make_per_library_sff.py – Make per-library sff files from ID lists¶
Description:
This script generates per-library sff files using a directory of text files, one per library, which list read ID’s to be included.
The ID list files should contain one read ID per line. If a line contains multiple words (separated by whitespace), then only the first word is used. A ‘>’ character is stripped from the beginning of the line, if present. Blank lines in the file are skipped.
Usage: make_per_library_sff.py [options]
Input Arguments:
Note
[REQUIRED]
- -i, --input_sff
- Input sff file (separate multiple files w/ comma)
- -l, --libdir
- Directory containing ID list text files, one per library
[OPTIONAL]
- -p, --sfffile_path
- Path to sfffile binary [default: use sfffile in $PATH]
- --use_sfftools
- Use external sfffile program instead of equivalent Python routines.
- --debug
- Print debugging output to stdout [default: False]
Output:
The result of this script generates sff files for each library.
Example:
Make per-library sff files using input.sff and a directory of libs where each file in the directory contains the id lists for each library:
make_per_library_sff.py -i input.sff -l libs