boopsboops

#!/usr/bin/env Rscript

# load libs
library("ape")
library("tidyverse")
library("magrittr")
library("ips")
library("phangorn")
library("rentrez")
library("bold")

boopsboops

#!/usr/bin/env Rscript
# script to subset and convert a reference library into fasta format

# load up libraries
library("tidyverse")
library("magrittr")
library("ape")

# load up the references using the `references-load.R` script
# loads objects: uk.species.table, uk.species.table.common, reflib.orig

boopsboops

# load libs
require("spider")
#source(file="sppDistMatrix2.R")#can source the function

# load the example data
data(dolomedes)
doloDist <- dist.dna(dolomedes)
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)

# you have three options for dist, which are min, mean and max

boopsboops

LOCUS       BB-002_CYTB              201 bp    DNA     linear   VRT 24-APR-2015
DEFINITION  Boops boops.
ACCESSION   
VERSION
KEYWORDS    .
SOURCE      mitochondrion Boops boops
  ORGANISM  Boops boops
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Neoteleostei;
            Acanthomorphata; Eupercaria; Spariformes; Sparidae; Boops.

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>BB-002_CYTB [organism=Boops boops] [Bio_material=BB-002] [Specimen-voucher=MNHN:1978-0632] [location=mitochondrion] [mgcode=2]
ATGGCTAGCCTTCGAAAAACGCACCCCCTATTAAAAATTGCTAATCACGCATTAGTTGATCTCCCTGCACCCTCCAATATTTCCGTCTGATGAAATTTTGGCTCCCTGCTTGGCCTCTGTCTTATTTCCCAGCTCCTTACAGGGCTATTCCTCGCCATACACTATACCTCCGATATCGCTACAGCCTTCTCTTCCGTTGCC
>BB-003_CYTB [organism=Boops boops] [Bio_material=BB-003] [Specimen-voucher=MNHN:1978-0632] [location=mitochondrion] [mgcode=2]
ATGGCTAGCCTTCGAAAAACGCACCCCCTATTAAAAATTGCTAATCACGCATTAGTTGATCTCCCTGCACCCTCCAATATTTCCGTCTGATGAAATTTTGGCTCCCTGCTTGGCCTCTGTCTTATTTCCCAGCTCCTTACAGGGCTATTCCTCGCCATACACTATACCTCCGATATCGCTACAGCCTTCTCTTCCGTTGCC
>BB-001_rRNA [organism=Boops boops] [Bio_material=BB-001] [Specimen-voucher=MNHN:1978-0632] [location=mitochondrion]
TATGGAGCTTAAGACGCCAGGGCAGCTCACGTTAAACGCCCCTAATAAAGGAATAAAACCTAGTGAATCCTGCTCTAATGTCTTTGGTTGGGGCGACCACGGGGAATCATAAAACCCCCACGTGGAATGGGAGCACCACACTCCTAAACCCAAGAGCTTCCGCTCTAATGAACAGAACTTCTGGCCATATTAGATCCGGT
>BB-003_rRNA [organism=Boops boops] [Bio_mater

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>Feature BB-002_CYTB
1	>201	gene
			gene	CYTB
1	>201	CDS		
			product	cytochrome b
			codon_start	1
>Feature BB-003_CYTB
1	>201	gene
			gene	CYTB
1	>201	CDS		

boopsboops

>Feature BB-002_CYTB
1	>201	gene
			gene	CYTB
1	>201	CDS		
			product	cytochrome b
			codon_start	1
>Feature BB-003_CYTB
1	>201	gene
			gene	CYTB
1	>201	CDS		

boopsboops

>BB-002_CYTB [organism=Boops boops] [Bio_material=BB-002] [Specimen-voucher=MNHN:1978-0632] [location=mitochondrion] [mgcode=2]
ATGGCTAGCCTTCGAAAAACGCACCCCCTATTAAAAATTGCTAATCACGCATTAGTTGATCTCCCTGCACCCTCCAATATTTCCGTCTGATGAAATTTTGGCTCCCTGCTTGGCCTCTGTCTTATTTCCCAGCTCCTTACAGGGCTATTCCTCGCCATACACTATACCTCCGATATCGCTACAGCCTTCTCTTCCGTTGCC
>BB-003_CYTB [organism=Boops boops] [Bio_material=BB-003] [Specimen-voucher=MNHN:1978-0632] [location=mitochondrion] [mgcode=2]
ATGGCTAGCCTTCGAAAAACGCACCCCCTATTAAAAATTGCTAATCACGCATTAGTTGATCTCCCTGCACCCTCCAATATTTCCGTCTGATGAAATTTTGGCTCCCTGCTTGGCCTCTGTCTTATTTCCCAGCTCCTTACAGGGCTATTCCTCGCCATACACTATACCTCCGATATCGCTACAGCCTTCTCTTCCGTTGCC

boopsboops

# Here we use -a flag to specify fasta file format type, 
# the -V flag to request verification (v) and a GenBank flatfile as part of the output (b), 
# and the -T flag to tell the program to generate the higher taxonomic classifications for our record.
# Use 'tbl2asn --help' for a full list of the options

# To run if in PATH 
tbl2asn -t template.sbt -i sequences.fsa -f features.tbl -a s -V vb -T
# To run if local
./tbl2asn -t template.sbt -i sequences.fsa -f features.tbl -a s -V vb -T

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reduced_table <- tab[-which(is.na(tab$nucleotides_16S)), ]
gene_name <- "rRNA"
prod_name <- "16S ribosomal RNA"
# note that we deleted the genetic code element, as this is not a coding sequence
# also note that 'append' is now set to 'TRUE' to add the data to previously written files
fasta_description <- paste0(">", paste0(reduced_table$otherCatalogNumbers, "_", gene_name), #
  " ", "[organism=", reduced_table$genus, " ", reduced_table$specificEpithet, "]", " ", #
  "[Bio_material=", reduced_table$otherCatalogNumbers, "]", " ", "[Specimen-voucher=", #
  reduced_table$institutionCode, ":", reduced_table$catalogNumber, "]", " ", "[location=mitochondrion]")
fasta_complete <- paste(fasta_description, reduced_table$nucleotides_16S, sep="\n")# add data to fasta