SEQPROG

Requires Python 3.6 with following packages:

• Argparse
• BioPython
• Pandas

Reads and writes sequences in common format

Using the program

Usage: python3 seqprog.py [-h] [-f PATH | -df [PATH]] [-e EMAIL] [-o PATH] [--allow-sub-species] [--no-allow-sub-species] [--remove_ids] [--keep_ids] [-rmdup [Optimal_Length Max_Length [Optimal_Length Max_Length ...]]] [-s [SEARCH_TERM]]

Process NCBI GenBank Records into custom format

optional arguments:
-h, --help            show this help message and exit
-f PATH, --input PATH
                        Input file of taxrecords
-df [PATH], --Taxonomy_info_csv [PATH]
                        Produce a CSV file of taxonomic information
-e EMAIL, --email EMAIL
                        Input email address
-o PATH, --output PATH
                        Path for output file
--allow-sub-species   Allow sub-species in taxonomic records
--no-allow-sub-species
                        Do not allow sub-species in taxonomic records
                        (default)
--remove_ids          Remove accession numbers from FASTA file (default)
--keep_ids            Keep accession numbers in FASTA file
-rmdup [Optimal_Length Max_Length [Optimal_Length Max_Length ...]], --remove_duplicates [Optimal_Length Max_Length [Optimal_Length Max_Length ...]]
                        Remove duplicate taxa records by optimal length
-s [SEARCH_TERM], --search_term [SEARCH_TERM]
                        Clade/Group term for NCBI GenBank Search (Required if
                        -f not used)