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