Source Code for Module weblogolib._cli

  1  #!/usr/bin/env python 
  2   
  3  # -------------------------------- WebLogo -------------------------------- 
  4   
  5  #  Copyright (c) 2003-2004 The Regents of the University of California. 
  6  #  Copyright (c) 2005 Gavin E. Crooks 
  7  #  Copyright (c) 2006-2011, The Regents of the University of California, through  
  8  #  Lawrence Berkeley National Laboratory (subject to receipt of any required 
  9  #  approvals from the U.S. Dept. of Energy).  All rights reserved. 
 10   
 11  #  This software is distributed under the new BSD Open Source License. 
 12  #  <http://www.opensource.org/licenses/bsd-license.html> 
 13  # 
 14  #  Redistribution and use in source and binary forms, with or without  
 15  #  modification, are permitted provided that the following conditions are met:  
 16  # 
 17  #  (1) Redistributions of source code must retain the above copyright notice,  
 18  #  this list of conditions and the following disclaimer.  
 19  # 
 20  #  (2) Redistributions in binary form must reproduce the above copyright  
 21  #  notice, this list of conditions and the following disclaimer in the  
 22  #  documentation and or other materials provided with the distribution.  
 23  # 
 24  #  (3) Neither the name of the University of California, Lawrence Berkeley  
 25  #  National Laboratory, U.S. Dept. of Energy nor the names of its contributors  
 26  #  may be used to endorse or promote products derived from this software  
 27  #  without specific prior written permission.  
 28  # 
 29  #  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"  
 30  #  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE  
 31  #  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  
 32  #  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE  
 33  #  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR  
 34  #  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF  
 35  #  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS  
 36  #  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN  
 37  #  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)  
 38  #  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE  
 39  #  POSSIBILITY OF SUCH DAMAGE.  
 40   
 41  # WebLogo Command Line Interface 
 42   
 43  import sys 
 44   
 45  from color import * 
 46  from colorscheme import ColorScheme, ColorGroup 
 47  from corebio.utils import * 
 48  from string import Template 
 49   
 50  from corebio import seq_io 
 51   
 52   
 53   
 54  import os  
 55  from corebio.utils.deoptparse import DeOptionParser 
 56  from optparse import OptionGroup 
 57   
 58  from weblogolib import LogoOptions, LogoData, LogoFormat 
 59  from weblogolib import parse_prior, description, release_description, formatters, default_formatter 
 60  from weblogolib import std_alphabets, std_units, std_sizes, std_color_schemes 
 61  from weblogolib import read_seq_data 
 62   
 63  # ====================== Main: Parse Command line ============================= 
 64 -def main():  
 65      """WebLogo command line interface """ 
 66       
 67      # ------ Parse Command line ------ 
 68      parser = _build_option_parser()                 
 69      (opts, args) = parser.parse_args(sys.argv[1:]) 
 70      if args : parser.error("Unparsable arguments: %s " % args) 
 71       
 72      if opts.serve: 
 73          httpd_serve_forever(opts.port) # Never returns? 
 74          sys.exit(0)  
 75     
 76               
 77      # ------ Create Logo ------ 
 78      try: 
 79          data = _build_logodata(opts) 
 80          format = _build_logoformat(data, opts) 
 81           
 82          formatter = opts.formatter 
 83          formatter(data, format, opts.fout) 
 84   
 85      except ValueError, err : 
 86          print >>sys.stderr, 'Error:', err 
 87          sys.exit(2) 
 88      except KeyboardInterrupt, err: 
 89          sys.exit(0) 
 90  # End main()             
 91           
 92   
 93 -def httpd_serve_forever(port=8080) : 
 94      """ Start a webserver on a local port.""" 
 95      import BaseHTTPServer 
 96      import CGIHTTPServer  
 97       
 98      class __HTTPRequestHandler(CGIHTTPServer.CGIHTTPRequestHandler): 
 99          # Modify CGIHTTPRequestHandler so that it will run the cgi script directly, instead of exec'ing 
100          # This bypasses the need for the cgi script to have execute permissions set, 
101          # since distutils install does not preserve permissions. 
102          def is_cgi(self) : 
103              self.have_fork = False          # Prevent CGIHTTPRequestHandler from using fork 
104              if self.path == "/create.cgi":  
105                  self.cgi_info = '', 'create.cgi' 
106                  return True 
107              return False 
108          def is_python(self,path):            # Let CGIHTTPRequestHandler know that cgi script is python 
109              return True 
110               
111       
112      # Add current directory to PYTHONPATH. This is 
113      # so that we can run the standalone server 
114      # without having to run the install script.       
115      pythonpath = os.getenv("PYTHONPATH", '') 
116      pythonpath += ":" + os.path.abspath(sys.path[0]).split()[0] 
117      os.environ["PYTHONPATH"] = pythonpath 
118   
119      htdocs = resource_filename(__name__, 'htdocs', __file__) 
120      os.chdir(htdocs)  
121   
122      HandlerClass = __HTTPRequestHandler 
123      ServerClass = BaseHTTPServer.HTTPServer 
124      httpd = ServerClass(('', port), HandlerClass) 
125      print "WebLogo server running at http://localhost:%d/" % port 
126       
127      try : 
128          httpd.serve_forever() 
129      except KeyboardInterrupt: 
130          sys.exit(0) 
131  # end httpd_serve_forever()   
132       
133       
134   
135 -def _build_logodata(options) : 
136       
137      if options.input_parser != "transfac": 
138          seqs = read_seq_data(options.fin,  
139              options.input_parser.read, 
140              alphabet=options.alphabet, 
141              ignore_lower_case = options.ignore_lower_case)    
142               
143          if options.reverse:  
144              seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet) 
145           
146          if options.complement : 
147              seqs= SeqList( [Seq(s,seqs.alphabet).complement() for s in seqs], seqs.alphabet) 
148   
149             
150           
151          prior = parse_prior( options.composition,seqs.alphabet, options.weight) 
152          data = LogoData.from_seqs(seqs, prior) 
153   
154      else : 
155          from corebio.matrix import Motif 
156       
157          if options.ignore_lower_case: 
158              raise ValueError("error: option --ignore-lower-case incompatible with matrix input") 
159           
160          #FIXME : implement 
161          if options.reverse: 
162              raise ValueError("error: option --reverse incompatible with matrix input") 
163           
164          #FIXME : implement 
165          if options.complement: 
166              raise ValueError("error: option --complement incompatible with matrix input") 
167                         
168          motif = Motif.read_transfac(options.fin, alphabet=options.alphabet) 
169          prior = parse_prior( options.composition,motif.alphabet, options.weight) 
170          data = LogoData.from_counts(motif.alphabet, motif, prior) 
171           
172      return data 
173        
174                
175 -def _build_logoformat( logodata, opts) : 
176      """ Extract and process relevant option values and return a  
177      LogoFormat object."""  
178   
179      args = {}   
180      direct_from_opts = [ 
181          "stacks_per_line",  
182          "logo_title", 
183          "yaxis_label",  
184          "show_xaxis", 
185          "show_yaxis",         
186          "xaxis_label",  
187          "show_ends", 
188          "fineprint",   
189          "show_errorbars",  
190          "show_boxes",   
191          "yaxis_tic_interval",  
192          "resolution",       
193          "alphabet", 
194          "debug", 
195          "show_ends", 
196          "default_color", 
197          #"show_color_key", 
198          "color_scheme", 
199          "unit_name", 
200          "logo_label", 
201          "yaxis_scale", 
202          "first_index", 
203          "logo_start", 
204          "logo_end", 
205          "scale_width",  
206          "annotate", 
207          "stack_width", 
208          "stack_aspect_ratio" 
209          ] 
210     
211      for k in direct_from_opts: 
212          args[k] = opts.__dict__[k] 
213   
214  #    logo_size = copy.copy(opts.__dict__['logo_size']) 
215  #    size_from_opts = ["stack_width", "stack_height"] 
216  #    for k in size_from_opts : 
217  #        length = getattr(opts, k) 
218  #        if length : setattr( logo_size, k, length ) 
219  #   args["size"] = logo_size     
220   
221   
222      if opts.colors: 
223          color_scheme = ColorScheme() 
224          for color, symbols, desc in opts.colors: 
225              try : 
226                  #c = Color.from_string(color) 
227                  color_scheme.groups.append( ColorGroup(symbols, color, desc)  ) 
228              except ValueError :  
229                  raise ValueError( 
230                       "error: option --color: invalid value: '%s'" % color )           
231                    
232          args["color_scheme"] = color_scheme 
233    
234    
235      if opts.annotate: 
236          args["annotate"] = opts.annotate.split(',') 
237    
238       
239      logooptions = LogoOptions()  
240      for a, v in args.iteritems() : 
241          setattr(logooptions,a,v) 
242   
243       
244      theformat =  LogoFormat(logodata, logooptions ) 
245      return theformat 
246   
247       
248      
249       
250      
251       
252  # ========================== OPTIONS ========================== 
253 -def _build_option_parser() : 
254      defaults = LogoOptions() 
255      parser = DeOptionParser(usage="%prog [options]  < sequence_data.fa > sequence_logo.eps", 
256          description = description, 
257          version     = release_description, 
258          add_verbose_options = False 
259          )     
260           
261      io_grp = OptionGroup(parser, "Input/Output Options",) 
262      data_grp = OptionGroup(parser, "Logo Data Options",) 
263      trans_grp = OptionGroup(parser, "Transformations", "Optional transformations of the sequence data.") 
264   
265    
266      format_grp = OptionGroup(parser, "Logo Format Options",  
267          "These options control the format and display of the logo.") 
268      color_grp = OptionGroup(parser, "Color Options",  
269          "Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc.") 
270      advanced_grp = OptionGroup(parser, "Advanced Format Options",  
271          "These options provide fine control over the display of the logo. ") 
272      server_grp = OptionGroup(parser, "WebLogo Server", 
273          "Run a standalone webserver on a local port.") 
274   
275   
276      parser.add_option_group(io_grp) 
277      parser.add_option_group(data_grp) 
278      parser.add_option_group(trans_grp)       
279      parser.add_option_group(format_grp)   
280      parser.add_option_group(color_grp) 
281      parser.add_option_group(advanced_grp) 
282      parser.add_option_group(server_grp) 
283       
284      # ========================== IO OPTIONS ========================== 
285       
286      io_grp.add_option( "-f", "--fin", 
287          dest="fin", 
288          action="store", 
289          type="file_in", 
290          default=sys.stdin, 
291          help="Sequence input file (default: stdin)", 
292          metavar="FILENAME") 
293   
294      # Add position weight matrix formats to input parsers by hand 
295      fin_choices = dict(seq_io.format_names()) 
296      fin_choices['transfac'] = 'transfac' 
297       
298      io_grp.add_option("-D", "--datatype",  
299          dest="input_parser", 
300          action="store", type ="dict", 
301          default = seq_io, 
302          choices = fin_choices,       # seq_io.format_names(), 
303          help="Type of multiple sequence alignment or position weight matrix file: (%s, transfac)" %  
304             ', '.join([ f.names[0] for f in seq_io.formats]), 
305          metavar="FORMAT") 
306   
307      io_grp.add_option("-o", "--fout", dest="fout", 
308          type="file_out", 
309          default=sys.stdout, 
310          help="Output file (default: stdout)", 
311          metavar="FILENAME") 
312   
313      io_grp.add_option( "-F", "--format", 
314          dest="formatter", 
315          action="store", 
316          type="dict", 
317          choices = formatters, 
318          metavar= "FORMAT", 
319          help="Format of output: eps (default), png, png_print, pdf, jpeg, svg, logodata", 
320          default = default_formatter) 
321   
322   
323      # ========================== Data OPTIONS ========================== 
324   
325   
326    
327      data_grp.add_option( "-A", "--sequence-type", 
328          dest="alphabet", 
329          action="store", 
330          type="dict", 
331          choices = std_alphabets, 
332          help="The type of sequence data: 'protein', 'rna' or 'dna'.", 
333          metavar="TYPE") 
334                          
335      data_grp.add_option( "-a", "--alphabet", 
336          dest="alphabet", 
337          action="store", 
338          help="The set of symbols to count, e.g. 'AGTC'. " 
339               "All characters not in the alphabet are ignored. " 
340               "If neither the alphabet nor sequence-type are specified then weblogo will examine the input data and make an educated guess. " 
341               "See also --sequence-type, --ignore-lower-case" )                        
342       
343          
344      data_grp.add_option( "-U", "--units", 
345          dest="unit_name", 
346          action="store", 
347          choices = std_units.keys(),     
348          type="choice", 
349          default = defaults.unit_name, 
350          help="A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit of free energy ('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for probabilities", 
351          metavar = "NUMBER")  
352   
353   
354      data_grp.add_option( "", "--composition", 
355          dest="composition", 
356          action="store", 
357          type="string", 
358          default = "auto", 
359          help="The expected composition of the sequences: 'auto' (default), 'equiprobable', 'none' (do not perform any compositional adjustment), a CG percentage, a species name (e.g. 'E. coli', 'H. sapiens'), or an explicit distribution (e.g. \"{'A':10, 'C':40, 'G':40, 'T':10}\"). The automatic option uses a typical distribution for proteins and equiprobable distribution for everything else. ", 
360          metavar="COMP.") 
361   
362      data_grp.add_option( "", "--weight", 
363          dest="weight", 
364          action="store", 
365          type="float", 
366          default = None, 
367          help="The weight of prior data.  Default: total pseudocounts equal to the number of monomer types.", 
368          metavar="NUMBER") 
369   
370      data_grp.add_option( "-i", "--first-index", 
371          dest="first_index", 
372          action="store", 
373          type="int", 
374          default = 1, 
375          help="Index of first position in sequence data (default: 1)", 
376          metavar="INDEX") 
377   
378      data_grp.add_option( "-l", "--lower", 
379          dest="logo_start", 
380          action="store", 
381          type="int", 
382          help="Lower bound of sequence to display", 
383          metavar="INDEX") 
384       
385      data_grp.add_option( "-u", "--upper", 
386          dest="logo_end", 
387          action="store", 
388          type="int", 
389          help="Upper bound of sequence to display", 
390          metavar="INDEX") 
391   
392      # ========================== Transformation OPTIONS ========================== 
393       
394   
395      # FIXME Add test?  
396      trans_grp.add_option( "", "--ignore-lower-case", 
397          dest="ignore_lower_case", 
398          action="store_true", 
399          default=False, 
400          help="Disregard lower case letters and only count upper case letters in sequences." 
401         ) 
402   
403      trans_grp.add_option( "", "--reverse", 
404          dest="reverse", 
405          action="store_true", 
406          default=False, 
407          help="reverse sequences", 
408          ) 
409   
410      trans_grp.add_option( "", "--complement", 
411          dest="complement", 
412          action="store_true", 
413          default=False, 
414          help="complement DNA sequences", 
415          ) 
416       
417   
418   
419      # ========================== FORMAT OPTIONS ========================== 
420   
421      format_grp.add_option( "-s", "--size", 
422          dest="stack_width", 
423          action="store", 
424          type ="dict", 
425          choices = std_sizes, 
426          metavar = "LOGOSIZE", 
427          default = defaults.stack_width, 
428          help="Specify a standard logo size (small, medium (default), large)" ) 
429               
430      format_grp.add_option( "-n", "--stacks-per-line", 
431          dest="stacks_per_line", 
432          action="store", 
433          type="int", 
434          help="Maximum number of logo stacks per logo line. (default: %default)", 
435          default = defaults.stacks_per_line, 
436          metavar="COUNT") 
437   
438      format_grp.add_option( "-t", "--title", 
439          dest="logo_title", 
440          action="store", 
441          type="string", 
442          help="Logo title text.", 
443          default = defaults.logo_title, 
444          metavar="TEXT") 
445   
446      format_grp.add_option( "", "--label", 
447          dest="logo_label", 
448          action="store", 
449          type="string", 
450          help="A figure label, e.g. '2a'", 
451          default = defaults.logo_label, 
452          metavar="TEXT") 
453   
454      format_grp.add_option( "-X", "--show-xaxis", 
455          action="store", 
456          type = "boolean", 
457          default= defaults.show_xaxis, 
458          metavar = "YES/NO", 
459          help="Display sequence numbers along x-axis? (default: %default)") 
460                          
461      format_grp.add_option( "-x", "--xlabel", 
462          dest="xaxis_label", 
463          action="store", 
464          type="string", 
465          default = defaults.xaxis_label, 
466          help="X-axis label", 
467          metavar="TEXT") 
468   
469      format_grp.add_option( "", "--annotate", 
470              dest="annotate", 
471              action="store", 
472              type="string", 
473              default = None, 
474              help="A comma separated list of custom stack annotations, e.g. '1,3,4,5,6,7'.  Annotation list must be same length as sequences.", 
475              metavar="TEXT") 
476   
477      format_grp.add_option( "-S", "--yaxis", 
478          dest="yaxis_scale", 
479          action="store", 
480          type="float", 
481          help="Height of yaxis in units. (Default: Maximum value with uninformative prior.)", 
482          metavar = "UNIT")  
483   
484      format_grp.add_option( "-Y", "--show-yaxis", 
485          action="store", 
486          type = "boolean", 
487          dest = "show_yaxis", 
488          default= defaults.show_yaxis, 
489          metavar = "YES/NO", 
490          help="Display entropy scale along y-axis? (default: %default)") 
491   
492      format_grp.add_option( "-y", "--ylabel", 
493          dest="yaxis_label", 
494          action="store", 
495          type="string", 
496          help="Y-axis label (default depends on plot type and units)", 
497          metavar="TEXT") 
498   
499      format_grp.add_option( "-E", "--show-ends", 
500          action="store", 
501          type = "boolean", 
502          default= defaults.show_ends, 
503          metavar = "YES/NO", 
504          help="Label the ends of the sequence? (default: %default)") 
505           
506      format_grp.add_option( "-P", "--fineprint", 
507          dest="fineprint", 
508          action="store", 
509          type="string", 
510          default= defaults.fineprint, 
511          help="The fine print (default: weblogo version)", 
512          metavar="TEXT") 
513   
514      format_grp.add_option( "", "--ticmarks", 
515          dest="yaxis_tic_interval", 
516          action="store", 
517          type="float", 
518          default= defaults.yaxis_tic_interval, 
519          help="Distance between ticmarks (default: %default)", 
520          metavar = "NUMBER") 
521   
522           
523      format_grp.add_option( "", "--errorbars", 
524          dest = "show_errorbars", 
525          action="store", 
526          type = "boolean", 
527          default= defaults.show_errorbars, 
528          metavar = "YES/NO", 
529          help="Display error bars? (default: %default)") 
530        
531          
532           
533      # ========================== Color OPTIONS ========================== 
534      # TODO: Future Feature 
535      # color_grp.add_option( "-K", "--color-key", 
536      #    dest= "show_color_key", 
537      #    action="store", 
538      #    type = "boolean", 
539      #    default= defaults.show_color_key, 
540      #    metavar = "YES/NO", 
541      #    help="Display a color key (default: %default)") 
542           
543           
544      color_scheme_choices = std_color_schemes.keys()     
545      color_scheme_choices.sort()     
546      color_grp.add_option( "-c", "--color-scheme", 
547          dest="color_scheme", 
548          action="store", 
549          type ="dict", 
550          choices = std_color_schemes, 
551          metavar = "SCHEME", 
552          default = None, # Auto 
553          help="Specify a standard color scheme (%s)" % \ 
554              ", ".join(color_scheme_choices) ) 
555               
556      color_grp.add_option( "-C", "--color", 
557          dest="colors", 
558          action="append", 
559          metavar="COLOR SYMBOLS DESCRIPTION ", 
560          nargs = 3, 
561          default=[], 
562          help="Specify symbol colors, e.g. --color black AG 'Purine' --color red TC 'Pyrimidine' ")     
563   
564      color_grp.add_option( "", "--default-color", 
565          dest="default_color", 
566          action="store", 
567          metavar="COLOR", 
568          default= defaults.default_color, 
569          help="Symbol color if not otherwise specified.") 
570   
571   
572      # ========================== Advanced options =========================    
573                   
574      advanced_grp.add_option( "-W", "--stack-width", 
575          dest="stack_width", 
576          action="store", 
577          type="float", 
578          default= defaults.stack_width, 
579          help="Width of a logo stack (default: %s)"% defaults.stack_width, 
580          metavar="POINTS" ) 
581   
582      advanced_grp.add_option( "", "--aspect-ratio", 
583          dest="stack_aspect_ratio", 
584          action="store", 
585          type="float", 
586          default= defaults.stack_aspect_ratio , 
587          help="Ratio of stack height to width (default: %s)"%defaults.stack_aspect_ratio, 
588          metavar="POINTS" )     
589   
590      advanced_grp.add_option( "", "--box", 
591          dest="show_boxes", 
592          action="store", 
593          type = "boolean", 
594          default=False,  
595          metavar = "YES/NO", 
596          help="Draw boxes around symbols? (default: no)") 
597   
598      advanced_grp.add_option( "", "--resolution", 
599          dest="resolution", 
600          action="store", 
601          type="float", 
602          default=96, 
603          help="Bitmap resolution in dots per inch (DPI).  (Default: 96 DPI, except png_print, 600 DPI) Low resolution bitmaps (DPI<300) are antialiased.", 
604          metavar="DPI")   
605   
606      advanced_grp.add_option( "", "--scale-width", 
607          dest="scale_width", 
608          action="store", 
609          type = "boolean", 
610          default= True,  
611          metavar = "YES/NO", 
612          help="Scale the visible stack width by the fraction of symbols in the column?  (I.e. columns with many gaps of unknowns are narrow.)  (Default: yes)") 
613      
614      advanced_grp.add_option( "", "--debug", 
615          action="store", 
616          type = "boolean", 
617          default= defaults.debug, 
618          metavar = "YES/NO", 
619          help="Output additional diagnostic information. (Default: %default)") 
620   
621   
622      # ========================== Server options =========================    
623      server_grp.add_option( "", "--serve", 
624          dest="serve", 
625          action="store_true", 
626          default= False, 
627          help="Start a standalone WebLogo server for creating sequence logos.")     
628       
629      server_grp.add_option( "", "--port", 
630          dest="port", 
631          action="store", 
632          type="int", 
633          default= 8080, 
634          help="Listen to this local port. (Default: %default)", 
635          metavar="PORT") 
636   
637      return parser 
638       
639      # END _build_option_parser 
640   
641   
642  ############################################################## 
643