コード例 #1
0
    def run_pipeline(self, R1, R2):  #, config_file
        r1 = tempfile.NamedTemporaryFile(suffix=".fastq")
        r1.write(R1)
        r1.seek(0)
        r2 = tempfile.NamedTemporaryFile(suffix=".fastq")
        r2.write(R2)
        r2.seek(0)

        args = [
            "--forward-reads", r1.name, "--reverse-reads", r2.name,
            "--summary-file", self.summary_fp, "--output-dir", self.output_dir
            #"--config-file", config_file.name
        ]

        main(args)
        return r1.name
コード例 #2
0
    def run_pipeline(self, R1, R2, config_file):
        r1 = tempfile.NamedTemporaryFile(suffix=".fastq")
        r1.write(R1)
        r1.seek(0)
        r2 = tempfile.NamedTemporaryFile(suffix=".fastq")
        r2.write(R2)
        r2.seek(0)
        
        args = [
            "--forward-reads", r1.name,
            "--reverse-reads", r2.name,
            "--summary-file", self.summary_fp,
            "--output-dir", self.output_dir,
            "--config-file", config_file.name
            ]

        main(args)
        return r1.name
コード例 #3
0
#!/usr/bin/env python
from pathfinderlib.main import main
main()