检查注释文件

SAW checkGTF

SAW count 的分析任务只接受标准格式的注释文件，所以在 SAW count 进行 reads 注释之前会自动校验文件的内容和格式。除了之外，还能够通过它实现特定注释信息内容的提取。

SAW 允许接入的注释文件的文件后缀名包括：gtf/gtf.gz、gff/gff.gz、gff3/gff3.gz 。

如果注释文件存在以下内容和格式问题（常见的错误），SAW checkGTF 将进行简单更正和问题提醒，以确保文件能够被正常使用。

Issue	Solution
In the seventh column indicating the sense and antisense strands, "-" and "_" symbols are mistakenly mixed.	Check each row of the annotation file and correct the error symbol "_" to "-".
A gene block lacks gene ID.	Discard the entire gene information and issue a warning.
A gene row is missing but the transcript row has information.	Discard the entire gene information and issue a warning.
A gene block lacks gene name.	Use gene ID to fill in the missing one.
A gene row exists but partial information of child rows is missing.	Child rows can inherit information from their gene rows.
A transcript ID is missing.	Fill it with its parent gene ID suffixed with a sequential number (e.g., XXX.1).
A row contains multiple attributes with the same name.	Only save the last <attribute:value> of the duplicated entries, for subsequent annotation.

*请注意，该程序默认假定输入注释文件已正确排序，并以基因块格式识别基因注释信息。

运行命令进行注释文件的格式检查：

saw checkGTF \
    --input-gtf=/path/to/input/GTF/or/GFF \
    --output-gtf=/path/to/output/GTF/or/GFF

假若不设置 --output-gtf 参数，程序将不会输出修正后的结果文件，请注意检查日志信息。

如果想要提取特定的注释信息，例如： gene_biotype:protein_coding 或 gene_biotype:lincRNA，可以这样运行程序：

saw checkGTF \
    --input-gtf=/path/to/input/GTF/or/GFF \
    --attribute=key1:value1,key2:value2,... \
    --output-gtf=/path/to/output/GTF/or/GFF

如果 --attribute 启用，SAW checkGTF 将提取特定的注释信息，但不进行文件格式的检查。