pyaragorn 0.1.0__cp37-cp37m-macosx_10_12_x86_64.whl

pyaragorn/tests/__init__.py

@@ -0,0 +1,10 @@
+from . import (
+    test_rna_finder,
+    test_doctest,
+)
+
+
+def load_tests(loader, suite, pattern):
+    suite.addTests(loader.loadTestsFromModule(test_rna_finder))
+    test_doctest.load_tests(loader, suite, pattern)
+    return suite

pyaragorn/tests/data/CP001621.default.txt

@@ -0,0 +1,95 @@
+>CP001621.1 Mycoplasma mycoides subsp. capri str. GM12 transgenic clone tetM-lacZ, complete genome
+31 genes found
+1   tRNA-Leu                c[87124,87207]	116.6	35  	(tag)
+gggggattggcggaattggcagacgcactagacttaggatctagcgtctttaacgtaagggttcaagtcccttatcccccacca
+(((((((ss(((ddddddddddd)))s(((((ccAAAcc)))))vvvvvvvvvvvv(((((ttttttt))))))))))))
+2   tRNA-Lys                c[87210,87285]	124.1	34  	(ttt)
+gactcgttagctcagccggtagagcaactggcttttaaccagtgggtccggggttcgaatccccgacgagtcacca
+(((((((ss((((dddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+3   tRNA-Lys              c[139027,139102]	117.7	34  	(ctt)
+gtctgattagcgcaactggcagagcaactgactcttaatcagtgggttgtgggttcgattcccacatcaggcacca
+(((((((ss((.(dddddddd).))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+4   tmRNA                  [198037,198447]	109.7		87,173	AEKNEENFEMPAFMINNASAGANYMFA**
+ggggatgtcatggatttgacaggatat|gtatcttggacgcgagttcgattctcgccatctccacca
+(((((((dddddddddddd((((((((|))))))))vvv(((((ttttttt))))))))))))aaaa
+5   tRNA-Ser               [355003,355092]	119.7	35  	(gct)
+gggttaatactcaagttggtgaagaggacaccctgctaaggtgttaggtcggtctccggcgcgagggttcgagtccctcttaacccgcca
+(((((((ss(((ddddddddddd)))((((((ccAAAcc))))))ss((((vvvvv))))ss(((((ttttttt))))))))))))
+6   tRNA-Gly               [371077,371150]	118.5	33  	(tcc)
+gcaggtgtagtttaatggcagaacttcagccttccaagctgattgtgagggttcgattcccttcacctgctcca
+(((((((ss((((ddddddd))))s(((((ccAAAcc)))))vvvv(((((ttttttt))))))))))))
+7   tRNA-Arg               [459024,459100]	118.0	35  	(tct)
+gcccatgtagctcagtaggatagagcacgcgccttctaagcgtgaggtcggaagttcgagccttctcgtgggcacca
+(((((((ss((((ddddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+8   tRNA-Leu               [521320,521404]	117.7	35  	(caa)
+gcccttttggcggaattggcagacgcattagactcaaaatctaacgaagaaattcgtatcggttcgaccccgataaagggcacca
+(((((((ss(((ddddddddddd)))s(((((ccAAAcc)))))((((vvvv))))s(((((ttttttt))))))))))))
+9   tRNA-Leu              c[611707,611795]	119.4	35  	(taa)
+ccccaagtggcggaataggtagacgcattggacttaaaatccaacgggcttaatatcctgtgccggttcaagtccggccttggggacca
+(((((((ss(((ddddddddddd)))s(((((ccAAAcc)))))((((vvvvvvvv))))s(((((ttttttt))))))))))))
+10  tRNA-Lys              c[611806,611881]	124.1	34  	(ttt)
+gactcgttagctcagccggtagagcaactggcttttaaccagtgggtccggggttcgaatccccgacgagtcacca
+(((((((ss((((dddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+11  tRNA-Gln              c[611886,611960]	116.0	33  	(ttg)
+tgggctatagccaagcggtaaggcaagggactttgactccctcatgcgccggttcgaatcctgctagcccaacca
+(((((((ss(((ddddddddd)))s(((((ccAAAcc)))))vvvvv((.((ttttttt)).)))))))))
+12  tRNA-Tyr              c[611967,612050]	120.5	35  	(gta)
+ggaggggtagcgaagtggctaaacgcgggtggctgtaacccacttccttacggttcgggggttcgaatccctccccctccacca
+(((((((ss(((ddddddddddd)))((((((ccAAAcc))))))vvvvvvvvvvv(((((ttttttt))))))))))))
+13  tRNA-Thr              c[612057,612132]	119.0	34  	(agt)
+gctgacttagctcagttggtagagcaattgactagtaatcaataggtcgaaggttcaaatcctttagtcagcacca
+(((((((ss((((dddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+14  tRNA-Trp              c[763746,763820]	118.0	33  	(cca)
+aggagagtagttcaatggtagaacgtcggtctccaaaaccgagcgttgagggttcgattcctttctctcctgcca
+(((((((ss((((ddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+15  tRNA-SeC              c[763858,763933]	118.2	34  	(tca)
+aggggcatagttcagtaggtagaacatcggtcttcaaaaccgagtgtcacgagttcgagtcttgttgcccctgcca
+(((((((ss((((dddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+16  tRNA-His              c[766239,766314]	113.8	34  	(gtg)
+gcgtaggtggtgaagtggttaacacatcaggttgtggctctgacatgcgcgggttcgatccccgttctacgcccca
+(((((((ss(((dddddddddd)))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+17  tRNA-Ile              c[778452,778528]	120.9	35  	(gat)
+cggaatatagctcagctggttagagcactccgctgataacggagaggtcgttggttcaagtccaattattccgacca
+(((((((ss((((ddddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+18  tRNA-Thr              c[813006,813081]	121.2	34  	(tgt)
+gctgacttagctcagcaggcagagcaactgacttgtaatcagtaggtcgtaggttcgattcctatagtcagcacca
+(((((((ss((((dddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+19  tRNA-Val              c[813094,813169]	122.2	34  	(tac)
+ggagtgttagctcagctgggagagctcctgccttacaagcaggcggtcataggttcaagtcctatacactccacca
+(((((((ss((((dddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+20  tRNA-Glu              c[813177,813252]	119.7	34  	(ttc)
+ggcctgttggtgaagcggttaacacacacggttttcatccgtggacacacgggttcgaaccccgtacaggctacca
+(((((((ss(((dddddddddd)))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+21  tRNA-Asn              c[813260,813335]	123.7	34  	(gtt)
+ggctttttagctcagcaggtagagcaaccggctgttaaccggtttgtcacaggttcgagccctgtaaaagccgcca
+(((((((ss((((dddddddd))))((((((ccAAAcc))))))vvvv(((((ttttttt))))))))))))
+22  tRNA-Arg               [856360,856436]	117.7	35  	(acg)
+gcgcccgtagatcaattggatagatcgcttgactacggatcaaaaggttgggggttcgagtccctccgggcgcacca
+(((((((ss((((ddddddddd))))s.((((ccAAAcc)))).vvvvv(((((ttttttt))))))))))))
+23  tRNA-Pro               [856484,856560]	121.2	35  	(tgg)
+cgggaagtggctcagtttggtagagcattcggtttgggaccgaagggtcgcaggttcaaatcctgtcttcccgacca
+(((((((ss((((ddddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+24  tRNA-Ala               [856571,856646]	121.1	34  	(tgc)
+gggcccttagctcagctgggagagcacctgccttgcacgcagggggtcgacggttcgatcccgttagggtccacca
+(((((((ss((((dddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+25  tRNA-Met               [856651,856727]	120.1	35  	(cat)
+ggcggggtagctcagttggttagagcgttcggttcatacccgaaaggtcgagagttcaactctctcccccgctacca
+(((((((ss((((ddddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+26  tRNA-Met               [856739,856815]	122.2	35  	(cat)
+ggacctttagctcagttggttagagcatccggctcataaccggacggtcattggttcaagtccaataaggtccacca
+(((((((ss((((ddddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+27  tRNA-Ser               [856858,856950]	117.2	37  	(tga)
+ggaagattacccaagtccggctgaagggatcggtcttgaaaaccgagagtcggggaaacccgagcgggggttcgaatccctcatcttccgcca
+(((((((ss(((.ddddddddddd.)))s(((((ccAAAcc)))))sss(((((vvvv)))))ss(((((ttttttt))))))))))))
+28  tRNA-Met               [856973,857048]	123.7	34  	(cat)
+cgcggggtagagcagttggtagctcgccgggctcataacccggaggccgcaggttcgagtcctgcccccgcaacca
+.((((((ss((((dddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))).
+29  tRNA-Asp               [857051,857127]	123.9	35  	(gtc)
+ggccccatagcgaagttggttatcgcgcctccctgtcacggaggagatcacgggttcgagtcccgttggggtcgcca
+(((((((ss((((ddddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+30  tRNA-Phe               [857136,857211]	119.3	34  	(gaa)
+ggtcgtgtagctcagtcggtagagcagcagactgaagctctgcgtgtcggcggttcaattccgtccacgaccacca
+(((((((ss((((dddddddd))))s(((((ccAAAcc)))))vvvvv(((((ttttttt))))))))))))
+31  tRNA-Cys               [975123,975197]	117.5	34  	(gca)
+ggcaatatagccaagcggctaaggcatgggtctgcaacaccctgatcgtcggttcgaatccgactattgcctcca
+(((((((ss(((dddddddddd)))s.((((ccAAAcc)))).vvvv(((((ttttttt))))))))))))

pyaragorn/tests/data/__init__.py

@@ -0,0 +1,30 @@
+import contextlib
+import gzip
+import io
+
+try:
+    try:
+        from importlib.resources import files
+    except ImportError:
+        from importlib_resources import files  # type: ignore
+except ImportError:
+    files = None  # type: ignore
+
+from ..fasta import parse, zopen
+
+@contextlib.contextmanager
+def load(name, mode="rb"):
+     with zopen(files(__name__).joinpath(name), mode=mode) as src:
+        yield src
+
+def load_record(name):
+    with load(name, mode="r") as f:
+        return next(parse(f))
+
+def load_records(name):
+    with load(name, mode="r") as f:
+        return list(parse(f))
+
+def load_text(name):
+    with load(name, mode="r") as f:
+        return f.read()

pyaragorn/tests/fasta.py

@@ -0,0 +1,86 @@
+import bz2
+import collections
+import contextlib
+import io
+import os
+
+
+
+_BZ2_MAGIC = b"BZh"
+_GZIP_MAGIC = b"\x1f\x8b"
+_XZ_MAGIC = b"\xfd7zXZ"
+_LZ4_MAGIC = b"\x04\x22\x4d\x18"
+_ZSTD_MAGIC = b"\x28\xb5\x2f\xfd"
+
+
+@contextlib.contextmanager
+def zopen(file, mode='r', encoding=None, errors=None, newline=None):
+    with contextlib.ExitStack() as ctx:
+
+        try:
+            path = os.fsencode(file)
+            file = ctx.enter_context(open(path, mode="rb"))
+        except TypeError:
+            raise
+
+        peek = file.peek()
+        if peek.startswith(_GZIP_MAGIC):
+            try:
+                from isal import igzip as gzip
+            except ImportError:
+                import gzip  # type: ignore
+            file = ctx.enter_context(gzip.open(file, mode="rb"))
+        elif peek.startswith(_BZ2_MAGIC):
+            import bz2
+            file = ctx.enter_context(bz2.open(file, mode="rb"))
+        elif peek.startswith(_XZ_MAGIC):
+            import lzma
+            file = ctx.enter_context(lzma.open(file, mode="rb"))
+        elif peek.startswith(_LZ4_MAGIC):
+            try:
+                import lz4.frame
+            except ImportError as err:
+                raise RuntimeError("File compression is LZ4 but lz4 is not installed") from err
+            file = ctx.enter_context(lz4.frame.open(file))
+        elif peek.startswith(_ZSTD_MAGIC):
+            try:
+                import zstandard
+            except ImportError as err:
+                raise RuntimeError("File compression is ZSTD but zstandard is not installed") from err
+            decompressor = zstandard.ZstdDecompressor()
+            file = decompressor.stream_reader(file)
+        if mode == "r":
+            file = io.TextIOWrapper(file, encoding=encoding, errors=errors, newline=newline)
+        yield file
+
+
+class Record(collections.namedtuple("Record", ["id", "seq", "description"])):
+    pass
+
+
+def parse(path):
+    with contextlib.ExitStack() as ctx:
+        try:
+            path = os.fsencode(path)
+            file = ctx.enter_context(zopen(path, "r"))
+        except TypeError:
+            file = path
+
+        # parse file
+        id_ = None
+        seq = []
+        for line in file:
+            l = line.strip()
+            if line.startswith(">"):
+                if id_ is not None:
+                    yield Record(id_, "".join(seq), desc)
+                fields = line[1:].split(maxsplit=1)
+                id_ = fields[0] if len(fields) > 0 else ""
+                desc = fields[1] if len(fields) > 1 else ""
+                seq = []
+            elif l:
+                seq.append(l)
+        if id_ is not None:
+            yield Record(id_, "".join(seq), desc)
+        elif seq:
+            raise ValueError("not in FASTA format")

pyaragorn/tests/requirements.txt

@@ -0,0 +1 @@
+importlib-resources ; python_version < '3.9'

pyaragorn/tests/test_doctest.py

@@ -0,0 +1,93 @@
+# coding: utf-8
+"""Test doctest contained tests in every file of the module.
+"""
+
+import configparser
+import doctest
+import importlib
+import json
+import gzip
+import os
+import pkgutil
+import re
+import shutil
+import sys
+import types
+import warnings
+from unittest import mock
+
+import pyaragorn
+
+from .fasta import parse
+
+
+def _load_tests_from_module(tests, module, globs, setUp=None, tearDown=None):
+    """Load tests from module, iterating through submodules."""
+    for attr in (getattr(module, x) for x in dir(module) if not x.startswith("_")):
+        if isinstance(attr, types.ModuleType):
+            suite = doctest.DocTestSuite(
+                attr,
+                globs,
+                setUp=setUp,
+                tearDown=tearDown,
+                optionflags=+doctest.ELLIPSIS,
+            )
+            tests.addTests(suite)
+    return tests
+
+
+def load_tests(loader, tests, ignore):
+    """`load_test` function used by unittest to find the doctests."""
+    _current_cwd = os.getcwd()
+    # demonstrate how to load sequences with Biopython without requiring Biopython
+    Bio = mock.Mock()
+    Bio.SeqIO = mock.Mock()
+    Bio.SeqIO.read = lambda file, format: next(parse(file))
+
+    # load sample record
+    data_folder = os.path.realpath(os.path.join(__file__, os.path.pardir, "data"))
+    with gzip.open(os.path.join(data_folder, "CP001621.fna.gz"), "rt") as f:
+        record = next(parse(f))
+
+    def setUp(self):
+        warnings.simplefilter("ignore")
+        os.chdir(data_folder)
+        sys.modules["Bio"] = Bio
+        sys.modules["Bio.SeqIO"] = Bio.SeqIO
+
+    def tearDown(self):
+        os.chdir(_current_cwd)
+        warnings.simplefilter(warnings.defaultaction)
+        sys.modules.pop("Bio")
+        sys.modules.pop("Bio.SeqIO")
+
+    # doctests are not compatible with `green`, so we may want to bail out
+    # early if `green` is running the tests
+    if sys.argv[0].endswith("green"):
+        return tests
+
+    # recursively traverse all library submodules and load tests from them
+    packages = [None, pyaragorn]
+    for pkg in iter(packages.pop, None):
+        for (_, subpkgname, subispkg) in pkgutil.walk_packages(pkg.__path__):
+            # do not import __main__ module to avoid side effects!
+            if subpkgname == "__main__" or subpkgname.startswith("tests") or subpkgname.startswith("cli"):
+                continue
+            # import the submodule and add it to the tests
+            module = importlib.import_module(".".join([pkg.__name__, subpkgname]))
+            globs = dict(pyaragorn=pyaragorn, json=json, gzip=gzip, Bio=Bio, record=record, **module.__dict__)
+            tests.addTests(
+                doctest.DocTestSuite(
+                    module,
+                    globs=globs,
+                    setUp=setUp,
+                    tearDown=tearDown,
+                    optionflags=+doctest.ELLIPSIS,
+                )
+            )
+            # if the submodule is a package, we need to process its submodules
+            # as well, so we add it to the package queue
+            if subispkg and subpkgname != "tests":
+                packages.append(module)
+
+    return tests

pyaragorn/tests/test_rna_finder.py

@@ -0,0 +1,69 @@
+import itertools
+import re
+import unittest
+
+from .. import RNAFinder, TMRNAGene, TRNAGene
+from . import data
+
+
+_TRNA_RX = re.compile(r"^(\d+)\s+tRNA-([A-Za-z]{3})\s+(c?)\[(\d+),(\d+)\]\s+([\d.]+)\s+(\d+)\s+\(([a-z]{2,4})\)")
+_TMRNA_RX = re.compile(r"^(\d+)\s+tmRNA\s+(c?)\[(\d+),(\d+)]\s+([\d.]+)\s+(\d+),(\d+)\s+([A-Z\*]+)")
+
+def batched(iterable, n, *, strict=False):
+    # batched('ABCDEFG', 3) → ABC DEF G
+    if n < 1:
+        raise ValueError('n must be at least one')
+    iterator = iter(iterable)
+    for batch in iter(lambda: tuple(itertools.islice(iterator, n)), ()):
+        if strict and len(batch) != n:
+            raise ValueError('batched(): incomplete batch')
+        yield batch
+
+class TestRNAFinder(unittest.TestCase):
+    
+    def test_default(self):
+        record = data.load_record("CP001621.fna.gz")
+        lines = data.load_text("CP001621.default.txt").splitlines()
+        
+        finder = RNAFinder(translation_table=11)
+        genes = finder.find_rna(str(record.seq))
+
+        for gene, expected in itertools.zip_longest(genes, batched(lines[2:], 3)):
+            self.assertIsNotNone(gene)
+            self.assertIsNotNone(expected)
+            result, seq, ss = expected
+            if gene.type == "tRNA":
+                matched = _TRNA_RX.match(result)
+                _, aa, complement, begin, end, energy, offset, anticodon = matched.groups()
+                self.assertEqual(gene.amino_acid, aa)
+                self.assertEqual(gene.begin, int(begin))
+                self.assertEqual(gene.end, int(end))
+                self.assertEqual(gene.anticodon_offset, int(offset))
+                self.assertEqual(gene.anticodon_length, len(anticodon))
+                self.assertEqual(gene.anticodon, anticodon)
+                self.assertEqual(gene.strand, -1 if complement == "c" else +1)
+                self.assertAlmostEqual(gene.energy, float(energy), places=1)
+                self.assertEqual(gene.sequence().lower(), seq)
+            elif gene.type == "tmRNA":
+                matched = _TMRNA_RX.match(result)
+                _, complement, begin, end, energy, cds_start, cds_end, peptide = matched.groups()
+                self.assertEqual(gene.begin, int(begin))
+                self.assertEqual(gene.end, int(end))
+                self.assertEqual(gene.cds_offset, int(cds_start))
+                self.assertEqual(gene.cds_offset + gene.cds_length, int(cds_end))
+                self.assertEqual(gene.peptide(), peptide)
+                self.assertEqual(gene.strand, -1 if complement == "c" else +1)
+                self.assertAlmostEqual(gene.energy, float(energy), places=1)
+                # self.assertEqual(gene.sequence().lower(), seq) # TODO
+
+    def test_trna(self):
+        record = data.load_record("CP001621.fna.gz")
+        finder = RNAFinder(translation_table=11, tmrna=False, trna=True)
+        for gene in finder.find_rna(str(record.seq)):
+            self.assertIsInstance(gene, TRNAGene)
+    
+    def test_tmrna(self):
+        record = data.load_record("CP001621.fna.gz")
+        finder = RNAFinder(translation_table=11, tmrna=True, trna=False)
+        for gene in finder.find_rna(str(record.seq)):
+            self.assertIsInstance(gene, TMRNAGene)