truncate_reverse_primer.py – Takes a demultiplexed fasta file, finds a specified reverse primer sequence, and truncates this primer and subsequent sequences following the reverse primer.

Description:

Takes input mapping file and fasta sequences which have already have been demultiplexed (via split_libraries.py, denoise_wrapper.py, ampliconnoise.py, etc.) with fasta labels that are in QIIME format, i.e., SampleID_#. This script will use the SampleID and a mapping file with a ReversePrimer column to find the reverse primer by local alignment and remove this and any subsequent sequence in a filtered output fasta file.

Usage: truncate_reverse_primer.py [options]

Input Arguments:

Note

[REQUIRED]

-f, --fasta_fp

Fasta file. Needs to have fasta labels in proper demultiplexed format.

-m, --mapping_fp

Mapping filepath. ReversePrimer field required. Reverse primers need to be in 5’->3’ orientation.

[OPTIONAL]

-o, --output_dir

Output directory. Will be created if does not exist. [default: .]

-z, --truncate_option

Truncation option. The default option, “truncate_only” will try to find the reverse primer to truncate, and if not found, will write the sequence unchanged. If set to “truncate_remove”, sequences where the reverse primer is not found will not be written. [default: truncate_only]

-M, --primer_mismatches

Number of mismatches allowed in the reverse primer. [default: 2]

Output:

Truncated version of the input fasta file (based on input name with ‘seqs_rev_primer_truncated’ appended) will be generated in the output directory, along with a .log file.

Example:

Find, truncate reverse primers from the fasta file seqs.fna, with the SampleIDs and reverse primers specified in Mapping_File_Rev_Primer.txt, writes output fasta file to the reverse_primer_removed directory:

truncate_reverse_primer.py -f seqs.fna -m Mapping_File_Rev_Primer.txt -o reverse_primer_removed/