Ejemplo n.º 1
0
    def _prepare_domains(self, dom_list):
        """Select domain subsequences from the entire protein sequences."""
        def prepare_domains(fasta_dic, dom_list, pfam_scan, out_folder):
            out_file_dic = {}
            for acc in dom_list:
                out_file_dic[acc] = open("%s/%s.fa" % (out_folder, acc), "w")

            f = open(pfam_scan)
            f.readline()
            for line in f:
                split = line.split()
                rbp = split[0]
                start = int(split[3])
                stop = int(split[4])
                acc = split[5].split('.')[0]
                if acc in out_file_dic.keys():
                    out_file_dic[acc].write(
                        ">%s:%i-%i\n%s\n" %
                        (rbp, start, stop, fasta_dic[rbp][start:stop]))
            f.close()

            for acc in dom_list:
                out_file_dic[acc].close()

        mkdir(self._dom_fold)
        fasta = fasta_utils.import_fasta(self.fasta)
        prepare_domains(fasta, dom_list, self.pfam_scan, self._dom_fold)
Ejemplo n.º 2
0
    def _prepare_domains(self, dom_list):
        """Select domain subsequences from the entire protein sequences."""
        def prepare_domains(fasta_dic, dom_list, pfam_scan, out_folder):
            out_file_dic = {}
            for acc in dom_list:
                out_file_dic[acc] = open("%s/%s.fa" % (out_folder, acc), "w")

            f = open(pfam_scan)
            f.readline()
            for line in f:
                split = line.split()
                rbp = split[0]
                start = int(split[3])
                stop = int(split[4])
                acc = split[5].split('.')[0]
                if acc in out_file_dic.keys():
                    out_file_dic[acc].write(
                        ">%s:%i-%i\n%s\n" % (rbp, start, stop,
                                             fasta_dic[rbp][start:stop]))
            f.close()

            for acc in dom_list:
                out_file_dic[acc].close()

        mkdir(self._dom_fold)
        fasta = fasta_utils.import_fasta(self.fasta)
        prepare_domains(fasta, dom_list, self.pfam_scan,
                        self._dom_fold)
Ejemplo n.º 3
0
    def _pfam_scan(self):
        """Scan the sequences against the Pfam database."""
        nf = open(self.pfam_scan, "w")
        nf.write(pfam_utils.search_header())

        fasta = fasta_utils.import_fasta(self.fasta)

        for rbp in sorted(fasta.keys()):
            seq = fasta[rbp]
            text = pfam_utils.sequence_search(rbp, seq)
            nf.write(text)

        nf.close()
Ejemplo n.º 4
0
    def _pfam_scan(self):
        """Scan the sequences against the Pfam database."""
        nf = open(self.pfam_scan, "w")
        nf.write(pfam_utils.search_header())

        fasta = fasta_utils.import_fasta(self.fasta)

        for rbp in sorted(fasta.keys()):
            seq = fasta[rbp]
            text = pfam_utils.sequence_search(rbp, seq)
            nf.write(text)

        nf.close()
Ejemplo n.º 5
0
    def _pfam_scan(self):
        """Scan the sequences against the Pfam database."""
        nf = open(self.pfam_scan, "w")
        nf.write(pfam_utils.search_header())

        fasta = fasta_utils.import_fasta(self.fasta)

        if len(fasta) != 1:
            sys.exit("""Fasta file must contain exactly one sequence.""")

        for rbp in sorted(fasta.keys()):
            seq = fasta[rbp]
            text = pfam_utils.sequence_search(rbp, seq)
            nf.write(text)

        nf.close()
Ejemplo n.º 6
0
    def _pfam_scan(self):
        """Scan the sequences against the Pfam database."""
        nf = open(self.pfam_scan, "w")
        nf.write(pfam_utils.search_header())

        fasta = fasta_utils.import_fasta(self.fasta)

        if len(fasta) != 1:
            sys.exit("""Fasta file must contain exactly one sequence.""")

        for rbp in sorted(fasta.keys()):
            seq = fasta[rbp]
            text = pfam_utils.sequence_search(rbp, seq)
            nf.write(text)

        nf.close()