Mercurial > repos > iuc > bioext_bealign
view copy_reference.py @ 10:4ad7321205c9 draft default tip
planemo upload for repository https://github.com/davebx/bioext-gx/ commit a7729ad7789e8b120055a9a9b53494acb826b371
author | iuc |
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date | Mon, 02 Sep 2024 10:14:49 +0000 |
parents | fb4975b507c6 |
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import argparse import os import shutil from BioExt.references import cov2, hxb2, nl4_3 references = { 'HXB2_env': hxb2.env, 'HXB2_gag': hxb2.gag, 'HXB2_int': hxb2.int, 'HXB2_nef': hxb2.nef, 'HXB2_pol': hxb2.pol, 'HXB2_pr': hxb2.pr, 'HXB2_prrt': hxb2.prrt, 'HXB2_rev': hxb2.rev, 'HXB2_rt': hxb2.rt, 'HXB2_tat': hxb2.tat, 'HXB2_vif': hxb2.vif, 'HXB2_vpr': hxb2.vpr, 'HXB2_vpu': hxb2.vpu, 'NL4-3_prrt': nl4_3.prrt, 'CoV2-3C': cov2.threeC, 'CoV2-E': cov2.E, 'CoV2-endornase': cov2.endornase, 'CoV2-exonuclease': cov2.exonuclease, 'CoV2-helicase': cov2.helicase, 'CoV2-leader': cov2.leader, 'CoV2-methyltransferase': cov2.methyltransferase, 'CoV2-M': cov2.M, 'CoV2-N': cov2.N, 'CoV2-nsp10': cov2.nsp10, 'CoV2-nsp2': cov2.nsp2, 'CoV2-nsp3': cov2.nsp3, 'CoV2-nsp4': cov2.nsp4, 'CoV2-nsp6': cov2.nsp6, 'CoV2-nsp7': cov2.nsp7, 'CoV2-nsp8': cov2.nsp8, 'CoV2-nsp9': cov2.nsp9, 'CoV2-ORF10': cov2.ORF10, 'CoV2-ORF1a': cov2.ORF1a, 'CoV2-ORF1b': cov2.ORF1b, 'CoV2-ORF3a': cov2.ORF3a, 'CoV2-ORF5': cov2.ORF5, 'CoV2-ORF6': cov2.ORF6, 'CoV2-ORF7a': cov2.ORF7a, 'CoV2-ORF7b': cov2.ORF7b, 'CoV2-ORF8': cov2.ORF8, 'CoV2-RdRp': cov2.RdRp, 'CoV2-S': cov2.S } parser = argparse.ArgumentParser() parser.add_argument('--reference', dest='reference', action='store', type=str) parser.add_argument('--dataset', dest='dataset', action='store', type=str) args = parser.parse_args() reference = os.path.abspath(references[args.reference]._seqpath) shutil.copy(reference, os.path.abspath(args.dataset))