add code for reader fasta in OOP style

source/_static/code/fasta_object.py

+class Sequence(object):
+
+    def __init__(self, id_, comment, sequence):
+        self.id = id_
+        self.comment = comment
+        self.sequence = sequence
+
+
+class FastaParser(object):
+
+
+    def __init__(self, fasta_path):
+        self.path = fasta_path
+        self._file = open(fasta_path)
+        self._current_id = ''
+        self._current_comment = ''
+        self._current_sequence = ''
+
+    def _parse_header(self, line):
+        header = line.split()
+        self._current_id = header[0]
+        self._current_comment = ' '.join(header[1:])
+        self._current_sequence = ''
+
+    def __iter__(self):
+        return self
+
+    def next(self):
+        for line in self._file:
+            if line.startswith('>'):
+                # a new sequence begin
+                if self._current_id != '':
+                    new_seq = Sequence(self._current_id,
+                                       self._current_comment,
+                                       self._current_sequence)
+                    self._parse_header(line)
+                    return new_seq
+                else:
+                    self._parse_header(line)
+            else:
+                self._current_sequence += line.strip()
+        if not self._current_id and not self._current_sequence:
+            self._file.close()
+            raise StopIteration()
+        else:
+            new_seq = Sequence(self._current_id,
+                               self._current_comment,
+                               self._current_sequence)
+            self._current_id = ''
+            self._current_sequence = ''
+            return new_seq
+
+
+if __name__ == '__main__':
+    import sys
+    import os.path
+
+    if len(sys.argv) != 2:
+        sys.exit("usage fasta_object fasta_path")
+    fasta_path = sys.argv[1]
+    if not os.path.exists(fasta_path):
+        sys.exit("No such file: {}".format(fasta_path))
+
+    fasta_parser = FastaParser(fasta_path)
+    for sequence in fasta_parser:
+        print "----------------"
+        print sequence.id
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