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Gentoo's Bugzilla – Attachment 101091 Details for
Bug 153766
Stabilisation request for EMBOSS 4.0.0 and related packages
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Small test suite for EMBOSS on Gentoo
emboss-test.sh (text/plain), 3.02 KB, created by
Olivier Fisette (RETIRED)
on 2006-11-02 13:51:15 UTC
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Description:
Small test suite for EMBOSS on Gentoo
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Creator:
Olivier Fisette (RETIRED)
Created:
2006-11-02 13:51:15 UTC
Size:
3.02 KB
patch
obsolete
>#!/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:"
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bug 153766
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