diff corebio/seq_io/nbrf_io.py @ 0:c55bdc2fb9fa

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/seq_io/nbrf_io.py	Thu Oct 27 12:09:09 2011 -0400
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+
+#  Copyright (c) 2006, The Regents of the University of California, through 
+#  Lawrence Berkeley National Laboratory (subject to receipt of any required
+#  approvals from the U.S. Dept. of Energy).  All rights reserved.
+
+#  This software is distributed under the new BSD Open Source License.
+#  <http://www.opensource.org/licenses/bsd-license.html>
+#
+#  Redistribution and use in source and binary forms, with or without 
+#  modification, are permitted provided that the following conditions are met: 
+#
+#  (1) Redistributions of source code must retain the above copyright notice, 
+#  this list of conditions and the following disclaimer. 
+#
+#  (2) Redistributions in binary form must reproduce the above copyright 
+#  notice, this list of conditions and the following disclaimer in the 
+#  documentation and or other materials provided with the distribution. 
+#
+#  (3) Neither the name of the University of California, Lawrence Berkeley 
+#  National Laboratory, U.S. Dept. of Energy nor the names of its contributors 
+#  may be used to endorse or promote products derived from this software 
+#  without specific prior written permission. 
+#
+#  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+#  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+#  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+#  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
+#  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+#  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+#  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+#  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+#  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+#  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+#  POSSIBILITY OF SUCH DAMAGE. 
+
+"""Sequence IO for NBRF/PIR format.
+
+The format is similar to fasta. The header line consistins of '>', a two-
+letter sequence type (P1, F1, DL, DC, RL, RC, or XX), a semicolon, and a
+sequence ID. The next line is a textual description of the sequence, 
+followed by one or more lines containing the sequence data. The end of 
+the sequence is marked by a "*" (asterisk) character.
+
+type_code -- A map between NBRF two letter type codes and Alphabets.
+
+
+see:  http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html
+
+--- Example NBRF File ---
+
+>P1;CRAB_ANAPL
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR 
+  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH 
+  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ 
+  SDVPERSIPI TREEKPAIAG AQRK*
+
+>P1;CRAB_BOVIN
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR 
+  PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV 
+  HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK 
+  QASGPERTIP ITREEKPAVT AAPKK*
+
+"""
+
+from corebio.utils import *
+from corebio.seq import *
+from corebio.seq_io import *
+
+names = ("nbrf", "pir",)
+extensions = ('nbrf', 'pir', 'ali')
+
+
+
+
+type_code = {
+    'P1' : protein_alphabet,   # Protein (complete)
+    'F1' : protein_alphabet,   # Protein (fragment)
+    'DL' : dna_alphabet,       # DNA (linear)
+    'DC' : dna_alphabet,       # DNA (circular)
+    'RC' : rna_alphabet,       # RNA (linear)
+    'RL' : rna_alphabet,       # RNA (circular)
+    'N3' : rna_alphabet,       # tRNA
+    'N1' : rna_alphabet,       # other functional RNA
+    'XX' : generic_alphabet
+    }
+
+def read(fin, alphabet=None):  
+    """Read and parse a NBRF seqquence file. 
+
+    Args:
+        fin -- A stream or file to read
+        alphabet -- The expected alphabet of the data. If not supplied, then
+                an appropriate alphabet will be inferred from the data.
+    Returns: 
+        SeqList -- A list of sequences
+    Raises: 
+        ValueError -- If the file is unparsable        
+    """
+    seqs = [ s for s in iterseq(fin, alphabet)]
+    return SeqList(seqs)
+
+
+        
+def iterseq(fin, alphabet=None):
+    """ Generate sequences from an NBRF file.
+    
+    arguments:
+        fin -- A stream or file to read
+        alphabet --    
+    yeilds :
+        Seq
+    raises :
+        ValueError -- On a parse error.
+    """
+        
+    body, header,sequence = range(3) # Internal states
+    
+    state = body
+    seq_id = None
+    seq_desc = None
+    seq_alpha = None
+    seqs = []
+
+    for lineno, line in enumerate(fin) :
+        if state == body :
+            if line == "" or line.isspace() :
+                continue
+            if line[0] == '>':
+                seq_type, seq_id = line[1:].split(';')
+                if alphabet :
+                    seq_alpha = alphabet
+                else :
+                    seq_alpha = type_code[seq_type]
+                state = header
+                continue
+            raise ValueError("Parse error on line: %d" % lineno)
+
+        elif state == header :
+            seq_desc = line.strip()
+            state = sequence
+            continue
+                          
+        elif state == sequence :
+            data = "".join(line.split()) # Strip out white space
+            if data[-1] =='*' :
+                # End of sequence data
+                seqs.append(data[:-1])   
+
+                seq = Seq( "".join(seqs), name = seq_id.strip(), 
+                    description = seq_desc, alphabet = seq_alpha)
+
+                yield seq
+                state= body
+                seq_id = None
+                seq_desc = None
+                seqs = []
+                continue
+            else :
+                seqs.append(data)
+                continue
+        else :       
+            # If we ever get here something has gone terrible wrong
+            assert(False)
+
+    # end for
+
+