codonlogo: weblogolib/__init_

comparison weblogolib/init.py @ 8:5149eb3a89c2

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author	davidmurphy
date	Fri, 20 Jan 2012 09:03:40 -0500
parents	4d47ab2b7bcc
children	f3462128e87c

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-:8d676bbd1f2d
+:5149eb3a89c2
 codon_alphabetT=['AAA', 'AAC', 'AAG', 'AAT', 'ACA', 'ACC', 'ACG', 'ACT', 'AGA', 'AGC', 'AGG', 'AGT', 'ATA', 'ATC', 'ATG', 'ATT', 'CAA', 'CAC', 'CAG', 'CAT', 'CCA', 'CCC', 'CCG', 'CCT', 'CGA', 'CGC', 'CGG', 'CGT', 'CTA', 'CTC', 'CTG', 'CTT', 'GAA', 'GAC', 'GAG', 'GAT', 'GCA', 'GCC', 'GCG', 'GCT', 'GGA', 'GGC', 'GGG', 'GGT', 'GTA', 'GTC', 'GTG', 'GTT', 'TAA', 'TAC', 'TAG', 'TAT', 'TCA', 'TCC', 'TCG', 'TCT', 'TGA', 'TGC', 'TGG', 'TGT', 'TTA', 'TTC', 'TTG', 'TTT']
 altype="codonsT"
 offset=0
 isreversed=False
+show_warnings=False
 col=[]
 __all__ = ['LogoSize',
 'colorscheme',
 ]
 description  = "Create sequence logos from biological sequence alignments."
-__version__ = "1.0"
+__version__ = "1.1"
 # These keywords are subsituted by subversion.
 # The date and revision will only  tell the truth after a branch or tag,
 # since different files in trunk will have been changed at different times
 release_date ="$Date: 2011-09-17 16:30:00 -0700 (Tue, 14 Oct 2008) $".split()[1]
 # The base stack width is set equal to 9pt Courier.
 # (Courier has a width equal to 3/5 of the point size.)
 # Check that can get 80 characters in journal page @small
 # 40 chacaters in a journal column
 std_sizes = {
-"small" : LogoSize( stack_width = 10, stack_height = 10*1*5),
+"small" : LogoSize( stack_width = 16.2, stack_height = 10*1*5),
-"medium" : LogoSize( stack_width = 10*2, stack_height = 10*2*5),
+"medium" : LogoSize( stack_width = 16.2*2, stack_height = 10*2*5),
-"large"  : LogoSize( stack_width = 10*3, stack_height = 10*3*5),
+"large"  : LogoSize( stack_width = 16.2*3, stack_height = 10*3*5),
 }
 std_alphabets = {
 'protein': unambiguous_protein_alphabet,
 self.yaxis_tic_interval = 1.
 self.yaxis_minor_tic_ratio = 5
 self.yaxis_scale = None
 self.show_xaxis = True
+self.strict=False
 self.xaxis_label = ""
 self.xaxis_tic_interval =1
 self.rotate_numbers = False
 self.number_interval = 5
 self.show_ends = False
 "xaxis_label",      "xaxis_tic_interval",   "number_interval",
 "fineprint",        "shrink_fraction",      "errorbar_fraction",
 "errorbar_width_fraction",
 "errorbar_gray",    "small_fontsize",       "fontsize",
 "title_fontsize",   "number_fontsize",      "text_font",
-"logo_font",        "title_font",
+"logo_font",        "title_font",           "strict",
 "logo_label",       "yaxis_scale",          "end_type",
 "debug",            "show_title",           "show_xaxis",
 "show_xaxis_label", "show_yaxis",           "show_yaxis_label",
 "show_boxes",       "show_errorbars",       "show_fineprint",
 "rotate_numbers",   "show_ends",            "altype",
 subsitutions["logo_data"] = "\n".join(data)
 # Create and output logo
 template = resource_string( __name__, 'template.eps', __file__)
 logo = Template(template).substitute(subsitutions)
 print >>fout, logo
 # map between output format names and logo
 	  while counter+offset<seq_length:
 	    for i in range(0,len(seqs)):
 if len(str(seqs[i][(counter):(counter+3)]))==3 and len(seqs[i][(counter):(counter+3)].strip("GATUC"))==0  :
 		if(str(seqs[i][(counter):(counter+3)]) in alphabet):
 x[counter/3][ (alphabet.index(str(seqs[i][(counter):(counter+3)]))) ]+=1
+elif show_warnings:
+		if len(seqs[i][(counter):(counter+3)].strip("GATUC"))==1 or len(seqs[i][(counter):(counter+3)].strip("GATUC"))==2 :
+		  print >>sys.stderr, 'Warning:Incomplete or non GATUC codon detected:', seqs[i][(counter):(counter+3)]
+		  print >>sys.stderr, 'Position:',counter
+		  print >>sys.stderr, 'Sequence:',i
+		  print >>sys.stderr, 'This will be treated as ---'
 	    counter=counter+3
 	  counts=asarray(x)
 else:
 	  counts = asarray(seqs.tally())
 while 1:
 line = finp.readline()
 if not line:
 break
 line = line.split()
-priordict[line[0]]=line[1]
-return priordict
+if(altype=="codonsT"):
+	priordict[line[0].upper().replace("U", "T")]=(float(line[1])/1000)*64
+else:
+	priordict[line[0].upper().replace("T", "U")]=(float(line[1])/1000)*64
+return priordict
 def _build_logodata(options) :
 global offset
 offset=options.frame
+global show_warnings
+show_warnings = options.strict
 options.alphabet = None
 options.ignore_lower_case = False
 #options.default_color = Color.by_name("black")
 options.color_scheme=None
 #options.colors=[]
 options.show_ends=False
 seqs = read_seq_data(options.fin,
 options.input_parser.read,
 alphabet=options.alphabet,
 ignore_lower_case = options.ignore_lower_case)
 if(options.priorfile!=None):
 if(altype=="CodonsT"):
 options.composition= str(read_priors(options.priorfile,codon_alphabetT))
 options.alphabet = codon_alphabetT
 else:
 direct_from_opts = [
 "stacks_per_line",
 "logo_title",
 "yaxis_label",
 "show_xaxis",
+"strict",
 "show_yaxis",
 "xaxis_label",
 "show_ends",
 "fineprint",
 "show_errorbars",
 dest="logo_end",
 action="store",
 type="int",
 help="Upper bound of sequence to display",
 metavar="INDEX")
+data_grp.add_option( "-G", "--strict",
+dest="strict",
+action="store",
+type="boolean",
+help="Issue warnings if partial codons are encountered. Default: %default",default = defaults.strict,
+metavar="True/False")
 # ========================== FORMAT OPTIONS ==========================
 format_grp.add_option( "-s", "--size",
 dest="logo_size",
 action="store",

Mercurial > repos > davidmurphy > codonlogo

comparison weblogolib/__init__.py @ 8:5149eb3a89c2

comparison weblogolib/init.py @ 8:5149eb3a89c2