1.1 --- a/test/usecase3.py	Fri Dec 17 16:36:00 2010 +0300
     1.2 +++ b/test/usecase3.py	Wed Jan 12 19:36:09 2011 +0300
     1.3 @@ -1,7 +1,67 @@
     1.4  from allpy import protein
     1.5 -alignment = protein.Alignment.from_fasta(open("aln.fasta"))
     1.6 +import sys
     1.7 +import optparse
     1.8 +
     1.9 +if len(sys.argv)==1:
    1.10 +    print("usercase3  shisfts left all letters in specified vertical block of input alignment")  
    1.11 +    print("\n Use python usercase3.py -h for help")
    1.12 +    exit()
    1.13 +
    1.14 +parser = optparse.OptionParser()
    1.15 +
    1.16 +parser.add_option("-i", "--in-file", help="Input alignment in fasta format", dest="in_file")
    1.17 +parser.add_option("-o", "--out-file", help="Output refined alignment in fasta format", dest="out_file", default='result.fasta')
    1.18 +parser.add_option("-f", "--_from", help="First position of refining block", dest="_from")
    1.19 +parser.add_option("-t", "--to", help="Last position of refining block", dest="to")
    1.20 +
    1.21 +options, args = parser.parse_args()
    1.22 +in_file = options.in_file
    1.23 +out_file = options.out_file
    1.24 +_from = options._from
    1.25 +to = options.to
    1.26 +
    1.27 +
    1.28 +if in_file==None or _from==None or to==None:
    1.29 +    print("Missed command line parameters.")
    1.30 +    print("Use python usercase3.py -h for help")
    1.31 +    exit()
    1.32 +
    1.33 +try:
    1.34 +    f = open(in_file)
    1.35 +except:
    1.36 +    print("File %s was not found" % in_file)
    1.37 +    exit()
    1.38 +
    1.39 +try:
    1.40 +    ifrom = int(_from)
    1.41 +    ito   = int(to)
    1.42 +except:
    1.43 +    print("Values -f %s and -t %s must be interer!" % (_from,to))
    1.44 +    exit()
    1.45 +
    1.46 +alignment = protein.Alignment.from_fasta(open(in_file))
    1.47 +
    1.48 +alignment.length = len(alignment.columns)
    1.49 +
    1.50 +if ito >= alignment.length:
    1.51 +    print("to must be smaller than alignment length!")
    1.52 +    exit()
    1.53 +
    1.54 +if ifrom >= ito :
    1.55 +    print("from must be greater than to!")
    1.56 +    exit()
    1.57 +
    1.58 +   
    1.59 +conservative = []
    1.60 +if ifrom > 1:
    1.61 +    conservative.append((0,int(_from)))
    1.62 +if ito < alignment.length:
    1.63 +    conservative.append((ito,alignment.length-1))
    1.64 +
    1.65 +print conservative
    1.66 +
    1.67  #conservative = [(10,20), (40,50)]
    1.68 -conservative = [(0,6),(18,37)]
    1.69 +#conservative = [(0,6),(18,37)]
    1.70  
    1.71  def ranges_to_markup(ranges):
    1.72      """Convert list of ranges to line of markup.
    1.73 @@ -31,6 +91,6 @@
    1.74      blocks = markup_to_blocks(markup)
    1.75      for block in blocks["-"]:
    1.76          block.flush_left()
    1.77 -    alignment.to_fasta(open("output.fasta", "w"))
    1.78 +    alignment.to_fasta(open(out_file, "w"))
    1.79  
    1.80  main()