def test_concat_alignments(alb_resources, hf): with pytest.raises(AttributeError) as e: Alb.concat_alignments(alb_resources.get_one("p o g"), '.*') assert "Please provide at least two alignments." in str(e) tester = alb_resources.get_one("o p g") tester.alignments.append(alb_resources.get_one("o p g").alignments[0]) with pytest.raises(ValueError) as e: Alb.concat_alignments(tester, 'foo') assert "No match found for record" in str(e) with pytest.raises(ValueError) as e: Alb.concat_alignments(tester, 'Panx') assert "Replicate matches" in str(e) tester = Sb.SeqBuddy("%sCnidaria_pep.nexus" % hf.resource_path) Sb.pull_recs(tester, "Ccr|Cla|Hec") tester = Alb.AlignBuddy(str(tester)) tester.alignments.append(tester.alignments[0]) assert hf.buddy2hash(Alb.concat_alignments(Alb.make_copy(tester))) == '32a507107b7dcd044ea7760c8812441c' tester.set_format("gb") tester2 = Alb.concat_alignments(Alb.make_copy(tester), "(.).(.)-Panx(.)") assert hf.buddy2hash(tester2) == 'cd2b6594b22c431aea67fa45899f933a' tester.set_format("gb") tester2 = Alb.concat_alignments(Alb.make_copy(tester), "(.).(.)-Panx(.)") assert hf.buddy2hash(tester2) == 'cd2b6594b22c431aea67fa45899f933a' tester.set_format("gb") tester2 = Alb.concat_alignments(Alb.make_copy(tester), "...", "Panx.*") assert hf.buddy2hash(tester2) == 'e49b26f695c910a93f93d70563fd9dd9' tester.set_format("gb") tester2 = Alb.concat_alignments(Alb.make_copy(tester), "...", "(P)an(x)(.)") assert hf.buddy2hash(tester2) == '3abfdf2217050ac2170c0de27352a8c6' shorten = Alb.delete_records(Alb.make_copy(tester), "Ccr") tester.alignments[1] = shorten.alignments[1] assert hf.buddy2hash(Alb.concat_alignments(Alb.make_copy(tester))) == '685f24ee1fc88860dd9465035040c91e'
def test_concat_alignments(alb_resources, hf): with pytest.raises(AttributeError) as e: Alb.concat_alignments(alb_resources.get_one("p o g"), '.*') assert "Please provide at least two alignments." in str(e) tester = alb_resources.get_one("o p g") tester.alignments.append(alb_resources.get_one("o p g").alignments[0]) with pytest.raises(ValueError) as e: Alb.concat_alignments(tester, 'foo') assert "No match found for record" in str(e) with pytest.raises(ValueError) as e: Alb.concat_alignments(tester, 'Panx') assert "Replicate matches" in str(e) tester = Sb.SeqBuddy("%sCnidaria_pep.nexus" % hf.resource_path) Sb.pull_recs(tester, "Ccr|Cla|Hec") tester = Alb.AlignBuddy(str(tester)) tester.alignments.append(tester.alignments[0]) assert hf.buddy2hash(Alb.concat_alignments( Alb.make_copy(tester))) == '32a507107b7dcd044ea7760c8812441c' tester.set_format("gb") tester2 = Alb.concat_alignments(Alb.make_copy(tester), "(.).(.)-Panx(.)") assert hf.buddy2hash(tester2) == '5ac908ebf7918a45664a31da480fda58' tester.set_format("gb") tester2 = Alb.concat_alignments(Alb.make_copy(tester), "(.).(.)-Panx(.)") assert hf.buddy2hash(tester2) == '5ac908ebf7918a45664a31da480fda58' tester.set_format("gb") tester2 = Alb.concat_alignments(Alb.make_copy(tester), "...", "Panx.*") assert hf.buddy2hash(tester2) == 'e754350b0397cf54f531421d1e85774f' tester.set_format("gb") tester2 = Alb.concat_alignments(Alb.make_copy(tester), "...", "(P)an(x)(.)") assert hf.buddy2hash(tester2) == '5c6653aec09489cadcbed68fbd2f7465' shorten = Alb.delete_records(Alb.make_copy(tester), "Ccr") tester.alignments[1] = shorten.alignments[1] assert hf.buddy2hash(Alb.concat_alignments( Alb.make_copy(tester))) == 'f3ed9139ab6f97042a244d3f791228b6'