fix different versions of fasta reader

source/_static/code/fasta_iterator.py

@@ -15,8 +15,9 @@ def fasta_iter(fasta_file):
    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] == ">"))
+      group = (x[1] for x in groupby(fasta_file , lambda line: line.startswith(">")))
       for header in group:
+         print header
          # drop the ">"
          header = header.next()[1:].strip()
          header = header.split()
@@ -35,4 +36,20 @@ def fasta_iter(fasta_file):
 # 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
+# it's better to put the fasta file opening out the fasta reader see fasta filter 
+
+if __name__ == '__main__':
+    import sys
+    import os.path
+    
+    if len(sys.argv) != 2:
+        sys.exit("usage multiple_fasta fasta_path")
+    fasta_path = sys.argv[1]
+    if not os.path.exists(fasta_path):
+        sys.exit("No such file: {}".format(fasta_path))
+        
+    with open(fasta_path, 'r') as fasta_input:    
+        for sequence in fasta_iter(fasta_input):
+            print "----------------"
+            print sequence
+            
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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_file):
+def fasta_reader(fasta_path):
     """
     :param fasta_path: the path to the file to parse
     :type fasta_path: string
@@ -10,24 +10,28 @@ def fasta_reader(fasta_file):
     :rtype: list of Sequence 
     """
     sequences = []
-    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
+    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()
                 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)
+    return sequences
 
-# 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
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+
+# The problem with this implementation is that we have to load all 
+# sequences in memory before to start to work with
+# it is better to return sequence one by one
+# and treat them as they are loaded.
+ 
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source/_static/code/multiple_fasta_reader2.py

+from collections import namedtuple 
+
+Sequence =  namedtuple("Sequence", "id comment sequence")
+
+def fasta_reader(fasta_file):
+    """
+    :param fasta_file: to the file in fasta format to parse
+    :type fasta_file: file object
+    :return: a sequence until they are sequences in the file
+    :rtype: a Sequence or None
+    """
+    id_ = ''
+    comment = ''
+    sequence = ''
+    # As we use seek or tell, we cannot use for line in file object
+    # Because in the last case tell is always at the end of file
+    # even if when we read the first line
+    # So I use readline
+    line = fasta_file.readline()
+    while line:
+        if line.startswith('>'):
+            # a new sequence begin
+            if id_ == '':
+                header = line.split()
+                id_ = header[0]
+                comment = ' '.join(header[1:])
+            else:
+                # I already parse a sequence
+                # So the begining of this sequence indicate the end of the
+                # previous sequence
+                # put the cursor one line in back for the next fasta_reader call
+                fasta_file.seek(-len(line),1)
+                # I return the previous sequence
+                return Sequence(id_ , comment, sequence)
+        else:
+            sequence += line.strip()
+        line = fasta_file.readline()
+    if id_ == '' and sequence == '':
+        return 
+    else:
+        return Sequence(id_ , comment, sequence)
+
+
+# to return sequence by sequence we had to open the file outside the fasta_reader
+# at each fasta_reader call the function return one sequence
+# unitl the end of file
+
+if __name__ == '__main__':
+    import sys
+    import os.path
+    
+    if len(sys.argv) != 2:
+        sys.exit("usage multiple_fasta fasta_path")
+    fasta_path = sys.argv[1]
+    if not os.path.exists(fasta_path):
+        sys.exit("No such file: {}".format(fasta_path))
+        
+    with open(fasta_path, 'r') as fasta_input:    
+        sequence = True
+        while sequence is not None:
+            sequence =  fasta_reader(fasta_input)
+            print "----------------"
+            print sequence
+            
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