--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/seq_io/phylip_io.py	Thu Oct 27 12:09:09 2011 -0400
@@ -0,0 +1,167 @@
+#!/usr/bin/env python
+
+#  Copyright (c) 2005 David D. Ding <dding@berkeley.edu>
+#
+#  This software is distributed under the MIT Open Source License.
+#  <http://www.opensource.org/licenses/mit-license.html>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a 
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+#  THE SOFTWARE.
+#
+
+"""Read Sequences in interleaved Phylip format (not sequential) and returns a
+list of sequences. Phylips is a very common phylogeny generating sequence type
+that has the following traits
+1) First line contains number of species and number of characters in a species'
+sequence. Options can may follow, and they can be spaced or unspaced. Options are
+simply letters such as A and W after the number of characters.
+2) Options doesn't have to contain U in order for a usertree to appear.
+3) If there are options then options appear first, then the sequences. For the
+first iteration of sequences the first ten spaces are reserved for names of
+options and species, the rest is for sequences.
+4) For the second and following iterations the names are removed, only
+sequence appears
+4) At end of file an usertree may appear. First there is a number that indicts
+the number of lines the usertree will take, and then the usertrees follow.
+
+Examples:
+  6   50   W
+W         0101001111 0101110101 01011	
+dmras1    GTCGTCGTTG GACCTGGAGG CGTGG	
+hschras   GTGGTGGTGG GCGCCGGCCG TGTGG
+ddrasa    GTTATTGTTG GTGGTGGTGG TGTCG
+spras     GTAGTTGTAG GAGATGGTGG TGTTG
+scras1    GTAGTTGTCG GTGGAGGTGG CGTTG
+scras2    GTCGTCGTTG GTGGTGGTGG TGTTG
+
+0101001111 0101110101 01011	
+GTCGTCGTTG GACCTGGAGG CGTGG	
+GTGGTGGTGG GCGCCGGCCG TGTGG
+GTTATTGTTG GTGGTGGTGG TGTCG
+GTAGTTGTAG GAGATGGTGG TGTTG
+GTAGTTGTCG GTGGAGGTGG CGTTG
+GTCGTCGTTG GTGGTGGTGG TGTTG
+
+1					
+((dmras1,ddrasa),((hschras,spras),(scras1,scras2)));
+
+
+"""
+
+from corebio.seq import *
+
+names = ( 'phylip',)
+extensions = ('phy',)
+
+def iterseq(fin, alphabet=None):
+    """Iterate over the sequences in the file."""
+    # Default implementation
+    return iter(read(fin, alphabet) )
+
+
+#Read takes in a phylip file name, read it, processes it, and returns a SeqList
+def read(fin, alphabet=None):
+    
+   
+    sequence=[] #where sequences are stored
+    idents=[]
+    num_seq=0
+    num_total_seq=0 #length of sequence of 1 species
+    tracker=0 #track what sequence the line is on
+    usertree_tracker=0 #track usertree lines
+    options='' #options
+    num_options=0 #number/lens of options - U
+
+    line=fin.readline()
+    while line:
+        s_line=line.split() #for ease of use, not used in all scenarios, but easier on the eye
+
+        if s_line == []: #see nothing do nothing
+            pass
+
+        elif (s_line[0].isdigit() and len(s_line) == 1 and len(sequence)==num_seq and len(sequence[0])==num_total_seq):    #identifies usertree
+            usertree_tracker = int(s_line[0])
+            pass
+        
+        elif num_options > 0:
+            if len(sequence) < num_seq:
+                if s_line[0][0] in options:
+                    num_options -= 1
+                    pass
+                else:
+                    raise ValueError('Not an option, but it should be one')
+            else:
+                num_options -= 1
+                pass
+    
+        elif usertree_tracker > 0:                    #baskically skip usertree
+            if len(sequence[num_seq-1]) == num_total_seq:
+                usertree_tracker -=1
+                pass
+            else:
+                raise ValueError('User Tree in Wrong Place')
+    
+        #####problems parse error unexpected
+        elif s_line[0].isdigit():
+            if len(s_line) >= 2 and len(sequence) == 0: #identifies first line of file
+                num_seq = int(s_line[0])               #get number of sequences
+                num_total_seq = int(s_line[1])         #get length of sequences
+                if len(s_line) > 2:                   #takes care of the options
+                    options= (''.join(s_line[2:]))
+                    num_options=len(options) - options.count('U')
+            else:
+                raise ValueError('parse error') 
+
+
+    #when options end, this take care of the sequence
+        elif num_options == 0:
+            if (num_seq==0):
+                raise ValueError("Empty File, or possibly wrong file")
+            elif tracker < num_seq:
+                if num_seq > len(sequence):
+                    sequence.append(''.join(line[10:].split())) #removes species name
+                    idents.append(line[0:10].strip())
+                    tracker +=1
+                    
+                else:
+                    sequence[tracker] += (''.join(s_line))      
+                    tracker +=1
+                    
+                if tracker == num_seq:
+                    tracker = 0
+                    num_options = len(options)-options.count('U')
+        
+        line=fin.readline()
+   
+    if len(sequence) != len(idents) or len(sequence)!=num_seq:
+        raise ValueError("Number of different sequences wrong") 
+    
+    seqs = []
+    for i in range (0, len(idents)):
+        if len(sequence[i])==num_total_seq:
+            seqs.append(Seq(sequence[i], alphabet, idents[i]))
+        else:
+            raise ValueError("extra sequence in list")
+    
+    return SeqList(seqs)
+
+
+        
+    
+    
+