Python fastaq_to_mira_xml示例

示例#1

文件： to_mira_xml.py 项目： jhh130910/code-test

def run(description):
    parser = argparse.ArgumentParser(
        description = description,
        usage = 'fastaq to_mira_xml <infile> <xml_out>')
    parser.add_argument('infile', help='Name of input fasta/q file')
    parser.add_argument('xml_out', help='Name of output xml file')
    options = parser.parse_args()
    tasks.fastaq_to_mira_xml(options.infile, options.xml_out)

示例#2

 def test_fastaq_to_mira_xml(self):
     '''check that fastaq_to_mira_xml makes the correct xml file from a fastq file'''
     tmp = 'tmp.mira.xml'
     tasks.fastaq_to_mira_xml(
         os.path.join(data_dir, 'sequences_test_good_file.fq'), tmp)
     self.assertTrue(
         filecmp.cmp(
             os.path.join(data_dir, 'sequences_test_good_file_mira.xml'),
             tmp))
     os.unlink(tmp)

示例#3

文件： to_mira_xml.py 项目： satta/Fastaq

def run(description):
    parser = argparse.ArgumentParser(description=description, usage="fastaq to_mira_xml <infile> <xml_out>")
    parser.add_argument("infile", help="Name of input fasta/q file")
    parser.add_argument("xml_out", help="Name of output xml file")
    options = parser.parse_args()
    tasks.fastaq_to_mira_xml(options.infile, options.xml_out)

示例#4

文件： tasks_test.py 项目： martinghunt/Fastaq

 def test_fastaq_to_mira_xml(self):
     '''check that fastaq_to_mira_xml makes the correct xml file from a fastq file'''
     tmp = 'tmp.mira.xml'
     tasks.fastaq_to_mira_xml(os.path.join(data_dir, 'sequences_test_good_file.fq'), tmp)
     self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_good_file_mira.xml'), tmp))
     os.unlink(tmp)