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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]
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.
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/