refactor fasta_reader to put open file outside function

source/_static/code/fasta_filter.py

@@ -5,57 +5,58 @@ from itertools import groupby
    
 Sequence =  namedtuple("Sequence", "id comment sequence")
 
-def fasta_iter(fasta_path):
-   """
-   :param fasta_file: the file containing all input sequences in fasta format.
-   :type fasta_file: file object
-   :author: http://biostar.stackexchange.com/users/36/brentp
-   :return: for a given fasta file, it returns an iterator which yields tuples
+def fasta_iter(fasta_file):
+    """
+    :param fasta_file: the file containing all input sequences in fasta format.
+    :type fasta_file: file object
+    :author: http://biostar.stackexchange.com/users/36/brentp
+    :return: for a given fasta file, it returns an iterator which yields tuples
           (string id, string comment, int sequence length)
-   :rtype: iterator
-   """
-   with open(fasta_path) as fasta_file:
-      # ditch the boolean (x[0]) and just keep the header or sequence since
-      # we know they alternate.
-      group = (x[1] for x in groupby(fasta_file , lambda line: line[0] == ">"))
-      for header in group:
-         # drop the ">"
-         header = header.next()[1:].strip()
-         header = header.split()
-         _id = header[0]
-         comment = ' '.join(header[1:])
-         seq = ''.join(s.strip() for s in group.next())
-         yield Sequence(_id, comment, seq)
+    :rtype: iterator
+    """
+    # ditch the boolean (x[0]) and just keep the header or sequence since
+    # we know they alternate.
+    group = (x[1] for x in groupby(fasta_file , lambda line: line[0] == ">"))
+    for header in group:
+       # drop the ">"
+       header = header.next()[1:].strip()
+       header = header.split()
+       _id = header[0]
+       comment = ' '.join(header[1:])
+       seq = ''.join(s.strip() for s in group.next())
+       yield Sequence(_id, comment, seq)
+         
          
-def fasta_writer(sequence, fasta_path):
+def fasta_writer(sequence, output_file):
     """
     write a sequence in a file in fasta format
 
     :param sequence: the sequence to print
     :type sequence: Sequence instance
-    :param fasta_path: the path to the file to print the sequence in
-    :type fasta_path: string
+    :param v: the file to print the sequence in
+    :type output_file: file object
     """
-    print "appel de fasta_writer ",sequence.id, " ",fasta_path
-    with open(fasta_path, 'w') as output:
-        output.write('>{0.id} {0.comment}\n'.format(seq))
-        start = 0
-        while start < len(seq.sequence):
-            end = start + 80
-            print start, " : ", end
-            output.write(seq.sequence[start: end + 1] + '\n')
-            start = end
+    output_file.write('>{0.id} {0.comment}\n'.format(seq))
+    start = 0
+    while start < len(seq.sequence):
+        end = start + 80
+        print start, " : ", end
+        output_file.write(seq.sequence[start: end + 1] + '\n')
+        start = end
+
 
 if __name__ == '__main__':
     if len(sys.argv) != 2:
         sys.exit("usage: fasta_filter path/to/fasta/file/to/read")
     input_path = sys.argv[1]
-
-    for seq in fasta_iter(input_path):
-        if seq.sequence.startswith('M') and seq.sequence.count('W') > 6:
-            if os.path.exists(seq.id):
-                print >> sys.stderr , "file {0} already exist: sequence {0} skipped".format(seq.id)
-                continue
-            else:
-                output_fasta = seq.id + ".fa"
-                fasta_writer(seq, output_fasta)
\ No newline at end of file
+    
+    with open(input_path, 'r') as input_file:
+        for seq in fasta_iter(input_path):
+            if seq.sequence.startswith('M') and seq.sequence.count('W') > 6:
+                if os.path.exists(seq.id):
+                    print >> sys.stderr , "file {0} already exist: sequence {0} skipped".format(seq.id)
+                    continue
+                else:
+                    output_fasta = seq.id + ".fa"
+                    with open(output_path, 'w') as output_file:
+                        fasta_writer(seq, output_file)
\ No newline at end of file

source/_static/code/fasta_iterator.py

@@ -3,7 +3,7 @@ from itertools import groupby
    
 Sequence =  namedtuple("Sequence", "id comment sequence")
 
-def fasta_iter(fasta_path):
+def fasta_iter(fasta_file):
    """
    :param fasta_file: the file containing all input sequences in fasta format.
    :type fasta_file: file object
@@ -30,4 +30,9 @@ def fasta_iter(fasta_path):
 #f.next()
 #or
 # for seq in fasta_iter('seq.fasta'):
-#   do something with seq
\ No newline at end of file
+#   do something with seq
+#The problem with this implementation is
+# something goes wrong in do something with seq
+# but we don't quit the program (we catch the exception for instance)
+# the fasta file is still open
+# it's better to put the fasta file opening out the fasta reader see fasta filter 
\ No newline at end of file

source/_static/code/fasta_reader.py

@@ -21,4 +21,4 @@ def fasta_reader(fasta_path):
                 in_sequence = True
             else:
                 sequence += line.strip()
-        return Sequence(id_ , comment, sequence)
\ No newline at end of file
+    return Sequence(id_ , comment, sequence)
\ No newline at end of file

source/_static/code/multiple_fasta_reader.py

@@ -2,7 +2,7 @@ from collections import namedtuple
 
 Sequence =  namedtuple("Sequence", "id comment sequence")
 
-def fasta_reader(fasta_path):
+def fasta_reader(fasta_file):
     """
     :param fasta_path: the path to the file to parse
     :type fasta_path: string
@@ -10,22 +10,24 @@ def fasta_reader(fasta_path):
     :rtype: list of Sequence 
     """
     sequences = []
-    with open(fasta_path, 'r') as fasta_infile:
-        id_ = ''
-        comment = ''
-        sequence = ''
-        for line in fasta_infile:
-            if line.startswith('>'):
-                # a new sequence begin
-                if id_ != '':
-                    # a sequence was already parsed so add it to the list
-                    sequences.append(Sequence(id_ , comment, sequence))
-                    sequence = ''
-                header = line.split()
-                id_ = header[0]
-                comment = ' '.join(header[1:])
-            else:
-                sequence += line.strip()
-        #append the last sequence of the file to the list    
-        sequences.append(Sequence(id_ , comment, sequence))
-    return sequences
\ No newline at end of file
+    id_ = ''
+    comment = ''
+    sequence = ''
+    for line in fasta_infile:
+        if line.startswith('>'):
+            # a new sequence begin
+            if id_ != '':
+                # a sequence was already parsed so add it to the list
+                sequences.append(Sequence(id_ , comment, sequence))
+                sequence = ''
+            header = line.split()
+            id_ = header[0]
+            comment = ' '.join(header[1:])
+        else:
+            sequence += line.strip()
+    return Sequence(id_ , comment, sequence)
+
+# if we open the file in the fasta reader we are forced
+# to read all the sequences and charge them in memory which can take huge space
+# it's better to read sequences one by one and treat it as one is ready.
+# see fasta_filter.py
\ No newline at end of file

source/_static/code/similarity.py

-from matrix import *
+import matrix
 
 lines = iter( ['  A G C U\n',
                'A 1.0 0.5 0.0 0.0\n',
@@ -11,14 +11,14 @@ def parse_similarity_file():
     """
     parse file containing RNA similarity matrix and return a matrix
     """
-    sim_matrix = matrix_maker(4, 4)
+    sim_matrix = matrix.create(4, 4)
     #skip first line
     lines.next()
     for row_no, line in enumerate(lines):
         line = line.strip()
         fields = line.split()
         values = [float(val) for val in fields[1:]]
-        matrix_replace_row(sim_matrix, row_no, values)
+        matrix.replace_row(sim_matrix, row_no, values)
     return sim_matrix
 
 def get_similarity(b1, b2, sim_matrix):
@@ -39,7 +39,7 @@ def get_similarity(b1, b2, sim_matrix):
         raise KeyError("unknown base b1: " + str(b1))
     if not b2 in bases:
         raise KeyError("unknown base b2: " + str(b2))
-    return matrix_get_cell(sim_matrix, bases[b1], bases[b2])
+    return matrix.get_cell(sim_matrix, bases[b1], bases[b2])
                            
 def compute_similarity(seq1, seq2, sim_matrix):
     """
@@ -63,7 +63,7 @@ if __name__ == '__main__':
     seq1 = 'AGCAUCUA'
     seq2 = 'ACCGUUCU'
     sim_matrix = parse_similarity_file()
-    print matrix_to_str(sim_matrix)
+    print matrix.to_str(sim_matrix)
     similarity = compute_similarity(seq1, seq2, sim_matrix)
     print similarity
             
\ No newline at end of file