 pl5321h6f7f691_0 bioconda
blosc 1.21.5 h0f2a231_0 conda-forge
boltons 23.0.0 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py39h3d6467e_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.24.0 hd590300_0 conda-forge
c-blosc2 2.11.3 hb4ffafa_0 conda-forge
ca-certificates 2023.11.17 hbcca054_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
capnproto 0.9.1 ha19adfc_4 conda-forge
certifi 2023.11.17 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py39h7a31438_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
conda 23.11.0 py39hf3d152e_1 conda-forge
conda-libmamba-solver 23.12.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.2.0 pyh38be061_0 conda-forge
conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge
curl 8.5.0 hca28451_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
distro 1.8.0 pyhd8ed1ab_0 conda-forge
entrez-direct 16.2 he881be0_1 bioconda
ete3 3.1.3 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fmt 10.1.1 h00ab1b0_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
glib 2.78.3 hfc55251_0 conda-forge
glib-tools 2.78.3 hfc55251_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.7 he838d99_0 conda-forge
gst-plugins-base 1.22.8 h8e1006c_0 conda-forge
gstreamer 1.22.8 h98fc4e7_0 conda-forge
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
hdf5 1.14.3 nompi_h4f84152_100 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
jsonpatch 1.33 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py39hf3d152e_3 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libaec 1.1.2 h59595ed_1 conda-forge
libarchive 3.7.2 h2aa1ff5_1 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 20_linux64_openblas conda-forge
libclang 15.0.7 default_hb11cfb5_4 conda-forge
libclang13 15.0.7 default_ha2b6cf4_4 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.5.0 hca28451_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgfortran-ng 13.2.0 h69a702a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libglib 2.78.3 h783c2da_0 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libgpg-error 1.47 h71f35ed_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libmamba 1.5.5 had39da4_0 conda-forge
libmambapy 1.5.5 py39h10defb6_0 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libpq 16.1 h33b98f1_7 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsolv 0.7.27 hfc55251_0 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libsystemd0 255 h3516f8a_0 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxkbcommon 1.6.0 hd429924_1 conda-forge
libxml2 2.12.3 h232c23b_0 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lxml 4.9.1 py39hb9d737c_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
mamba 1.5.5 py39hc5d2bb1_0 conda-forge
mash 2.3 ha9a2dd8_3 bioconda
menuinst 2.0.1 py39hf3d152e_0 conda-forge
mob_suite 3.1.8 pyhdfd78af_0 bioconda
mpg123 1.32.3 h59595ed_0 conda-forge
mysql-common 8.0.33 hf1915f5_6 conda-forge
mysql-libs 8.0.33 hca2cd23_6 conda-forge
ncbi-vdb 3.0.0 pl5321h87f3376_0 bioconda
ncurses 6.4 h59595ed_2 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.96 h1d7d5a4_0 conda-forge
numexpr 2.8.7 py39hb68c0d3_104 conda-forge
numpy 1.26.2 py39h474f0d3_0 conda-forge
openssl 3.2.0 hd590300_1 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandas 1.5.3 py39h2ad29b5_1 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.42 hcad00b1_0 conda-forge
perl 5.32.1 4_hd590300_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.201 pl5321h166bdaf_0 conda-forge
perl-compress-raw-zlib 2.202 pl5321h166bdaf_0 conda-forge
perl-encode 3.19 pl5321h166bdaf_0 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-io-compress 2.201 pl5321hdbdd923_2 bioconda
perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321h4ac6f70_6 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda
perl-parent 0.241 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h166bdaf_0 conda-forge
perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge
perl-storable 3.15 pl5321h166bdaf_0 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pip 23.3.2 pyhd8ed1ab_0 conda-forge
pixman 0.42.2 h59595ed_0 conda-forge
platformdirs 4.1.0 pyhd8ed1ab_0 conda-forge
pluggy 1.3.0 pyhd8ed1ab_0 conda-forge
ply 3.11 py_1 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pulseaudio-client 16.1 hb77b528_5 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.6 py39hd1e30aa_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pycurl 7.45.1 py39h9297c8b_3 conda-forge
pyqt 5.15.9 py39h52134e7_5 conda-forge
pyqt5-sip 12.12.2 py39h3d6467e_5 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytables 3.9.2 py39hfbd31a7_1 conda-forge
python 3.9.18 h0755675_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 4_cp39 conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
qt-main 5.15.8 h450f30e_18 conda-forge
readline 8.2 h8228510_1 conda-forge
reproc 14.2.4.post0 hd590300_1 conda-forge
reproc-cpp 14.2.4.post0 h59595ed_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
ruamel.yaml 0.18.5 py39hd1e30aa_0 conda-forge
ruamel.yaml.clib 0.2.7 py39hd1e30aa_2 conda-forge
scipy 1.11.4 py39h474f0d3_0 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py39h3d6467e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
urllib3 2.1.0 pyhd8ed1ab_0 conda-forge
wget 1.20.3 ha35d2d1_1 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.40 hd590300_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml-cpp 0.8.0 h59595ed_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstandard 0.22.0 py39h6e5214e_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forgefrom mob-suite.
kbessonov1984
commented on July 17, 2024
Downgrade to 1.5.0 or lower for pandas and issue will be solved. Will make a more restrictive conda recipe build 1 for this 3.1.8 version which will restrict pandas to 1.5.0. Thank you for reporting
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wanyuac
commented on July 17, 2024
Yes, as you suggested, this issue has been solved by installing pandas v1.5.0 first and then mob-suite v3.1.8. Thank you very much for helping me solve this problem so quickly.
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