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conda安装kofamscan

conda安装kofamscan

作者: 沈梦圆1993 | 来源:发表于2021-05-27 11:20 被阅读0次

    官网的安装依赖的方法还是有些麻烦,直接用conda安装!避免报错~

    下载数据库

    mkdir -p /project/shenmy/biosoftware/kofamscan/db
    cd /project/shenmy/biosoftware/kofamscan/db
    wget ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz  
    wget ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz  
    gunzip ko_list.gz 
    tar xvzf profiles.tar.gz  
    

    安装环境

    conda create  -n kofamscan -c bioconda kofamscan
    

    运行

    ./exec_annotation -h
    Usage: exec_annotation [options] <query>
      <query>                    FASTA formatted query sequence file
      -o <file>                  File to output the result  [stdout]
      -p, --profile <path>       Profile HMM database
      -k, --ko-list <file>       KO information file
      --cpu <num>                Number of CPU to use  [1]
      -c, --config <file>        Config file
      --tmp-dir <dir>            Temporary directory  [./tmp]
      -E, --e-value <e_value>    Largest E-value required of the hits
      -T, --threshold-scale <scale>
                                 The score thresholds will be multiplied by this value
      -f, --format <format>      Format of the output [detail]
          detail:          Detail for each hits (including hits below threshold)
          detail-tsv:      Tab separeted values for detail format
          mapper:          KEGG Mapper compatible format
          mapper-one-line: Similar to mapper, but all hit KOs are listed in one line
      --[no-]report-unannotated  Sequence name will be shown even if no KOs are assigned
                                 Default is true when format=mapper or mapper-all,
                                 false when format=detail
      --create-alignment         Create domain annotation files for each sequence
                                 They will be located in the tmp directory
                                 Incompatible with -r
      -r, --reannotate           Skip hmmsearch
                                 Incompatible with --create-alignment
      --keep-tabular             Neither create tabular.txt nor delete K number files
                                 By default, all K number files will be combined into
                                 a tabular.txt and delete them
      --keep-output              Neither create output.txt nor delete K number files
                                 By default, all K number files will be combined into
                                 a output.txt and delete them
                                 Must be with --create-alignment
    

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