mmagnus / rna-tools

    def __init__(self):

        pass

    def cmscan(self, seq, verbose=False):

        """Run cmscan on the seq.

        Usage::

           >>> seq = RNASequence("GGCGCGGCACCGUCCGCGGAACAAACGG")

           >>> rs = RfamSearch()

           >>> hit = rs.cmscan(seq)

           >>> print(hit)  #doctest: +ELLIPSIS

           # cmscan :: search sequence(s) against a CM database...

        :param seq: string

        :returns: result

        :rtype: string """

        #if verbose:

        print('RFAM_DB_PATH', RFAM_DB_PATH)

        # make tmp file

        tf = tempfile.NamedTemporaryFile(delete=False)

        tf.name += '.fa'

        with open(tf.name, 'w') as f:

            f.write('>target\n')

            f.write(seq.seq + '\n')

        # make output file

        of = tempfile.NamedTemporaryFile(delete=False)

        # run cmscan

        cmd = 'cmscan -E 1 ' + RFAM_DB_PATH + ' ' + tf.name + '  > ' + of.name

        print(cmd)

        o = subprocess.Popen(

            cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)

        # out = o.stdout.read().strip()

        err = o.stderr.read().strip()

        if err:

            raise RfamSearchError(err)

        self.output = open(of.name).read()

        # os.chdir(old_pwd)

        return self.output

# main

        if outputfn:

            self.output = open(outputfn).read().strip().split('\n')

    def run_cmalign(self, seq, cm, verbose=True):

        """Run cmalign and process the result.

        :param seq: seq string

        :param cm: cm fn

        Run::

            $ cmalign RF01831.cm 4lvv.seq

            # STOCKHOLM 1.0

            #=GF AU Infernal 1.1.2

            4lvv         -GGAGAGUA-GAUGAUUCGCGUUAAGUGUGUGUGA-AUGGGAUGUCG-UCACACAACGAAGC---GAGA---GCGCGGUGAAUCAUU-GCAUCCGCUCCA

            #=GR 4lvv PP .********.******************9999998.***********.8999999******8...5555...8**************.************

            #=GC SS_cons (((((----(((((((((((,,,,,<<-<<<<<<<<___________>>>>>>>>>>,,,<<<<______>>>>,,,)))))))))))-------)))))

            #=GC RF      ggcaGAGUAGggugccgugcGUuAAGUGccggcgggAcGGGgaGUUGcccgccggACGAAgggcaaaauugcccGCGguacggcaccCGCAUcCgCugcc

            //

        .. warning :: requires cmalign to be set in your shell

        """

        tf = tempfile.NamedTemporaryFile(delete=False)

        tf.name += '.seq'

        with open(tf.name, 'w') as f:

            f.write('>target\n')

            f.write(seq + '\n')

        cmd = 'cmalign -g ' + cm + ' ' + tf.name  # global

        if verbose:

            print('cmd' + cmd)

        o = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)

        stdout = o.stdout.read().strip()

        stderr = o.stderr.read().strip()

        if verbose:

            print(stdout)

        self.output = stdout.split('\n')

    def get_gc_rf(self):

        """Get ``#=GC RF``.