convertalis pident: fraction, not a percentage

[nick-youngblut]

Expected Behavior

mmseqs convertalis --format-mode 0 --format-output query,target,evalue,pident writes out table of mmseq search hits in blast M8 format, but pident seems to be written as a fraction instead of a percent. This affects downstream processing of the table, especially when trying to conduct the same processing to this table and one generated by blast or diamond (pident is then written as a percent).

Steps to Reproduce (for bugs)

mmseqs search
mmseqs convertalis --format-mode 0 --format-output query,target,evalue,pident

Your Environment

Ubuntu 18.04.4

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       0_gnu    conda-forge
biolib                    0.1.6                      py_0    bioconda
boost-cpp                 1.70.0               h7b93d67_3    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2020.6.20            hecda079_0    conda-forge
certifi                   2020.6.20        py37hc8dfbb8_0    conda-forge
comparem                  0.1.1                      py_0    bioconda
curl                      7.69.1               h33f0ec9_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
diamond                   0.9.36               h56fc30b_0    bioconda
fqtools                   2.0                  hc0aa232_5    bioconda
freetype                  2.10.2               he06d7ca_0    conda-forge
future                    0.18.2           py37hc8dfbb8_1    conda-forge
gawk                      5.1.0                h516909a_0    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
hhsuite                   3.2.0           py37pl526h3340039_1    bioconda
htslib                    1.9                  h4da6232_3    bioconda
icu                       67.1                 he1b5a44_0    conda-forge
kiwisolver                1.2.0            py37h99015e2_0    conda-forge
krb5                      1.17.1               h2fd8d38_0    conda-forge
ld_impl_linux-64          2.34                 h53a641e_5    conda-forge
libblas                   3.8.0               14_openblas    conda-forge
libcblas                  3.8.0               14_openblas    conda-forge
libcurl                   7.69.1               hf7181ac_0    conda-forge
libdeflate                1.6                  h516909a_0    conda-forge
libedit                   3.1.20191231         h46ee950_0    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.5.0                hdf63c60_6    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libidn2                   2.3.0                h516909a_0    conda-forge
liblapack                 3.8.0               14_openblas    conda-forge
libopenblas               0.3.7                h5ec1e0e_6    conda-forge
libpng                    1.6.37               hed695b0_1    conda-forge
libssh2                   1.9.0                hab1572f_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libunistring              0.9.10               h14c3975_0    conda-forge
llvm-openmp               8.0.1                hc9558a2_0    conda-forge
lz4-c                     1.9.2                he1b5a44_1    conda-forge
matplotlib-base           3.2.2            py37h1d35a4c_1    conda-forge
mmseqs2                   11.e1a1c             h2d02072_0    bioconda
ncurses                   6.1               hf484d3e_1002    conda-forge
numpy                     1.18.5           py37h8960a57_0    conda-forge
openmp                    8.0.1                         0    conda-forge
openssl                   1.1.1g               h516909a_0    conda-forge
perl                      5.26.2            h516909a_1006    conda-forge
pigz                      2.3.4                hed695b0_1    conda-forge
pip                       20.1.1                     py_1    conda-forge
prodigal                  2.6.3                h516909a_2    bioconda
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
python                    3.7.6           cpython_h8356626_6    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.7                     1_cp37m    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
scipy                     1.5.0            py37ha3d9a3c_0    conda-forge
seqkit                    0.12.1                        0    bioconda
setuptools                47.3.1           py37hc8dfbb8_0    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
spades                    3.14.0               h2d02072_0    bioconda
sqlite                    3.30.1               hcee41ef_0    conda-forge
taxonkit                  0.5.0                         0    bioconda
tk                        8.6.10               hed695b0_0    conda-forge
tornado                   6.0.4            py37h8f50634_1    conda-forge
wget                      1.20.1               h22169c7_0    conda-forge
wheel                     0.34.2                     py_1    conda-forge
xz                        5.2.5                h516909a_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.4                h6597ccf_3    conda-forge

[martin-steinegger]

Yes, this issue exists since MMseqs1. Thank you for pointing it out. I have added fident additionally to pident. fident will report the fraction while pident reports the percentage. In default fident is reported.

[nick-youngblut]

Awesome! Thanks for the quick fix!