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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
212 lines
7.8 KiB
Python
212 lines
7.8 KiB
Python
# Copyright 2013 by Saket Choudhary. Based on test_Clustalw_tool.py by Peter
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# Cock .
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#
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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 calling BWA."""
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import os
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import sys
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import unittest
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import warnings
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from Bio import BiopythonDeprecationWarning
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from Bio import MissingExternalDependencyError
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with warnings.catch_warnings():
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warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
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# TODO from Bio.Sequencing.Applications import BwaBwaswCommandline
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from Bio.Sequencing.Applications import BwaAlignCommandline
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from Bio.Sequencing.Applications import BwaIndexCommandline
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from Bio.Sequencing.Applications import BwaMemCommandline
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from Bio.Sequencing.Applications import BwaSampeCommandline
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from Bio.Sequencing.Applications import BwaSamseCommandline
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#################################################################
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# Try to avoid problems when the OS is in another language
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os.environ["LANG"] = "C"
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bwa_exe = None
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if sys.platform == "win32":
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# TODO - Check the path?
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try:
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# This can vary depending on the Windows language.
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prog_files = os.environ["PROGRAMFILES"]
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except KeyError:
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prog_files = r"C:\Program Files"
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likely_dirs = ["bwa", "bwa-0.6.2", ""]
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likely_exes = ["bwa"]
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for folder in likely_dirs:
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if os.path.isdir(os.path.join(prog_files, folder)):
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for filename in likely_exes:
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if os.path.isfile(os.path.join(prog_files, folder, filename)):
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bwa_exe = os.path.join(prog_files, folder, filename)
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break
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if bwa_exe:
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break
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else:
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from subprocess import getoutput
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output = getoutput("bwa")
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# Since "not found" may be in another language, try and be sure this is
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# really the bwa tool's output
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bwa_found = False
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if "not found" not in output and "not recognized" not in output:
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if "bwa" in output and "alignment via Burrows-Wheeler transformation" in output:
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bwa_exe = "bwa"
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skip_aln_tests = False
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aln_output = getoutput("bwa aln")
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if "unrecognized" in aln_output:
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skip_aln_tests = True
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print("'bwa aln' is unrecognized, skipping aln/samse/sampe tests")
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if not bwa_exe:
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raise MissingExternalDependencyError(
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"Install bwa and correctly set"
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" the file path to the program if"
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" you want to use it from Biopython"
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)
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class BwaTestCase(unittest.TestCase):
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"""Class for implementing BWA test cases."""
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def setUp(self):
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self.reference_file = "BWA/human_g1k_v37_truncated.fasta"
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self.reference_extensions = ["amb", "ann", "bwt", "pac", "sa"]
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self.infile1 = "BWA/HNSCC1_1_truncated.fastq"
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self.infile2 = "BWA/HNSCC1_2_truncated.fastq"
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self.saifile1 = "BWA/1.sai"
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self.saifile2 = "BWA/2.sai"
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self.samfile1 = "BWA/1.sam"
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self.samfile2 = "BWA/2.sam"
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self.samfile = "BWA/out.sam"
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self.files_to_clean = [
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self.saifile1,
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self.saifile2,
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self.samfile1,
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self.samfile2,
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self.samfile,
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]
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def tearDown(self):
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for filename in self.files_to_clean:
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if os.path.isfile(filename):
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os.remove(filename)
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for extension in self.reference_extensions:
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index_file = self.reference_file + "." + extension
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if os.path.exists(index_file):
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os.remove(index_file)
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def test_index(self):
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"""Test for creating index files for the reference genome fasta file."""
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cmdline = BwaIndexCommandline(bwa_exe)
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cmdline.set_parameter("infile", self.reference_file)
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cmdline.set_parameter("algorithm", "bwtsw")
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stdout, stderr = cmdline()
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for extension in self.reference_extensions:
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index_file = self.reference_file + "." + extension
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self.assertTrue(
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os.path.exists(index_file), f"Index File {index_file} not found"
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)
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self.assertIn(
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"Finished constructing BWT",
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str(stdout) + str(stderr),
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f"FASTA indexing failed:\n{cmdline}\nStdout:{stdout}\nStderr:{stderr}\n",
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)
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def do_aln(self, in_file, out_file):
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"""Test for generating sai files given the reference and read file."""
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cmdline = BwaAlignCommandline(bwa_exe)
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cmdline.set_parameter("reference", self.reference_file)
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cmdline.read_file = in_file
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self.assertTrue(os.path.isfile(in_file))
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stdout, stderr = cmdline(stdout=out_file)
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self.assertNotIn(
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"fail to locate the index",
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str(stderr) + str(stdout),
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"Error aligning sequence to reference:\n%s\nStdout:%s\nStderr:%s\n"
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% (cmdline, stdout, stderr),
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)
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def create_fasta_index(self):
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"""Test for generating index for fasta file.
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BWA requires an indexed fasta for each alignment operation.
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This should be called to create an index before any alignment
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operation.
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"""
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cmdline = BwaIndexCommandline(bwa_exe)
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cmdline.set_parameter("infile", self.reference_file)
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cmdline.set_parameter("algorithm", "bwtsw")
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stdout, stderr = cmdline()
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if not skip_aln_tests:
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def test_samse(self):
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"""Test for single end sequencing."""
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self.create_fasta_index()
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self.do_aln(self.infile1, self.saifile1)
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cmdline = BwaSamseCommandline(bwa_exe)
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cmdline.set_parameter("reference", self.reference_file)
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cmdline.set_parameter("read_file", self.infile1)
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cmdline.set_parameter("sai_file", self.saifile1)
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stdout, stderr = cmdline(stdout=self.samfile1)
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with open(self.samfile1) as handle:
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headline = handle.readline()
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self.assertTrue(
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headline.startswith("@SQ"),
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f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
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)
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def test_sampe(self):
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"""Test for generating samfile by paired end sequencing."""
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self.create_fasta_index()
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# Generate sai files from paired end data
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self.do_aln(self.infile1, self.saifile1)
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self.do_aln(self.infile2, self.saifile2)
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cmdline = BwaSampeCommandline(bwa_exe)
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cmdline.set_parameter("reference", self.reference_file)
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cmdline.set_parameter("sai_file1", self.saifile1)
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cmdline.set_parameter("sai_file2", self.saifile2)
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cmdline.set_parameter("read_file1", self.infile1)
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cmdline.set_parameter("read_file2", self.infile2)
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stdout, stderr = cmdline(stdout=self.samfile)
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with open(self.samfile) as handle:
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headline = handle.readline()
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self.assertTrue(
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headline.startswith("@SQ"),
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f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
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)
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def test_mem(self):
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"""Test for generating samfile by paired end sequencing using BWA-MEM."""
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self.create_fasta_index()
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cmdline = BwaMemCommandline(bwa_exe)
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cmdline.set_parameter("reference", self.reference_file)
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cmdline.set_parameter("read_file1", self.infile1)
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cmdline.set_parameter("read_file2", self.infile2)
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stdout, stderr = cmdline(stdout=self.samfile)
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with open(self.samfile) as handle:
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headline = handle.readline()
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self.assertTrue(
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headline.startswith("@SQ"),
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f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
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)
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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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