From 89baab96128b7c469bae27a4ae7a0c870292f507 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 3 Mar 2020 09:06:16 +0000 Subject: [PATCH] JAL-3547 groovy script to get the conservation sequence and output it as fasta --- examples/groovy/exportconsensus.groovy | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 examples/groovy/exportconsensus.groovy diff --git a/examples/groovy/exportconsensus.groovy b/examples/groovy/exportconsensus.groovy new file mode 100644 index 0000000..36e8475 --- /dev/null +++ b/examples/groovy/exportconsensus.groovy @@ -0,0 +1,32 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + +// export a consensus sequence +// execute this script via command line for an alignment - e.g. +// jalview -groovy exportconsensus.groovy -headless -open examples/uniref50.fa + +def alf = Jalview.getAlignFrames(); +for (ala in alf) +{ + // ala is an jalview.gui.AlignFrame object + jalview.datamodel.SequenceI seq = ala.viewport.getConsensusSeq(); + print new jalview.io.FastaFile().print(((jalview.datamodel.SequenceI[]) [seq]),false)+"\n"; +} \ No newline at end of file -- 1.7.10.2