update to support python3
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2
README
2
README
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@ -6,7 +6,7 @@ Installation:
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"tiger_fns_102.py" to /usr/local/bin. This will allow access to
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the executable from any location in the filesystem.
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* Please ensure that you are using Python version 2.5 or 2.6.
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* Please ensure that you are using Python version 2.5 or 2.6. [Note: Now I update the python script, so, now please use python3.x]
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76
tiger
76
tiger
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@ -38,7 +38,7 @@ for opt in range(len(options)):
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try:
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file = open(file_name)
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except IOError:
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print "File \"" + file_name + "\" not found..."
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print ("File \"" + file_name + "\" not found...")
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sys.exit(0)
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elif options[opt] == "-b":
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@ -54,18 +54,18 @@ for opt in range(len(options)):
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numbered = True
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elif options[opt] == "-v":
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print "TIGER version 1.02"
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print ("TIGER version 1.02")
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sys.exit(0)
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elif options[opt] == "-rl":
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write_rates = True
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write_rates = True
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try:
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rate_file = options[opt+1]
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if rate_file[0] == "-":
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print "\n\nPlease specify file name for -rl option.\n\n"
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print ("\n\nPlease specify file name for -rl option.\n\n")
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sys.exit(0)
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except IndexError:
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print "\n\nPlease specify file name for -rl option.\n\n"
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print ("\n\nPlease specify file name for -rl option.\n\n")
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sys.exit(0)
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elif options[opt] == "-pl":
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@ -73,10 +73,10 @@ for opt in range(len(options)):
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try:
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pval_file = options[opt+1]
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if pval_file[0] == "-":
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print "\n\nPlease specify file name for -pl option.\n\n"
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print ("\n\nPlease specify file name for -pl option.\n\n")
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sys.exit(0)
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except IndexError:
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print "\n\nPlease specify file name for -pl option.\n\n"
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print ("\n\nPlease specify file name for -pl option.\n\n")
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sys.exit(0)
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elif options[opt] == "-ptp":
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@ -94,7 +94,7 @@ for opt in range(len(options)):
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if not file:
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print "No file specified (-in option)"
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print ("No file specified (-in option)")
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sys.exit(0)
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@ -104,12 +104,12 @@ seqs = []
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if ">" in file.readline():
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tmp = FastaParse(file_name)
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else:
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print """
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print ("""
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*******************************
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File not in correct format!
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TIGER accepts FastA format.
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*******************************
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"""
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""")
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sys.exit(0)
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import re
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@ -121,11 +121,11 @@ seqs = tmp[1]
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lns = [len(l) for l in seqs]
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lns.sort()
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if lns[0] != lns[-1]:
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print "\n\nUneven sequence lengths. Ensure sequences have been aligned!\n\n"
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print ("\n\nUneven sequence lengths. Ensure sequences have been aligned!\n\n")
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sys.exit(0)
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datatype = DNAdetect(seqs[0])
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datatype = DNAdetect(seqs[0])
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#Create array of site patterns
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patterns = []
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@ -236,12 +236,12 @@ for n, nm in enumerate(names):
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filled_names[n] = nm_r+ filler[:(20 -len(nm_r))]
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#print in correct format.... :(
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print "#NEXUS\n\n[This file contains data that has been analysed for site specific rates]"
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print "[using TIGER, developed by Carla Cummins in the laboratory of]"
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print "[Dr James McInerney, National University of Ireland, Maynooth]\n\n"
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#print in correct format.... (
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print ("#NEXUS\n\n[This file contains data that has been analysed for site specific rates]")
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print ("[using TIGER, developed by Carla Cummins in the laboratory of]")
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print ("[Dr James McInerney, National University of Ireland, Maynooth]\n\n")
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print "[Histograms of number of sites in each category:]"
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print ("[Histograms of number of sites in each category:]")
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Hnames = []
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counts = []
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for b in range(binNo):
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@ -249,15 +249,15 @@ for b in range(binNo):
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counts.append(binStr.count(str(b+1)))
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histogram(counts, Hnames)
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print "\n\n"
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print ("\n\n")
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print "\n\n\nBEGIN TAXA;"
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print "\tDimensions NTax = ", len(seqs), ";"
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print "\tTaxLabels ", " ".join(filled_names), ";\nEND;\n"
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print ("\n\n\nBEGIN TAXA;")
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print ("\tDimensions NTax = "), len(seqs), ";"
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print ("\tTaxLabels "), " ".join(filled_names), ";\nEND;\n"
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print "BEGIN CHARACTERS;"
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print "\tDimensions nchar = ", len(seqs[0]), ";"
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print "\tFormat datatype = ", datatype, " gap = - interleave;\nMatrix\n"
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print ("BEGIN CHARACTERS;")
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print ("\tDimensions nchar = "), len(seqs[0]), ";"
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print ("\tFormat datatype = "), datatype, " gap = - interleave;\nMatrix\n"
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sorted = range(len(seqs[0]))
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@ -274,7 +274,7 @@ if formSort == 1:
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sorted[ind] = x
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sr[ind] = "|"
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print sortD
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print (sortD)
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if doPTP:
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@ -294,7 +294,7 @@ for xy in range(0, len(seqs[0]), 60):
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for j in sorted[xy:xy+60]:
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ln = ln + seqs[xz][j].upper()
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print ln
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print (ln)
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if formRate == 0:
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for x in range(len(str(binNo))):
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@ -312,7 +312,7 @@ for xy in range(0, len(seqs[0]), 60):
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bnls = bnls + str(binStr[s])[x]
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else:
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break
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print bnls + "]"
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print (bnls + "]")
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else:
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for c in range(5):
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@ -328,7 +328,7 @@ for xy in range(0, len(seqs[0]), 60):
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rtls = rtls + str(ranks[sorted[d]])[c]
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else:
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break
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print rtls + "]"
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print (rtls + "]")
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if numbered:
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digits = len(str(len(sorted)))
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@ -343,14 +343,14 @@ for xy in range(0, len(seqs[0]), 60):
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colnms = "[" + filler + "\t"
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nms = [str(n)[c] for n in srted[xy:xy+60]]
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colnms += "".join(nms)
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print colnms + "]"
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print (colnms + "]")
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print "\n"
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print "\n"
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print ("\n")
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print ("\n")
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print ";\nEND;\n\nBEGIN PAUP;"
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print (";\nEND;\n\nBEGIN PAUP;")
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if formSort:
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lower_bound = 1
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for c in range(1, binNo + 1):
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@ -360,7 +360,7 @@ if formSort:
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upper_bound = lower_bound + (binStr.count(str(c))) - 1
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charset = charset + str(lower_bound) + "-" + str(upper_bound) + ";"
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lower_bound = upper_bound + 1
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print charset
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print (charset)
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else:
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for x in range(1, binNo + 1):
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tmpL = []
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@ -368,13 +368,13 @@ else:
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for y in range(len(binStr)):
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if str(binStr[y]) == str(x):
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tmpL.append(str(y + 1))
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print "\tCharset Bin" + str(x) + " = ", " ".join(tmpL) + ";"
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print ("\tCharset Bin" + str(x) + " = ", " ".join(tmpL) + ";")
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if doPTP:
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print "\tCharset Sig_Disagreement = " + " ".join([str(i) for i in sig_dis]) + ";"
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print ("\tCharset Sig_Disagreement = " + " ".join([str(i) for i in sig_dis]) + ";")
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print "END;"
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print ("END;")
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lt_F = time.localtime()
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print "[START TIME:", lt_S[3], ":", lt_S[4],":", lt_S[5], "]"
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print "[FINISH TIME:", lt_F[3], ":", lt_F[4],":", lt_F[5], "]"
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print ("[START TIME:", lt_S[3], ":", lt_S[4],":", lt_S[5], "]")
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print ("[FINISH TIME:", lt_F[3], ":", lt_F[4],":", lt_F[5], "]")
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@ -72,10 +72,10 @@ def getPattern(site, unknown):
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for x in range(len(site)):
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if site[x] not in unknown:
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if site[x] in considered:
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pattern[considered.index(site[x])].append(str(x))
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else:
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considered.append(site[x])
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pattern.append([str(x)])
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pattern[considered.index(site[x])].append(str(x))
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else:
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considered.append(site[x])
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pattern.append([str(x)])
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patStr = "|".join([",".join(g) for g in pattern])
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@ -99,7 +99,7 @@ def DNAdetect(seq):
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seq = seq.upper()
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oLen = float(len(seq))
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seq_C = ""
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seq_C = seq.replace("A", "")
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seq_C = seq_C.replace("C", "")
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seq_C = seq_C.replace("G", "")
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@ -136,7 +136,7 @@ def histogram(num_list, name_list):
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pr = pr + "="*(p+1) + (" "*(60 - p))
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break
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low = hi
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print "[" + pr + "|" + str(n) + " "*(pad-len(str(n))) + "]"
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print ("[" + pr + "|" + str(n) + " "*(pad-len(str(n))) + "]")
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def FastaParse(file_name):
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@ -155,7 +155,7 @@ def FastaParse(file_name):
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def printHelp():
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print """
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print ("""
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****************
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TIGER Help:
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****************
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@ -226,4 +226,4 @@ TIGER: Tree-Independent Generation of Evolutionary Rates
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randomised 1,000 times and pass the test if their p-value is <0.01. All ? and * characters
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encountered in the alignment will be ommitted from the analysis.
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"""
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""")
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