Mercurial > repos > iuc > bioext_bam2msa

annotate copy_reference.py @ 10:767943cd85bf draft default tip

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit a7729ad7789e8b120055a9a9b53494acb826b371
author iuc
date Mon, 02 Sep 2024 10:14:57 +0000
parents b226e0c805a5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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diff changeset
1 import argparse
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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2 import os
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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3 import shutil
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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5 from BioExt.references import cov2, hxb2, nl4_3
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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8 references = {
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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9 'HXB2_env': hxb2.env,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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10 'HXB2_gag': hxb2.gag,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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11 'HXB2_int': hxb2.int,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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12 'HXB2_nef': hxb2.nef,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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13 'HXB2_pol': hxb2.pol,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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14 'HXB2_pr': hxb2.pr,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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15 'HXB2_prrt': hxb2.prrt,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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16 'HXB2_rev': hxb2.rev,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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17 'HXB2_rt': hxb2.rt,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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18 'HXB2_tat': hxb2.tat,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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19 'HXB2_vif': hxb2.vif,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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20 'HXB2_vpr': hxb2.vpr,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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21 'HXB2_vpu': hxb2.vpu,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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22 'NL4-3_prrt': nl4_3.prrt,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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23 'CoV2-3C': cov2.threeC,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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24 'CoV2-E': cov2.E,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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25 'CoV2-endornase': cov2.endornase,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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26 'CoV2-exonuclease': cov2.exonuclease,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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27 'CoV2-helicase': cov2.helicase,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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28 'CoV2-leader': cov2.leader,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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29 'CoV2-methyltransferase': cov2.methyltransferase,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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30 'CoV2-M': cov2.M,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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31 'CoV2-N': cov2.N,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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32 'CoV2-nsp10': cov2.nsp10,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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33 'CoV2-nsp2': cov2.nsp2,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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34 'CoV2-nsp3': cov2.nsp3,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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35 'CoV2-nsp4': cov2.nsp4,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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36 'CoV2-nsp6': cov2.nsp6,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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37 'CoV2-nsp7': cov2.nsp7,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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38 'CoV2-nsp8': cov2.nsp8,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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39 'CoV2-nsp9': cov2.nsp9,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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40 'CoV2-ORF10': cov2.ORF10,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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41 'CoV2-ORF1a': cov2.ORF1a,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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42 'CoV2-ORF1b': cov2.ORF1b,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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43 'CoV2-ORF3a': cov2.ORF3a,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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44 'CoV2-ORF5': cov2.ORF5,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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45 'CoV2-ORF6': cov2.ORF6,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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46 'CoV2-ORF7a': cov2.ORF7a,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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47 'CoV2-ORF7b': cov2.ORF7b,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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48 'CoV2-ORF8': cov2.ORF8,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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49 'CoV2-RdRp': cov2.RdRp,
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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50 'CoV2-S': cov2.S
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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51 }
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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52
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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53 parser = argparse.ArgumentParser()
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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54 parser.add_argument('--reference', dest='reference', action='store', type=str)
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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55 parser.add_argument('--dataset', dest='dataset', action='store', type=str)
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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56 args = parser.parse_args()
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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57 reference = os.path.abspath(references[args.reference]._seqpath)
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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58
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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59 shutil.copy(reference, os.path.abspath(args.dataset))