anusha026

library("reutils")

# NB: to grab FASTA of accession number x, do this:
#
#    f <- content(efetch(x, db="nuccore", rettype="fasta", retmode="text"))
#
# Result is a string, with \n separators.

grab.results <- function (term) {
        # Search for the given term on nuccore. This gives us a list of

anusha026

# Download FASTA sequences from GenBank
# Copyright (C) 2015 Anusha Beer <anbeer29@gmail.com>
#
# Permission to use, copy, modify, and/or distribute this software for
# any purpose with or without fee is hereby granted, provided that the
# above copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR

anusha026

# Convert CSV into Excel with highlighting
# Copyright (C) 2015 Anusha Beer <anbeer29@gmail.com>
#
# Permission to use, copy, modify, and/or distribute this software for
# any purpose with or without fee is hereby granted, provided that the
# above copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR

anusha026

# Genbank scraping functions
# Copyright (C) 2015 Anusha Beer <anbeer29@gmail.com>
#
# Permission to use, copy, modify, and/or distribute this software for
# any purpose with or without fee is hereby granted, provided that the
# above copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR