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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
278 lines
10 KiB
Python
278 lines
10 KiB
Python
# Copyright 2014 by Kevin Wu.
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# Copyright 2014 by Peter Cock.
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# All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Tests for online functionality of the KEGG module."""
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# Builtins
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import io
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import unittest
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import requires_internet
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from Bio import SeqIO
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from Bio.KEGG.KGML import KGML_parser
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from Bio.KEGG.REST import kegg_conv
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from Bio.KEGG.REST import kegg_find
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from Bio.KEGG.REST import kegg_get
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from Bio.KEGG.REST import kegg_info
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from Bio.KEGG.REST import kegg_link
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from Bio.KEGG.REST import kegg_list
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requires_internet.check()
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class KEGGTests(unittest.TestCase):
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"""Tests for KEGG REST API."""
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def test_info_kegg(self):
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with kegg_info("kegg") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/info/kegg")
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def test_info_pathway(self):
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with kegg_info("pathway") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/info/pathway")
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def test_list_pathway(self):
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with kegg_list("pathway") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/pathway")
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def test_pathway_hsa(self):
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with kegg_list("pathway", "hsa") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/pathway/hsa")
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def test_list_organism(self):
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with kegg_list("organism") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/organism")
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def test_list_hsa(self):
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with kegg_list("hsa") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/hsa")
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def test_list_T01001(self):
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with kegg_list("T01001") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/T01001")
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def test_list_hsa_10458_plus_ece_Z5100(self):
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with kegg_list("hsa:10458+ece:Z5100") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/hsa:10458+ece:Z5100")
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def test_list_hsa_10458_list_ece_Z5100(self):
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with kegg_list(["hsa:10458", "ece:Z5100"]) as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/hsa:10458+ece:Z5100")
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def test_list_cpd_C01290_plus_gl_G0009(self):
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with kegg_list("cpd:C01290+gl:G00092") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/cpd:C01290+gl:G00092")
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def test_list_cpd_C01290_list_gl_G0009(self):
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with kegg_list(["cpd:C01290", "gl:G00092"]) as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/cpd:C01290+gl:G00092")
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def test_list_C01290_plus_G00092(self):
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with kegg_list("C01290+G00092") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/C01290+G00092")
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def test_list_C01290_list_G00092(self):
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with kegg_list(["C01290", "G00092"]) as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/list/C01290+G00092")
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def test_find_genes_shiga_plus_toxin(self):
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with kegg_find("genes", "shiga+toxin") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/find/genes/shiga+toxin")
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def test_find_genes_shiga_list_toxin(self):
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with kegg_find("genes", ["shiga", "toxin"]) as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/find/genes/shiga+toxin")
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def test_find_compound_C7H10O5_formula(self):
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with kegg_find("compound", "C7H10O5", "formula") as handle:
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handle.read()
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/find/compound/C7H10O5/formula"
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)
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def test_find_compound_O5C7_formula(self):
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with kegg_find("compound", "O5C7", "formula") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/find/compound/O5C7/formula")
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def test_find_compound_exact_mass(self):
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with kegg_find("compound", "174.05", "exact_mass") as handle:
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handle.read()
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/find/compound/174.05/exact_mass"
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)
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def test_find_compound_weight(self):
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with kegg_find("compound", "300-310", "mol_weight") as handle:
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handle.read()
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/find/compound/300-310/mol_weight"
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)
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def test_get_br_ko00002(self):
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with kegg_get("br:ko00002", "json") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/get/br:ko00002/json")
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def test_get_cpd_C01290_plus_gl_G00092(self):
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with kegg_get("cpd:C01290+gl:G00092") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/get/cpd:C01290+gl:G00092")
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def test_get_cpd_C01290_list_gl_G00092(self):
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with kegg_get(["cpd:C01290", "gl:G00092"]) as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/get/cpd:C01290+gl:G00092")
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def test_get_C01290_plus_G00092(self):
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with kegg_get(["C01290+G00092"]) as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/get/C01290+G00092")
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def test_get_C01290_list_G00092(self):
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with kegg_get(["C01290", "G00092"]) as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/get/C01290+G00092")
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def test_get_hsa_10458_plus_ece_Z5100(self):
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with kegg_get("hsa:10458+ece:Z5100") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/get/hsa:10458+ece:Z5100")
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def test_get_hsa_10458_list_ece_Z5100(self):
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with kegg_get(["hsa:10458", "ece:Z5100"]) as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/get/hsa:10458+ece:Z5100")
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def test_get_hsa_10458_plus_ece_Z5100_as_aaseq(self):
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with kegg_get("hsa:10458+ece:Z5100", "aaseq") as handle:
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data = SeqIO.parse(handle, "fasta")
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self.assertEqual(len(list(data)), 2)
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/get/hsa:10458+ece:Z5100/aaseq"
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)
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def test_get_hsa_10458_list_ece_Z5100_as_aaseq(self):
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with kegg_get(["hsa:10458", "ece:Z5100"], "aaseq") as handle:
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data = SeqIO.parse(handle, "fasta")
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self.assertEqual(len(list(data)), 2)
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/get/hsa:10458+ece:Z5100/aaseq"
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)
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def test_get_hsa_10458_plus_ece_Z5100_as_ntseq(self):
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with kegg_get("hsa:10458+ece:Z5100", "ntseq") as handle:
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data = SeqIO.parse(handle, "fasta")
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self.assertEqual(len(list(data)), 2)
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/get/hsa:10458+ece:Z5100/ntseq"
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)
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def test_get_hsa_10458_list_ece_Z5100_as_ntseq(self):
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with kegg_get(["hsa:10458", "ece:Z5100"], "ntseq") as handle:
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data = SeqIO.parse(handle, "fasta")
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self.assertEqual(len(list(data)), 2)
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/get/hsa:10458+ece:Z5100/ntseq"
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)
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def test_get_hsa05130_image(self):
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with kegg_get("hsa05130", "image") as handle:
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data = handle.read()
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self.assertEqual(data[:4], b"\x89PNG")
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self.assertEqual(handle.url, "https://rest.kegg.jp/get/hsa05130/image")
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def test_conv_eco_ncbi_geneid(self):
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with kegg_conv("eco", "ncbi-geneid") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/conv/eco/ncbi-geneid")
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def test_conv_ncbi_geneid_eco(self):
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with kegg_conv("ncbi-geneid", "eco") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/conv/ncbi-geneid/eco")
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def test_conv_ncbi_gi_hsa_10458_plus_ece_Z5100(self):
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with kegg_conv("ncbi-gi", "hsa:10458+ece:Z5100") as handle:
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handle.read()
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/conv/ncbi-gi/hsa:10458+ece:Z5100"
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)
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def test_conv_ncbi_gi_hsa_10458_list_ece_Z5100(self):
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with kegg_conv("ncbi-gi", ["hsa:10458", "ece:Z5100"]) as handle:
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handle.read()
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/conv/ncbi-gi/hsa:10458+ece:Z5100"
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)
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def test_link_pathway_hsa(self):
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with kegg_link("pathway", "hsa") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/link/pathway/hsa")
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def test_link_hsa_pathway(self):
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with kegg_link("hsa", "pathway") as handle:
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handle.read()
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self.assertEqual(handle.url, "https://rest.kegg.jp/link/hsa/pathway")
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def test_pathway_hsa_10458_plus_ece_Z5100(self):
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with kegg_link("pathway", "hsa:10458+ece:Z5100") as handle:
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handle.read()
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/link/pathway/hsa:10458+ece:Z5100"
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)
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def test_pathway_hsa_10458_list_ece_Z5100(self):
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with kegg_link("pathway", ["hsa:10458", "ece:Z5100"]) as handle:
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handle.read()
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self.assertEqual(
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handle.url, "https://rest.kegg.jp/link/pathway/hsa:10458+ece:Z5100"
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)
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class KGMLPathwayTests(unittest.TestCase):
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"""Tests with metabolic maps."""
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def test_parse_remote_pathway(self):
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"""Download a KEGG pathway from the KEGG server and parse KGML."""
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with kegg_get("ko03070", "kgml") as handle:
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pathway = KGML_parser.read(handle)
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self.assertEqual(pathway.name, "path:ko03070")
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def test_parser_roundtrip(self):
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"""Download a KEGG pathway, write local KGML and check roundtrip."""
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with kegg_get("ko00680", "kgml") as remote_handle:
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pathway = KGML_parser.read(remote_handle)
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with io.StringIO(pathway.get_KGML()) as local_handle:
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roundtrip = KGML_parser.read(local_handle)
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self.assertEqual(pathway.name, roundtrip.name)
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self.assertEqual(len(pathway.relations), len(roundtrip.relations))
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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