#!/bin/bash

# Copyright 1999-2006 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2

# emboss-test.sh - A small test suite for EMBOSS 4.0.0 on Gentoo
# Olivier Fisette <ribosome@gentoo.org> 2006-11-02

source "/sbin/functions.sh"

einfo "EMBOSS version (from \"embossversion\"): $(embossversion -auto)"

echo
einfo "Use \"seqret\" to store a sequence in GenBank format, in lowercase."
einfo "Add a title using \"descseq\" and convert to Fasta format. Print it"
einfo "on screen in EMBL format."
echo
seqret -auto -slower "raw::stdin" "genbank::phikz-lys.gb" <<- EOF
	ATGAAAGTATTACGCAAAGGCGATAGGGGTGATGAGGTATGTCAACTCCAGACACTCTTA
	AATTTATGTGGCTATGATGTTGGAAAGCCAGATGGTATTTTTGGAAATAACACCTTTAAT
	CAGGTAGTTAAATTTCAAAAAGATAATTGTCTAGATAGTGATGGTATTGTAGGTAAGAAT
	ACTTGGGCTGAATTATTCAGTAAATATTCTCCACCTATTCCTTATAAAACTATCCCTATG
	CCAACTGCAAATAAATCACGTGCAGCTGCAACTCCAGTTATGAATGCAGTAGAAAATGCT
	ACTGGCGTTCGTAGCCAGTTGCTACTAACATTTGCTTCTATTGAATCAGCATTCGATTAC
	GAAATAAAAGCTAAGACTTCATCAGCTACTGGTTGGTTCCAATTCCTTACTGGAACATGG
	AAAACAATGATTGAAAATTATGGCATGAAGTATGGCGTACTTACTGATCCAACTGGGGCA
	TTACGTAAAGATCCACGTATAAGTGCTTTAATGGGTGCCGAACTAATTAAAGAGAATATG
	AATATTCTTCGTCCTGTCCTTAAACGTGAACCAACTGATACTGATCTTTATTTAGCTCAC
	TTCTTTGGGCCTGGTGCAGCCCGTCGTTTCCTGACCACTGGCCAGAATGAATTAGCTGCT
	ACCCATTTCCCAAAAGAAGCTCAGGCAAACCCATCTATTTTTTATAACAAAGATGGGTCA
	CCTAAAACCATTCAAGAAGTTTATAACTTAATGGATGGTAAAGTTGCAGCACATAGAAAA
	TAA
EOF
descseq -auto "phikz-lys.gb" "fasta::phikz-lys.fasta" \
		-name "PhiKZ-ORF144 Putative endolysin, complete CDA"
seqret -auto "phikz-lys.fasta" "embl::stdout"

echo
einfo "Search for common restriction sites (using \"restrict\" and the Rebase"
einfo "database). We expect to find only a few since viral DNA has evolved to"
einfo "protect itself from restriction enzymes. (There is only one hit, for"
einfo "the EcoRII enzyme, starting at 610.)"
echo
restrict -auto -enzymes "BamHI, EcoRI, EcoRII" -sitelen 4 "phikz-lys.fasta" \
		"stdout"

echo
einfo "Could we mutate the sequence to make the viral DNA even more robust to"
einfo "restriction systems whilst keeping the same translation product? This"
einfo "is investigated using \"recoder\". (There are seven possible mutations.)"
echo
recoder -auto -enzymes "EcoRII" "phikz-lys.fasta" "stdout"

echo
einfo "Translate gene to protein sequence. We trim the termination \"*\""
einfo "character from the end of the translation. We use \"transeq\". The"
einfo "translation product is printed on screen in SwissProt format."
echo
transeq -auto -trim "phikz-lys.fasta" "phikz-lys-pep.fasta"
seqret -auto "phikz-lys-pep.fasta" "swiss::stdout"

echo
einfo "Show a few basic statistics about the protein using \"pepstats\"."
einfo "Molecular weight of the protein is 28814.90 Da (in 260 residues)."
einfo "Create an hydropathy plot in PNG format to search for transmembrane"
einfo "helices. The PNG graph shows three maxima at around residues 75, 100"
einfo "and 135."
echo
pepstats -auto "phikz-lys-pep.fasta" "stdout"
octanol -auto -send1 125 -graph png -goutfile2 "phikz-lys-pep.octanol" \
		-send1 125 "phikz-lys-pep.fasta:"