extract_seqs_by_sample_id.py – Extract sequences based on the SampleID

Description:

This script creates a fasta file which will contain only sequences that ARE associated with a set of sample IDs, OR all sequences that are NOT associated with a set of sample IDs (-n)

Usage: extract_seqs_by_sample_id.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fasta_fp

Path to the input fasta file

-o, --output_fasta_fp

The output fasta file

[OPTIONAL]

-n, --negate

Negate the sample ID list (i.e., output sample ids not passed via -s) [default: False]

-s, --sample_ids

Comma-separated sample_ids to include in output fasta file (or exclude if –negate), or string describing mapping file states defining sample ids (mapping_fp must be provided for the latter)

-m, --mapping_fp

The mapping filepath

Output:

The script produces a fasta file containing containing only the specified SampleIDs.

Examples:

Create the file outseqs.fasta (-o), which will be a subset of inseqs.fasta (-i) containing only the sequences THAT ARE associated with sample ids S2, S3, S4 (-s). As always, sample IDs are case-sensitive:

extract_seqs_by_sample_id.py -i inseqs.fasta -o outseqs_by_sample.fasta -s S2,S3,S4

Create the file outseqs.fasta (-o), which will be a subset of inseqs.fasta (-i) containing only the sequences THAT ARE NOT (-n) associated with sample ids S2, S3, S4 (-s). As always, sample IDs are case-sensitive:

extract_seqs_by_sample_id.py -i inseqs.fasta -o outseqs_by_sample_negated.fasta -s S2,S3,S4 -n

Create the file outseqs.fasta (-o), which will be a subset of inseqs.fasta (-i) containing only the sequences THAT ARE associated with sample ids whose “Treatment” value is “Fast” in the mapping file:

extract_seqs_by_sample_id.py -i inseqs.fasta -o outseqs_by_mapping_field.fasta -m map.txt -s "Treatment:Fast"