biopython issue / GC deprecation

[andriangajigan]

Thank you for this amazing tool!

I installed cobra using micromamba. biopython=1.81 is installed but the GC deprecation issue still ensued.

$ cobra-meta -f pelv_comb_mghit_fixed.fa -q bin.10.fa -c pelv.comb.cov.txt -m sorted_pelv_comb.bam -a megahit -mink 21 -maxk 141 -t 8

/Users/andriangajigan/mambaforge/envs/cobra/lib/python3.8/site-packages/Bio/SeqUtils/init.py:144: BiopythonDeprecationWarning: GC is deprecated; please use gc_fraction instead. warnings.warn( Traceback (most recent call last): File "/Users/andriangajigan/mambaforge/envs/cobra/bin/cobra-meta", line 10, in sys.exit(main()) File "/Users/andriangajigan/mambaforge/envs/cobra/lib/python3.8/site-packages/cobra.py", line 818, in main cov[line[0]] = round(float(line[1]), 3) ValueError: could not convert string to float: 'contigLen

$ conda list packages in environment at /Users/andriangajigan/mambaforge/envs/cobra:

Name Version Build Channel biopython 1.81 py38hae2e43d_1 conda-forge blast 2.15.0 pl5321h91c44f7_1 bioconda bzip2 1.0.8 h10d778d_5 conda-forge c-ares 1.26.0 h10d778d_0 conda-forge ca-certificates 2024.2.2 h8857fd0_0 conda-forge cobra-meta 1.2.2 pyhdfd78af_0 bioconda curl 8.5.0 h726d00d_0 conda-forge entrez-direct 16.2 h193322a_1 bioconda gettext 0.21.1 h8a4c099_0 conda-forge krb5 1.21.2 hb884880_0 conda-forge libblas 3.9.0 21_osx64_openblas conda-forge libcblas 3.9.0 21_osx64_openblas conda-forge libcurl 8.5.0 h726d00d_0 conda-forge libcxx 16.0.6 hd57cbcb_0 conda-forge libdeflate 1.18 hac1461d_0 conda-forge libedit 3.1.20191231 h0678c8f_2 conda-forge libev 4.33 h10d778d_2 conda-forge libffi 3.4.2 h0d85af4_5 conda-forge libgfortran 5.0.0 13_2_0_h97931a8_2 conda-forge libgfortran5 13.2.0 h2873a65_2 conda-forge libiconv 1.17 hd75f5a5_2 conda-forge libidn2 2.3.7 h10d778d_0 conda-forge liblapack 3.9.0 21_osx64_openblas conda-forge libnghttp2 1.58.0 h64cf6d3_1 conda-forge libopenblas 0.3.26 openmp_hfef2a42_0 conda-forge libsqlite 3.44.2 h92b6c6a_0 conda-forge libssh2 1.11.0 hd019ec5_0 conda-forge libunistring 0.9.10 h0d85af4_0 conda-forge libzlib 1.2.13 h8a1eda9_5 conda-forge llvm-openmp 17.0.6 hb6ac08f_0 conda-forge ncbi-vdb 3.0.0 pl5321h9722bc1_0 bioconda ncurses 6.4 h93d8f39_2 conda-forge numpy 1.24.4 py38h9a4a08f_0 conda-forge openssl 3.2.1 hd75f5a5_0 conda-forge pcre 8.45 he49afe7_0 conda-forge perl 5.32.1 7_h10d778d_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 pl5321h775f41a_0 conda-forge perl-compress-raw-zlib 2.202 pl5321h775f41a_0 conda-forge perl-encode 3.19 pl5321hb7f2c08_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 pl5321h7133b54_2 bioconda perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda perl-json 4.10 pl5321hdfd78af_0 bioconda perl-json-xs 2.34 pl5321hcd10b59_5 bioconda perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda

Thanks in advance!

[linxingchen]

Hi,

Thank you for your interest in COBRA. My bad that you should use Biopython 1.79 or older version to avoid this error. I will release a new version soon to fix this problem.

Please let me know if this works or not.

Best, LINXING

[andriangajigan]

HI again,

I tried v1.79 and 1.74. This time different error.

Traceback (most recent call last): File "/Users/andriangajigan/mambaforge/envs/cobra/bin/cobra-meta", line 10, in sys.exit(main()) File "/Users/andriangajigan/mambaforge/envs/cobra/lib/python3.8/site-packages/cobra.py", line 818, in main cov[line[0]] = round(float(line[1]), 3) ValueError: could not convert string to float: 'contigLen'

[linxingchen]

Hi, it looks like your contig depth/coverage file contains header that the second column is not a number but "contigLen", please check it and remove the first line.

[andriangajigan]

It worked! Thank you. I used coverage.transfer.py to convert my coverage file.

[linxingchen]

Do you mean that the output file of coverage.transfer.py still has the header line with "contigLen"? If yes, could you please show me your original depth file, probably just the first 5 lines? Thank you.

[andriangajigan]

It worked now. I meant I used the coverage.transfer.py to convert the jgi_summarize_bam_contig_depths coverage file as suggested in the main instruction: python coverage.transfer.py -i original.coverage.txt -o coverage.txt

[linxingchen]

Did you mean when you used the coverage.transfer.py script, then everything is fine right?