AOP-tk wrappers for download, chemical identification + matching + normalization, PDF parsing, relationship finding#728
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rdurnik wants to merge 54 commits intoRECETOX:masterfrom
Open
AOP-tk wrappers for download, chemical identification + matching + normalization, PDF parsing, relationship finding#728rdurnik wants to merge 54 commits intoRECETOX:masterfrom
rdurnik wants to merge 54 commits intoRECETOX:masterfrom
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rdurnik
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hechth
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Feb 2, 2026
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This could be rewritten as a direct galaxy tool wrapper using the following syntax
with open($input_file, "r") as f_in, open($output_file, "w") as f_out:
f_out.write("id\ttext\tchemicals\n")
for row in csv.DictReader(f_in, delimiter="\t"):
chemicals = Spacy().find_chemical(row["text"])
chemicals_str = (
"|".join(set([chem.name for chem in chemicals])) if chemicals else ""
)
f_out.write(f"{row['id']}\t{row['text']}\t{chemicals_str}\n")
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AOP-tk wrappers for download, chemical identification + matching + normalization, PDF parsing, relationship finding