Python io.execute函数代码示例

 def build_bowtie_index(self):
     io.execute([
             'bowtie2-build',
             self.reference_fasta_filename(),
             self/'bowtie',
             ],
         )

 def build_snpeff(self):
     jar = io.find_jar('snpEff.jar')
     
     with open(self/'snpeff.config','wb') as f:
         print >> f, 'data_dir = snpeff'
         print >> f, 'genomes : ' + self.name
         print >> f, self.name + '.genome : ' + self.name 
     
     snpwork = io.Workspace(self/'snpeff',must_exist=False)
     snpwork_genome = io.Workspace(snpwork/self.name,must_exist=False)
     snpwork_genomes = io.Workspace(snpwork/'genomes',must_exist=False)
     
     annotations = self.annotations_filename()
     assert annotations
     with open(snpwork_genome/'genes.gff','wb') as f:
         for record in annotation.read_annotations(annotations):
             if record.end <= record.start: continue
             if not record.attr:
                 record.attr['attributes'] = 'none'
             print >> f, record.as_gff()
     
     with open(snpwork_genomes/(self.name+'.fa'),'wb') as f:
         for name, seq in io.read_sequences(self.reference_fasta_filename()):
             io.write_fasta(f, name, seq)
             
     io.execute('java -jar JAR build NAME -gff3 -c CONFIG',
         JAR=jar, NAME=self.name, CONFIG=self/'snpeff.config')

 def run(self):
     genome = self.genome
     if os.path.isdir(genome):
         genome = os.path.join(genome, os.path.split(genome)[1]+'.genome')
         print genome
     
     #pref_filename = os.path.join(os.path.expanduser('~'),'igv','prefs.properties')
     #if os.path.exists(pref_filename):
     #    with open(pref_filename,'rb') as f:
     #        lines = f.readlines()
     #    with open(pref_filename,'wb') as f:
     #        for line in lines:
     #            if line.startswith('DEFAULT_GENOME_KEY='):
     #                #line = 'DEFAULT_GENOME_KEY=\n'
     #                continue
     #            f.write(line)
     
     with workspace.tempspace() as temp:
         with open(temp/'batch.txt','wb') as f:
             print >> f, 'new'
             print >> f, 'preference LAST_TRACK_DIRECTORY', os.getcwd()
             print >> f, 'preference LAST_GENOME_IMPORT_DIRECTORY', os.getcwd()
             print >> f, 'genome '+os.path.abspath(genome)
             for filename in self.files:
                 print >> f, 'load '+os.path.abspath(filename)
         
         io.execute(['java','-Xmx32000m',
                     #Flags from igb.sh script:
                     '-Dproduction=true','-Dapple.laf.useScreenMenuBar=true','-Djava.net.preferIPv4Stack=true',
                     '-jar',io.find_jar('igv.jar'),'-b',temp/'batch.txt'])

def sort_and_index(in_filename, out_prefix):
    io.execute([
        'samtools', 'sort', in_filename, out_prefix
    ])
    
    io.execute([
        'samtools', 'index', out_prefix + '.bam'
    ])

 def build_bowtie_index(self, log_to=sys.stdout):
     io.execute([
             'bowtie2-build',
             self.reference_fasta_filename(),
             self/'bowtie',
             ],
         stdout = log_to,
         )

def index_vcf(filename):
    """ IGV index a VCF file. 
        Don't fail if igvtools fails (eg not installed).
    """
    try:
        io.execute('igvtools index FILENAME',FILENAME=filename)
    except (OSError, AssertionError):
        print >> sys.stderr, 'Failed to index VCF file with igvtools. Continuing.'

def sort_bam(in_filename, out_prefix, by_name=False, cores=8):
    cores = min(cores, legion.coordinator().get_cores())
    megs = max(10, 800 // cores)
    
    io.execute(
        [ 'samtools', 'sort', '[email protected]', '%d' % cores, '-m', '%dM' % megs ] +
        ([ '-n' ] if by_name else [ ]) +
        [ in_filename, out_prefix ], cores=cores)

    def run(self):
        base = os.path.split(self.prefix)[1]
        
        annotations = [ ]
        sequences = [ ]
        
        for filename in self.filenames:
            any = False
            if io.is_sequence_file(filename):
                sequences.append(filename)
                any = True
            if annotation.is_annotation_file(filename):
                annotations.append(filename)
                any = True
            assert any, 'File is neither a recognized sequence or annotation file'

        cytoband_filename = os.path.join(self.prefix,base+'_cytoband.txt')
        property_filename = os.path.join(self.prefix,'property.txt')
        gff_filename = os.path.join(self.prefix,base+'.gff')
        output_filenames = [ cytoband_filename, property_filename, gff_filename ] 

        if not os.path.exists(self.prefix):
            os.mkdir(self.prefix)
            
        f = open(property_filename,'wb')
        print >> f, 'ordered=true'
        print >> f, 'id=%s' % base
        print >> f, 'name=%s' % (self.name or base)
        print >> f, 'cytobandFile=%s_cytoband.txt' % base
        print >> f, 'geneFile=%s.gff' % base
        print >> f, 'sequenceLocation=%s' % base
        f.close()
        
        trivia.As_gff(output=gff_filename,
               filenames=annotations,
               exclude=[ 'gene', 'source' ]
        ).run()
        
        f_cyt = open(cytoband_filename,'wb')
        for filename in sequences:
            for name, seq in io.read_sequences(filename):
                assert '/' not in name
                f = open(os.path.join(self.prefix, name + '.txt'), 'wb')
                f.write(seq)
                f.close()
                print >> f_cyt, '%s\t0\t%d' % (name, len(seq))
        f_cyt.close()
        
        genome_filename = self.prefix + '.genome'
        if os.path.exists(genome_filename):
            os.unlink(genome_filename)
        io.execute(
            ['zip', '-j', io.abspath(genome_filename)] +
            [ io.abspath(item) for item in output_filenames ]
        )
        for filename in output_filenames:
            if os.path.exists(filename):
                os.unlink(filename)

 def run(self):
     with workspace.tempspace() as temp:
         with open(temp/'batch.txt','wb') as f:
             print >> f, 'new'
             print >> f, 'genome '+os.path.abspath(self.genome)
             for filename in self.files:
                 print >> f, 'load '+os.path.abspath(filename)
         
         io.execute(['java','-jar',io.find_jar('igv.jar'),'-b',temp/'batch.txt'])

 def build_shrimp_mmap(self, cs=False):
     suffix = '-cs' if cs else '-ls'
     
     grace.status('Building SHRiMP mmap')
     io.execute([
         'gmapper' + suffix,
         '--save', self.object_filename('reference' + suffix),
         self.reference_fasta_filename(),
     ])
     grace.status('')

 def run(self):
     from nesoni import io
     
     f_in = self.begin_input()
     f_out = self.begin_output()
     try:
         io.execute(self.command, stdin=f_in, stdout=f_out)
     finally:
         self.end_output(f_out)
         self.end_input(f_in)

 def run(self):
     with workspace.tempspace() as temp:
         with open(temp/'batch.txt','wb') as f:
             print >> f, 'new'
             print >> f, 'preference LAST_TRACK_DIRECTORY', os.getcwd()
             print >> f, 'preference LAST_GENOME_IMPORT_DIRECTORY', os.getcwd()
             print >> f, 'genome '+os.path.abspath(self.genome)
             for filename in self.files:
                 print >> f, 'load '+os.path.abspath(filename)
         
         io.execute(['java','-jar',io.find_jar('igv.jar'),'-b',temp/'batch.txt'])

    def run(self):
        reference = reference_directory.Reference(self.reference, must_exist=True)
        
        jar = io.find_jar('snpEff.jar')
        
        with open(self.prefix + '.vcf','wb') as f:
            io.execute('java -jar JAR eff GENOME VCF -c CONFIG',
                JAR=jar, GENOME=reference.name, VCF=self.vcf, CONFIG=reference/'snpeff.config',
                stdout=f)

        index_vcf(self.prefix+'.vcf')

 def run(self):
     work = self.get_workspace()
     acc = self.run_accession
     io.execute(
         'wget -c URL',
         URL='http://ftp-private.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/%s/%s/%s/%s.sra'
             % (acc[:3],acc[:6],acc,acc),
         cwd=work.working_dir,
         )
     
     io.execute(
         'fastq-dump --split-files --bzip2 FILENAME',
         FILENAME=acc+'.sra',
         cwd=work.working_dir,
         )

 def run(self):
     from nesoni import io
     
     assert self.command, 'Nothing to execute!'
     
     print self.ident()
     
     f_in = self.begin_input()
     f_out = self.begin_output()
     try:
         io.execute(self.command[:1] + self.execution_options + self.command[1:], 
                    stdin=f_in, stdout=f_out)
     finally:
         self.end_output(f_out)
         self.end_input(f_in)