1.1 --- a/sbbs_2009/blocks_finder.py	Mon Jul 11 22:15:50 2011 +0400
     1.2 +++ b/sbbs_2009/blocks_finder.py	Fri Jul 29 19:08:21 2011 +0400
     1.3 @@ -78,19 +78,22 @@
     1.4      return blocks_for_print
     1.5  
     1.6  
     1.7 +sys.path.append(os.path.dirname(__file__)+"/../utils")
     1.8 +from timesup import *
     1.9 +@timesup
    1.10  def blocks2homology_file(blocks, homology_file):
    1.11      sys.path.append(os.path.dirname(__file__)+"/../allpy/")
    1.12      from homology import MonomerHomology
    1.13      class_counter = 0
    1.14      for b in blocks:
    1.15          if b[0].content[0].state == "aligned":
    1.16 -            for sa in b[0].content[0].sequence_indexes_a:
    1.17 -                sequence_name = b[0].content[0].alignment.sequences[b[0].content[0].alignment.sequence_indexes_s[sa]].name
    1.18 -                for pa in b[0].content[0].position_indexes_a:
    1.19 +            for pa in b[0].content[0].position_indexes_a:
    1.20 +                for sa in b[0].content[0].sequence_indexes_a:
    1.21 +                    sequence_name = b[0].content[0].alignment.sequences[b[0].content[0].alignment.sequence_indexes_s[sa]].name
    1.22                      if b[0].content[0].alignment.get_aa(sa,pa)!=None:
    1.23 -                        monomer_id = (sequence_name, pa+1)
    1.24 -                        MonomerHomology.write_monomer(homology_file, monomer_id, class_counter)
    1.25 -            class_counter+=1
    1.26 +                        monomer_id = (sequence_name, b[0].content[0].alignment.body[sa][pa]+1)
    1.27 +                        MonomerHomology.write_monomer(homology_file, monomer_id, class_counter, pa+1)
    1.28 +                class_counter+=1
    1.29          else:
    1.30              if b[0].content[0].state == "no_alignment":
    1.31                  #print each monomer as a separate class
    1.32 @@ -98,8 +101,8 @@
    1.33                      sequence_name = b[0].content[0].alignment.sequences[b[0].content[0].alignment.sequence_indexes_s[sa]].name
    1.34                      for pa in b[0].content[0].position_indexes_a:
    1.35                          if b[0].content[0].alignment.get_aa(sa, pa) != None:
    1.36 -                            monomer_id = (sequence_name, pa+1)
    1.37 -                            MonomerHomology.write_monomer(homology_file, monomer_id, class_counter)
    1.38 +                            monomer_id = (sequence_name, b[0].content[0].alignment.body[sa][pa]+1)
    1.39 +                            MonomerHomology.write_monomer(homology_file, monomer_id, class_counter, pa+1)
    1.40                              class_counter+=1
    1.41  
    1.42  

     2.1 --- a/sbbs_2009/modules/block.py	Mon Jul 11 22:15:50 2011 +0400
     2.2 +++ b/sbbs_2009/modules/block.py	Fri Jul 29 19:08:21 2011 +0400
     2.3 @@ -376,7 +376,7 @@
     2.4          elif mode == "semiexternal":
     2.5              mat = self.create_distance_matrix()
     2.6              #if mat.max() == 0: return False
     2.7 -            f=open(os.path.dirname(__file__)+"/../jobs/temptree.dist","w")
     2.8 +            f=open(""+os.path.dirname(__file__)+"/../jobs/temptree.dist","w")
     2.9              f.write(str(mat))
    2.10              f.close()
    2.11              os.system("fneighbor "+os.path.dirname(__file__)+"/../jobs/temptree.dist -outfile "+os.path.dirname(__file__)+"/../jobs/temptree.nj -outtreefile "+os.path.dirname(__file__)+"/../jobs/temptree.tre -treetype u 2>>"+os.path.dirname(__file__)+"/../jobs/temptree.log >>"+os.path.dirname(__file__)+"/../jobs/temptree.log")

     3.1 --- a/sequence_based_blocks_search/blocks_finder.py	Mon Jul 11 22:15:50 2011 +0400
     3.2 +++ b/sequence_based_blocks_search/blocks_finder.py	Fri Jul 29 19:08:21 2011 +0400
     3.3 @@ -105,12 +105,12 @@
     3.4          candidate_preblocks+=addition_to_candidate_preblocks
     3.5          #remove from candidates those preblocks that share the same set of sequences with others, but are shorter and have lower scores
     3.6          #print index_of_column, len(candidate_preblocks),
     3.7 -        print index_of_column, len(candidate_preblocks)        
     3.8 -        if len(candidate_preblocks)>1000:
     3.9 -            import cProfile
    3.10 -            cProfile.runctx('remove_contained_preblocks(candidate_preblocks)',globals(),locals())
    3.11 -        else:
    3.12 -            remove_contained_preblocks(candidate_preblocks)
    3.13 +        #print index_of_column, len(candidate_preblocks)
    3.14 +#        if len(candidate_preblocks)>1000:
    3.15 +#            import cProfile
    3.16 +#            cProfile.runctx('remove_contained_preblocks(candidate_preblocks)',globals(),locals())
    3.17 +#        else:
    3.18 +        remove_contained_preblocks(candidate_preblocks)
    3.19          #print len(candidate_preblocks)
    3.20          #remove_bad_candidates(candidate_preblocks, index_of_column, 0.5, 10)
    3.21          #for those preblocks ending with a conserved position and having the score above threshold, add new links
    3.22 @@ -377,7 +377,7 @@
    3.23      created by create_links function"""
    3.24      try:
    3.25          markup_file = open(markup_file_name,'w')
    3.26 -    except E:
    3.27 +    except Exception as E:
    3.28          print E
    3.29          sys.exit()
    3.30      #creating markups

     4.1 --- a/sequence_based_blocks_search/test_homology.py	Mon Jul 11 22:15:50 2011 +0400
     4.2 +++ b/sequence_based_blocks_search/test_homology.py	Fri Jul 29 19:08:21 2011 +0400
     4.3 @@ -17,5 +17,13 @@
     4.4      find_links(groups_content, alignment)
     4.5      create_file_with_monomer_homology(alignment, output_file_name)
     4.6  
     4.7 +def timeout(signum, frame):
     4.8 +    print sys.argv[1]+" time-out!!!"
     4.9 +    sys.exit(1)
    4.10 +
    4.11  if __name__ == "__main__":
    4.12 +    import signal
    4.13 +    signal.signal(signal.SIGALRM, timeout)
    4.14 +    signal.alarm(90)
    4.15 +    print sys.argv[1]
    4.16      alignment_file2homology_file(sys.argv[1], sys.argv[2])