Added MCA-Parser

Author: Christian Schudoma

mca2bracket2.py

@@ -0,0 +1,164 @@
+#!/usr/bin/python
+
+import re 
+import os
+import sys
+import math
+
+import minilib as biolib
+import mdg_dt as MDGDT
+
+ix_pattern = re.compile('([A-Za-z]|\'[0-9]\')-?[0-9]+(\.[A-Z])?')
+
+###
+def read_data(fn):
+    sequence = []
+    structure = []
+
+    unidentified = set([])
+
+    edge_re = re.compile('W[a-z]/W[a-z]')
+    pair_re = re.compile('([AG]-U)|(C-G)|(G-[CU])|(U-[AG])')
+
+    fi = open(fn)
+    mode = 'ignore'
+    while True:
+        line = fi.readline()
+        if not line: break
+
+        line = line.strip()
+        if line.endswith('----'):
+            if line.startswith('Residue conformations'):                
+                mode = 'sequence'
+                if len(sequence) > 0:
+                    """ ignore multimodels """
+                    break
+            elif line.startswith('Base-pairs'):
+                mode = 'structure'
+            else:
+                mode = 'ignore'
+                pass
+            continue
+            pass
+
+        
+        if mode == 'ignore': continue
+        elif mode == 'sequence':            
+            line = line.split()
+
+
+            base = line[2].strip()
+            if base in biolib.BASEDICT:
+                base = biolib.BASEDICT[base]
+                sequence.append((line[0], base))
+            else:
+                unidentified.add(base)
+                
+        elif mode == 'structure':
+            is_ss_pair = 'antiparallel' in line and \
+                         'cis' in line and \
+                         edge_re.search(line) and \
+                         pair_re.search(line)
+            if is_ss_pair:
+                line = line.split()
+                line = line[0]
+
+
+                try:
+                    base1 = ix_pattern.search(line)
+                    line = line[base1.end():]
+                    base2 = ix_pattern.search(line)
+                    structure.append([base1.group(), base2.group()])
+                except:
+                    print line, 'fail'
+                    pass
+
+                """
+                if len(tmp) == len(line) - 1:
+                    structure.append(line[0].split('-'))
+                elif len(tmp) == len(line) - 2:
+                    pass
+                else:
+                    p = line.find('-')
+                """
+            
+        else:
+            continue
+        
+        pass
+
+    if len(unidentified) > 0:
+        sys.stderr.write('UNIDENTIFIED RESIDUES: %s\n' % \
+                         str(list(unidentified)))
+        pass
+
+    
+    return sequence, structure
+
+
+
+###
+def create_brackets(structure, sequence):    
+    brackets = ['.' for i in xrange(len(sequence))]
+
+    index = [x[0] for x in sequence]
+    
+    structure = [(index.index(b1), index.index(b2))
+                 for b1, b2 in structure]
+    ss_tree = MDGDT.MDG_Stem()
+    ss_tree.assemble(sorted(structure), outp=sys.stderr)
+    
+    knotless = sorted(ss_tree.preorder())
+    if ss_tree.has_tertiary_pairs() and ss_tree.has_tertiary_stem():
+        print ss_tree.te_contacts
+        return None
+    # print 'KLESS', knotless
+
+    def write_structure(structure, n):
+        brackets = ['.' for i in xrange(n)]
+        
+        for i, j in structure:
+            if brackets[i] != '.' or brackets[j] != '.':
+                sys.stderr.write('%s %s %i %i already occupied\n' % \
+                                 (b1, b2, i, j))
+                if brackets[i] == '(' or brackets[i] == '<':
+                    brackets[i] = '<'
+                elif brackets[i] == ')' or brackets[i] == '>':
+                    brackets[i] ='#'
+
+                if brackets[j] == '(' or brackets[j] == '<':
+                    brackets[j] = '@'
+                elif brackets[j] == ')' or brackets[j] == '>':
+                    brackets[j] ='>'
+
+            else:
+                brackets[i] = '('
+                brackets[j] = ')'
+                
+            pass
+
+        # sys.stderr.write('***\n')
+        return ''.join(brackets)
+    
+    return (write_structure(structure, len(sequence)), 
+            write_structure(knotless, len(sequence)))
+
+###
+def main(argv):
+#
+    if len(argv) < 1:
+        sys.stderr.write('Usage: python mca2bracket2.py <MC-Annotate-file>\n')
+        sys.exit(1)
+    elif not os.path.exists(argv[0]):
+        sys.stderr.write('Error: file %s does not exist. Aborting.\n' % argv[0])
+        sys.exit(1)
+    
+    seq, struc = read_data(argv[0])
+    brackets = create_brackets(struc, seq)
+
+    print 'Structure with knots:\n%s\nKnotless:\n%s\n' % brackets
+
+
+    return None
+
+if __name__ == '__main__': main(sys.argv[1:])