Mercurial > repos > iuc > bioext_bam2msa

comparison copy_reference.py @ 3:b226e0c805a5 draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
author iuc
date Fri, 20 Aug 2021 21:03:56 +0000
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2:0a4ad829d87a 3:b226e0c805a5
1 import argparse
2 import os
3 import shutil
4
5 from BioExt.references import cov2, hxb2, nl4_3
6
7
8 references = {
9 'HXB2_env': hxb2.env,
10 'HXB2_gag': hxb2.gag,
11 'HXB2_int': hxb2.int,
12 'HXB2_nef': hxb2.nef,
13 'HXB2_pol': hxb2.pol,
14 'HXB2_pr': hxb2.pr,
15 'HXB2_prrt': hxb2.prrt,
16 'HXB2_rev': hxb2.rev,
17 'HXB2_rt': hxb2.rt,
18 'HXB2_tat': hxb2.tat,
19 'HXB2_vif': hxb2.vif,
20 'HXB2_vpr': hxb2.vpr,
21 'HXB2_vpu': hxb2.vpu,
22 'NL4-3_prrt': nl4_3.prrt,
23 'CoV2-3C': cov2.threeC,
24 'CoV2-E': cov2.E,
25 'CoV2-endornase': cov2.endornase,
26 'CoV2-exonuclease': cov2.exonuclease,
27 'CoV2-helicase': cov2.helicase,
28 'CoV2-leader': cov2.leader,
29 'CoV2-methyltransferase': cov2.methyltransferase,
30 'CoV2-M': cov2.M,
31 'CoV2-N': cov2.N,
32 'CoV2-nsp10': cov2.nsp10,
33 'CoV2-nsp2': cov2.nsp2,
34 'CoV2-nsp3': cov2.nsp3,
35 'CoV2-nsp4': cov2.nsp4,
36 'CoV2-nsp6': cov2.nsp6,
37 'CoV2-nsp7': cov2.nsp7,
38 'CoV2-nsp8': cov2.nsp8,
39 'CoV2-nsp9': cov2.nsp9,
40 'CoV2-ORF10': cov2.ORF10,
41 'CoV2-ORF1a': cov2.ORF1a,
42 'CoV2-ORF1b': cov2.ORF1b,
43 'CoV2-ORF3a': cov2.ORF3a,
44 'CoV2-ORF5': cov2.ORF5,
45 'CoV2-ORF6': cov2.ORF6,
46 'CoV2-ORF7a': cov2.ORF7a,
47 'CoV2-ORF7b': cov2.ORF7b,
48 'CoV2-ORF8': cov2.ORF8,
49 'CoV2-RdRp': cov2.RdRp,
50 'CoV2-S': cov2.S
51 }
52
53 parser = argparse.ArgumentParser()
54 parser.add_argument('--reference', dest='reference', action='store', type=str)
55 parser.add_argument('--dataset', dest='dataset', action='store', type=str)
56 args = parser.parse_args()
57 reference = os.path.abspath(references[args.reference]._seqpath)
58
59 shutil.copy(reference, os.path.abspath(args.dataset))