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Changes in XML parser to allow partial content - #189

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google_xml_parser
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Changes in XML parser to allow partial content#189
LeonardoGonzales wants to merge 5 commits into
mainfrom
google_xml_parser

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@LeonardoGonzales
LeonardoGonzales marked this pull request as draft August 1, 2023 08:30
@LeonardoGonzales

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Good morning, this is what I was able to generate:

This is the input XML from google: https://drive.google.com/corp/drive/folders/114FyEediJZZNmnupwoyyxOiSTV79aVC3

This is the XML after a few required changes to make it work:
"\n" +
"<uniprot xmlns="http://uniprot.org/uniprot\" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/docs/uniprot.xsd\">\n" +
"\n" +
"A0A2E0WTX0\n" +
"TEMPLATE_VALUE\n" +
"\n" +
"\n" +
"NAD(P)H-dependent oxidoreductase\n" +
"\n" +
"\n" +
"<comment type="similarity">\n" +
"Belongs to the nitroreductase family.\n" +
"\n" +
"" +
""

This is the example of the output Flat file:
ID TEMPLATE_VALUE Unreviewed; 0 AA.
AC A0A2E0WTX0;
DT 31-JUL-2023, integrated into UniProtKB.
DT 31-JUL-2023, sequence version 0.
DT 31-JUL-2023, entry version 0.
DE SubName: Full=NAD(P)H-dependent oxidoreductase;
OS .
OC unclassified.
OX NCBI_TaxID=0;
CC -!- SIMILARITY: Belongs to the nitroreductase family.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
PE UNKNOWN;
SQ SEQUENCE 0 AA; 18 MW; 0000000000000000 CRC64;

//

I think there is room for improvement, but it is a good start point

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2 participants