GenBase - Documentation

工具

目前，GenBaseTools为通用序列和新冠序列的序列校验提供了两个独立工具。

Usage: gbt <COMMAND>
Commands:
  seqvalcom    Validate common sequences
  seqvalcovid  Validate COVID19 sequences
  help         Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

通用序列校验

使用以下命令行校验通用序列：

gbt seqvalcom common_seq.fsa -o val_out

COVID-19序列校验

使用以下命令行校验COVID-19序列：

gbt seqvalcovid covid_seq.fsa -o val_out

校验程序将会输出如下汇总信息：

LOG->ERROR: Found 7 errors
LOG->ERROR: Found 0 warnings

如果校验有错，将产生如下校验结果文件：

val_out.error.txt  
val_out.warning.txt

文件内容将以表格形式显示。例如：

Error Type	Message
Nucleotide	Found invalid char '@' at Line 2, Column 18
Nucleotide	Found invalid char '@' at Line 2, Column 19
Nucleotide	Found invalid char '@' at Line 2, Column 20
Nucleotide	Found invalid '>' at Line 2, Column 34 in sequence(seqid:'>ssss'). This symbol is not allowed in the sequence. Please check whether the new-line character is missing.
Nucleotide	Found invalid '>' at Line 1164, Column 24 in sequence(seqid:'>Beijing-AAA-2022'). This symbol is not allowed in the sequence. Please check whether the new-line character is missing.
Defline	Found duplicated sequence id: '>ssss'
Defline	Found duplicated sequence id: '>asdf'