make_library_id_lists.py – Make library id lists

Description:

Makes a list of the ids corresponding to each library represented in the input fasta file. Assumes that the libraries are the output of split_libraries.py and that they contain the 454 read id for each sequence as is standard in the split_libraries.py output. Produces a separate file for each library.

Usage: make_library_id_lists.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fasta

The path to a FASTA file containing input sequences

[OPTIONAL]

-s, --screened_rep_seqs

The path to a FASTA file containing screened representative seqs[DEFAULT: None]

-u, --otus

The path to an OTU file mapping OTUs onto rep seqs[DEFAULT: None]

-o, --outdir

The base directory to save results (one file per library).

-f, --field

Index of space-delimited field to read id from [DEFAULT: 1]

--debug

Show debug output.

Output:

This script produces a separate file for each library.

Example:

Create a list containing library ids for a fasta file (seqs.fna):

make_library_id_lists.py -i seqs.fna -o results/