Analyse option

analyse or analyze

analyse allow users to generate secondary reports without having to generate the main report again, saving time.

Input

-i --input
Any kind of main report from TAPES either txt (tab separated) or csv (comma separated) file.

Output

-o --output Will output a txt (tab separated) or csv (comma separated) file containing the desired report

Examples

python tapes.py analyse -i /path/to/main_report.csv -o /path/to/new_report.csv --by_gene
python tapes.py analyze -i /path/to/main_report.csv -o /path/to/new_report.txt --by_sample
python tapes.py analyse -i /path/to/main_report.txt -o /path/to/new_report.txt --enrichr GO_Molecular_Function_2018

Warning

analyse will only work with one report/option at a time. For example:
python tapes.py analyse -i /path/to/main_report.csv -o /path/to/new_report.csv --by_gene --by_sample will not work.

Available Report Options

See the entire details of options at the sort function page.

• --by_gene
• --by_sample
• --list and --kegg
• --enrichr
• --disease

Analysis strategies

Filtering options such as --disease, --list and --kegg will output a file with a similar format to the main report. The output file will only keep genes passing a filter.

This means that those can be used with other options such as --by_gene or --by_sample.

For example:
python tapes.py analyse -i ./main_report.txt -o ./only_cancer_genes.txt --disease cancer
then
python tapes.py analyse -i ./only_cancer_genes.txt -o ./cancer_sample.txt --by_sample
Will give, for each sample, the 5 most pathogenic variant only in genes that are involved in cancer pathways.