Mercurial > repos > jpayne > seqsero2s

annotate patch_stringmlst.sh @ 20:4dbbf92ff30a draft default tip

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planemo upload commit 936a627c4fc706080f07ec678f89e8256a7e7895-dirty
author jpayne
date Fri, 15 May 2026 17:55:16 +0000
parents 4c4899031795
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env bash
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2
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3 # patch stringMLST.py log path: replace dbPrefix reference with cwd.
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4 # patches all occurrences (at line 1464 and predict section at line 1478).
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5
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6 set -euo pipefail
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7
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8 STRINGMLST="$PREFIX/bin/stringMLST.py"
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10 if [ ! -f "$STRINGMLST" ]; then
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11 echo "SKIP: $STRINGMLST not found"
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12 exit 0
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13 fi
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14
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15 python3 << 'PATCH_WITH_PY'
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16 import os
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17
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18 p = os.path.join(os.environ["PREFIX"], "bin", "stringMLST.py")
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19 with open(p) as f:
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20 lines = f.readlines()
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21
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22 original = " log = dbPrefix+'.log'\n"
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23 commented = " # log = dbPrefix+'.log'\n"
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24 replacement = ' log = os.path.join(os.getcwd(), "kmer.log")\n'
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25
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26 # Count occurrences BEFORE modifying
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27 occurrences = lines.count(original)
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28
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29 if occurrences == 0:
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30 print("SKIP: stringMLST.py has 0 occurrences, expected at least 1")
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31 exit(0)
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33 out = []
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34 for line in lines:
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35 if line.rstrip("\n") == original.rstrip("\n"):
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36 out.append(commented)
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37 out.append(replacement)
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38 else:
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39 out.append(line)
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40
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41 with open(p, "w") as f:
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42 f.writelines(out)
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43
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44 print("PATCHED: stringMLST.py log path fixed (%d occurrences)" % occurrences)
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45 PATCH_WITH_PY