SANPRO

Programs designed for managing the iSanXoT results.

File structure

|
├── basic
│   ├── diff_tables.py
│   ├── filter_table.py
│   ├── sort_table.py
│   ├── get_n_rows.py
├── positioner
│   ├── add_pep_position.py
├── potpurri
│   ├── convert_bed_to_fasta.py
├── README.md
└── .gitignore

tests folder contains test files. Note: This folder may not exist.

potpourri is a folder for discarding. It is a mixture of programs without an objective.

Programs

basic: programs for handling large files

• get_n_rows: Retrieve the N rows from the given file.

Usage:

python basic/get_n_rows.py -c conf/config.ini

• diff_tables: Retrieve the rows that differ based on specified columns from two tabular-separated files.

Usage:

python basic/diff_tables.py -c conf/config.ini

• filter_table: Filter the given table file based on the provided conditions (header, operator, value).

Usage:

python basic/filter_table.py -c conf/config.ini

• sort_table: Sort the table file (in tabular-separated format) based on the specified columns.

Usage:

python basic/sort_table.py -c conf/config.ini

• remove_cols: Remove the specified columns from the table.

Usage:

python basic/remove_cols.py -c conf/config.ini

• select_cols: Select the specified columns from the table.

Usage:

python basic/select_cols.py -c conf/config.ini

positioner: programs that add positions

• add_pep_position: Include the peptide position within the protein in the report.

Usage:

python positioner/add_pep_position.py -i tests/test4/Npep2prot.tsv  -f tests/test4/mouse_202206_uni-sw-tr.target.fasta  -hp "peptide"  -hq "protein" -o tests/test4/Npep2prot.new.tsv

python positioner/add_pep_position.py -i tests/test6/LIMMA_Quanprot_Quanpep_Normpep_Nscanpep.tsv  -f tests/test6/rabbit_202306_pro-sw-tr.target.fasta  -hp "peptide"  -hq "protein" -o tests/test6/LIMMA_Quanprot_Quanpep_Normpep_Nscanpep.new.tsv

• get_appris: Retrieve APPRIS annotations for the given protein and positions

Usage:

python positioner/get_appris.py  -i tests/test7/Paths_PDMTableMaker_PDMTable_GM_2.txt  -c "q,b,e"  -d tests/test7/human_202306.appris.gtf -o tests/test7/appris_annots.gtf

python positioner/get_appris.py  -i tests/test8/LIMMA_NM_pgmqfall_table.tsv  -c "q,b,e"  -d data/202310/appris.gtf -o tests/test8/LIMMA_NM_pgmqfall_table.appris.tsv

potpourri: programs that possess multiple applications without a specific general focus