1.1 --- a/allpy/util.py	Sun Jun 10 16:08:47 2012 +0400
     1.2 +++ b/allpy/util.py	Thu Jun 14 19:05:28 2012 +0400
     1.3 @@ -3,6 +3,8 @@
     1.4  import sys
     1.5  import warnings
     1.6  import os
     1.7 +import inspect
     1.8 +import functools
     1.9  from tempfile import mkstemp
    1.10  from StringIO import StringIO
    1.11  
    1.12 @@ -43,10 +45,43 @@
    1.13      """Clone of str that user may add attributes to."""
    1.14      pass
    1.15  
    1.16 -def deprecated(message):
    1.17 +def deprecated(message=None, what=None, in_favor=None, removed_in=None):
    1.18      """Warn about function being deprecated."""
    1.19 +    if not message:
    1.20 +        if what is None:
    1.21 +            frame = inspect.currentframe().f_back
    1.22 +            caller = []
    1.23 +            if inspect.getmodule(frame):
    1.24 +                caller.append(inspect.getmodule(frame).__name__)
    1.25 +            if 'self' in frame.f_locals:
    1.26 +                caller.append(frame.f_locals['self'].__class__.__name__)
    1.27 +            elif 'cls' in frame.f_locals:
    1.28 +                caller.append(frame.f_locals['cls'].__name__)
    1.29 +            caller.append(frame.f_code.co_name)
    1.30 +            what = ".".join(caller) + "(...)"
    1.31 +        message = "{0} is deprecated".format(what)
    1.32 +    if in_favor:
    1.33 +        message = "{0} in favor of {1}".format(message, in_favor)
    1.34 +    if removed_in:
    1.35 +        message = "{0}; will be removed in allpy version {1}".format(message, removed_in)
    1.36      warnings.warn(message, DeprecationWarning, stacklevel=2)
    1.37  
    1.38 +def Deprecated(message=None, in_favor=None, removed_in=None):
    1.39 +    def decorator(function):
    1.40 +        @functools.wraps(function)
    1.41 +        def decorated(*args, **kws):
    1.42 +            text = "{0} is deprecated".format(function)
    1.43 +            if in_favor:
    1.44 +                text = "{0} in favor of {1}".format(text, in_favor)
    1.45 +            if removed_in:
    1.46 +                text = "{0}\n\nWill be removed in allpy version {1}.".format(text, removed_in)
    1.47 +            if message:
    1.48 +                text = "{0}\n\n{1}".format(text, message)
    1.49 +            warnings.warn(text, DeprecationWarning, stacklevel=2)
    1.50 +            return function(*args, **kws)
    1.51 +        return decorated
    1.52 +    return decorator
    1.53 +
    1.54  class Silence(object):
    1.55      """Context manager for use with `with`.
    1.56  

     2.1 --- a/utils/markup_to_file.py	Sun Jun 10 16:08:47 2012 +0400
     2.2 +++ b/utils/markup_to_file.py	Thu Jun 14 19:05:28 2012 +0400
     2.3 @@ -3,51 +3,53 @@
     2.4  import sys
     2.5  import optparse
     2.6  import copy
     2.7 -from allpy import protein, markups
     2.8 +from allpy import protein, markups, util
     2.9  
    2.10 -parser = optparse.OptionParser()
    2.11 -parser.add_option("--input-format", default="markup",
    2.12 -    help="Format of the input file")
    2.13 -parser.add_option("-f", "--output-format", default="fasta",
    2.14 -    help="Format of the output file")
    2.15 -parser.add_option("-i", "--input-file",
    2.16 -    help="Input file (defaults to stdin)")
    2.17 -parser.add_option("-o", "--output-file",
    2.18 -    help="Output file (defaults to stdout)")
    2.19 -parser.add_option("-m", "--markup",
    2.20 -    help="Markup to save as a sequence")
    2.21 -options, args = parser.parse_args()
    2.22 +def add_markup(alignment, sequence, markup):
    2.23 +    new = copy.deepcopy(sequence)
    2.24 +    new.name = "markup_{0}|{1}".format(markup.name, sequence.name)
    2.25 +    for new_monomer, monomer in zip(new, sequence):
    2.26 +        new_monomer.code1 = str(markup.get(monomer, '-'))
    2.27 +        assert len(new_monomer.code1) == 1
    2.28 +        assert new_monomer.code1 not in (markup.separator, markup.quotes)
    2.29  
    2.30 -if not options.markup:
    2.31 -    parser.error("You must specify -m argument")
    2.32 +    sequence.add_markup('index')
    2.33 +    for column in alignment.columns:
    2.34 +        if sequence in column:
    2.35 +            column[new] = new[column[sequence].index]
    2.36 +    sequence.remove_markup('index')
    2.37  
    2.38 -infile, outfile = sys.stdin, sys.stdout
    2.39 -if options.input_file is not None:
    2.40 -    infile = open(options.input_file)
    2.41 -if options.output_file is not None:
    2.42 -    outfile = open(options.output_file, "w")
    2.43 +    alignment.sequences.insert(alignment.sequences.index(sequence)+1, new)
    2.44  
    2.45 -aln = protein.Alignment().append_file(infile, format=options.input_format)
    2.46 +def main():
    2.47 +    aln = protein.Alignment().append_file(
    2.48 +        util.open(options.input_file), format=options.input_format)
    2.49  
    2.50 -mseqs = copy.deepcopy(aln.sequences)
    2.51 -for mseq in mseqs:
    2.52 -    mseq.name = "markup_%s|%s" % (options.markup, mseq.name)
    2.53 -    for monomer in mseq:
    2.54 -        monomer.code1 = str(getattr(monomer, options.markup, '-'))
    2.55 -seqs = aln.sequences
    2.56 +    for seq in list(aln.sequences):
    2.57 +        for markup in seq.markups.values():
    2.58 +            if not options.markups or markup.name in options.markups:
    2.59 +                add_markup(aln, seq, markup)
    2.60  
    2.61 -for seq, mseq in zip(seqs, mseqs):
    2.62 -    seq.add_markup('index')
    2.63 -    for column in aln.columns:
    2.64 -        if seq in column:
    2.65 -            column[mseq] = mseq[column[seq].index]
    2.66 -    seq.remove_markup('index')
    2.67 +    aln.to_file(util.open(options.output_file, "w"), format=options.output_format)
    2.68  
    2.69 -aln.sequences = []
    2.70 -for seq, mseq in zip(seqs, mseqs):
    2.71 -    aln.sequences.append(seq)
    2.72 -    aln.sequences.append(mseq)
    2.73 +if __name__ == "__main__":
    2.74  
    2.75 -aln.to_file(outfile)
    2.76 +    parser = optparse.OptionParser()
    2.77 +    parser.add_option("--input-format", default="markup",
    2.78 +        help="Format of the input file")
    2.79 +    parser.add_option("-f", "--output-format", default="fasta",
    2.80 +        help="Format of the output file")
    2.81 +    parser.add_option("-i", "--input-file", default="-",
    2.82 +        help="Input file (defaults to stdin)")
    2.83 +    parser.add_option("-o", "--output-file", default="-",
    2.84 +        help="Output file (defaults to stdout)")
    2.85 +    parser.add_option("-m", "--markups", "--markup",
    2.86 +        help="Optional comma (,) separated list of sequence markups to convert")
    2.87 +    options, args = parser.parse_args()
    2.88 +
    2.89 +    if options.markups:
    2.90 +        options.markups = options.markups.split(",")
    2.91 +
    2.92 +    main()
    2.93  
    2.94  # vim: set et ts=4 sts=4 sw=4: