--- ./doc/examples/sample_opal_scripts/FimoClient.py (original) +++ ./doc/examples/sample_opal_scripts/FimoClient.py (refactored) @@ -13,7 +13,7 @@ from os import mkdir from subprocess import call from time import sleep -from urlparse import urlparse +from urllib.parse import urlparse from ZSI.TC import String @@ -67,35 +67,35 @@ req._inputFile = inputFiles # Launch a non-blocking job -print "Launching non-blocking FIMO job" +print("Launching non-blocking FIMO job") resp = appServicePort.launchJob(req) jobID = resp._jobID -print "Received Job ID:", jobID +print("Received Job ID:", jobID) # Poll for job status status = resp._status -print "Polling job status" +print("Polling job status") while 1: # print current status - print "Status:" - print "\tCode:", status._code - print "\tMessage:", status._message - print "\tOutput Base URL:", status._baseURL + print("Status:") + print("\tCode:", status._code) + print("\tMessage:", status._message) + print("\tOutput Base URL:", status._baseURL) if (status._code == 8) or (status._code == 4): # STATUS_DONE || STATUS_FAILED break - print "Waiting 30 seconds" + print("Waiting 30 seconds") sleep(30) # Query job status status = appServicePort.queryStatus(queryStatusRequest(jobID)) if status._code == 8: # 8 = GramJob.STATUS_DONE - print "\nDownloading Outputs (using wget):\n\n"; + print("\nDownloading Outputs (using wget):\n\n"); output_dir = 'fimo_out' - dir_count = sum(1 for _ in filter(None, urlparse(status._baseURL).path.split("/"))) + dir_count = sum(1 for _ in [_f for _f in urlparse(status._baseURL).path.split("/") if _f]) index_url = status._baseURL + '/index.html' call(["wget", "-r", "-nc", "-p", "-np", "-nH", "--cut-dirs=" + str(dir_count), "-P", output_dir, index_url]) -print "\nJob Complete\n\n"; +print("\nJob Complete\n\n"); --- ./doc/examples/sample_opal_scripts/MemeClient.py (original) +++ ./doc/examples/sample_opal_scripts/MemeClient.py (refactored) @@ -13,7 +13,7 @@ from os import mkdir from subprocess import call from time import sleep -from urlparse import urlparse +from urllib.parse import urlparse from ZSI.TC import String # Set the location of our service @@ -64,35 +64,35 @@ req._inputFile = inputFiles # Launch non-blocking job and retrieve job ID -print "Launching remote MEME job" +print("Launching remote MEME job") resp = appServicePort.launchJob(req) jobID = resp._jobID -print "Received Job ID:", jobID +print("Received Job ID:", jobID) # Poll for job status status = resp._status -print "Polling job status" +print("Polling job status") while 1: # print current status - print "Status:" - print "\tCode:", status._code - print "\tMessage:", status._message - print "\tOutput Base URL:", status._baseURL + print("Status:") + print("\tCode:", status._code) + print("\tMessage:", status._message) + print("\tOutput Base URL:", status._baseURL) if (status._code == 8) or (status._code == 4): # STATUS_DONE || STATUS_FAILED break - print "Waiting 30 seconds" + print("Waiting 30 seconds") sleep(30) # Query job status status = appServicePort.queryStatus(queryStatusRequest(jobID)) if status._code == 8: # 8 = GramJob.STATUS_DONE - print "\nDownloading Outputs (using wget):\n\n"; + print("\nDownloading Outputs (using wget):\n\n"); output_dir = 'meme_out' - dir_count = sum(1 for _ in filter(None, urlparse(status._baseURL).path.split("/"))) + dir_count = sum(1 for _ in [_f for _f in urlparse(status._baseURL).path.split("/") if _f]) index_url = status._baseURL + '/index.html' call(["wget", "-r", "-nc", "-p", "-np", "-nH", "--cut-dirs=" + str(dir_count), "-P", output_dir, index_url]) -print "\nJob Complete\n\n"; +print("\nJob Complete\n\n"); --- ./scripts/alphabet.py (original) +++ ./scripts/alphabet.py (refactored) @@ -1,6 +1,6 @@ #!@WHICHPYTHON@ -from __future__ import with_statement + import collections, itertools, json, math, re, string, sys from xml.sax.saxutils import quoteattr @@ -9,7 +9,7 @@ def alphabetSymbolCompare(x, y): """Compares 2 strings of alphabet symbols""" if len(x) == len(y): - for a, b in itertools.izip(x, y): + for a, b in zip(x, y): # letters before numbers and symbols if a.isalpha(): if b.isalpha(): @@ -302,7 +302,7 @@ comprise_lookup[sym.comprise].append(sym) else: comprise_lookup[sym.comprise] = [sym] - for comprise, syms in comprise_lookup.iteritems(): + for comprise, syms in comprise_lookup.items(): if len(comprise) == 1: # alias for a core symbol core_sym = self.sym_lookup[comprise] @@ -356,7 +356,7 @@ value = 0.4 step = 360 / ncolours colours = [] - for i in xrange(ncolours): + for i in range(ncolours): rgb = _hsv2rgb(step * i, sat, value) colours.append((rgb, _rgb2lab(rgb))) # for each of the unique colours find the closest colour in the generated colours and remove it @@ -364,8 +364,8 @@ best_dist = None best_i = None best_j = None - for i in xrange(len(uniques)): - for j in xrange(len(colours)): + for i in range(len(uniques)): + for j in range(len(colours)): dist = _lab_dist(uniques[i], colours[j][1]) if best_dist == None or dist < best_dist: best_dist = dist @@ -448,15 +448,15 @@ # check assumptions if self.parsed: raise RuntimeError("Parsing is already done!") - if not(isinstance(symbol, basestring) and len(symbol) == 1): + if not(isinstance(symbol, str) and len(symbol) == 1): raise RuntimeError("Expected symbol to be a single character") - if name != None and not(isinstance(name, basestring)): + if name != None and not(isinstance(name, str)): raise RuntimeError("Expected name to be a string") - if colour != None and not(isinstance(colour, (int, long))): + if colour != None and not(isinstance(colour, int)): raise RuntimeError("Expected colour to be a unsigned 24 bit number") - if complement != None and not(isinstance(complement, basestring) and len(complement) == 1): + if complement != None and not(isinstance(complement, str) and len(complement) == 1): raise RuntimeError("Expected complement symbol to be a single character") - if comprise != None and not(isinstance(comprise, basestring)): + if comprise != None and not(isinstance(comprise, str)): raise RuntimeError("Expected name to be a string") if complement != None and comprise != None: raise RuntimeError("Expected only comprise or complement not both") @@ -677,7 +677,7 @@ alph_sym_1.complement = alph_sym_2.index # link comprising symbols # core symbols have themselves in the comprise list - for i in xrange(self.ncore): + for i in range(self.ncore): self.symbols[i].comprise = frozenset([i]) # ambiguous symbols link to the core symbols for sym_obj in reader.ambig_syms: @@ -701,11 +701,11 @@ for alph_sym in self.symbols: self.comp_symbols[alph_sym.symbol] = self.getComplement(alph_sym.symbol) # try to determine a pair of symbols that make up each ambiguous symbol - symbols_by_count = [[] for _ in xrange(self.ncore + 1)] + symbols_by_count = [[] for _ in range(self.ncore + 1)] for alph_sym in self.symbols: symbols_by_count[len(alph_sym.comprise)].append(alph_sym) for alph_sym in self.symbols[self.ncore:]: - for j in xrange(1, len(alph_sym.comprise)): + for j in range(1, len(alph_sym.comprise)): for part in symbols_by_count[j]: if not(part.comprise < alph_sym.comprise): continue @@ -740,7 +740,7 @@ def getColour(self, sym): """Get the colour for this symbol""" - if isinstance(sym, (int, long)): + if isinstance(sym, int): if sym < len(self.symbols): return self.symbols[sym].colour raise RuntimeError("Symbol index " + sym + " does not exist in alphabet") @@ -751,7 +751,7 @@ def getMutedColour(self, sym): """Get the muted colour for this symbol""" - if isinstance(sym, (int, long)): + if isinstance(sym, int): if sym < len(self.symbols): return _lighten(self.symbols[sym].colour) raise RuntimeError("Symbol index " + str(sym) + " does not exist in alphabet") @@ -807,7 +807,7 @@ def getComprisingIndexes(self, sym): """Retrieve the indexes of the comprising core symbols (immutable)""" - if isinstance(sym, (int, long)): + if isinstance(sym, int): if sym < len(self.symbols): return self.symbols[sym].comprise else: @@ -817,7 +817,7 @@ def getPairIndexes(self, sym): """Retrieve the indexes of the comprising core symbols (immutable)""" - if isinstance(sym, (int, long)): + if isinstance(sym, int): if sym < len(self.symbols): return self.symbols[sym].pair else: @@ -868,7 +868,7 @@ def getComplementIndex(self, sym): """Retrieve the index of the complement of the symbol""" - if isinstance(sym, (int, long)): + if isinstance(sym, int): if sym < len(self.symbols): return self.symbols[sym].complement else: @@ -941,7 +941,7 @@ """Create the text representation of the alphabet""" out = [] # output core symbols with complements - for i in xrange(self.ncore): + for i in range(self.ncore): sym1 = self.symbols[i] # check symbol has a complement (which we assume is symetric) if sym1.complement == None: @@ -954,14 +954,14 @@ out.append(sym2.asText()) out.append("\n") # output core symbols without complements - for i in xrange(self.ncore): + for i in range(self.ncore): sym = self.symbols[i] if sym.complement != None: continue out.append(sym.asText()) out.append("\n") # output ambiguous symbols - for i in xrange(self.ncore, len(self.symbols)): + for i in range(self.ncore, len(self.symbols)): sym = self.symbols[i] comprise_str = "".join(sorted([self.symbols[symi].symbol for symi in sym.comprise], cmp=alphabetSymbolCompare)) out.append(sym.asText()) @@ -975,7 +975,7 @@ out.append(comprise_str) out.append("\n") # output aliases for core symbols - for i in xrange(self.ncore): + for i in range(self.ncore): sym = self.symbols[i] if sym.aliases != None: for alias in sym.aliases: @@ -1139,7 +1139,7 @@ prime = 0 alt = 0 other = 0 - for sym, count in counts.iteritems(): + for sym, count in counts.items(): if alphabet.isCoreSymbol(sym): seen.add(alphabet.getIndex(sym)) if alphabet.isPrimeSymbol(sym): --- ./scripts/hypergeometric.py (original) +++ ./scripts/hypergeometric.py (refactored) @@ -16,7 +16,7 @@ psyco_found = False pass if psyco_found: - print >> sys.stderr, "Using psyco..." + print("Using psyco...", file=sys.stderr) # global constants _log10 = log(10) @@ -170,7 +170,7 @@ return 0.0 key = str(n) - if _lnfact_hash.has_key(key): + if key in _lnfact_hash: return _lnfact_hash[key] result = lngamm(n+1.0) @@ -230,29 +230,29 @@ # no arguments: print usage if len(sys.argv) == 1: - print >> sys.stderr, usage; sys.exit(1) + print(usage, file=sys.stderr); sys.exit(1) # parse command line i = 1 while i < len(sys.argv): arg = sys.argv[i] if (arg == "-h"): - print >> sys.stderr, usage; sys.exit(1) + print(usage, file=sys.stderr); sys.exit(1) else: if (i==1): try: p = string.atoi(sys.argv[i]) - except: print >> sys.stderr, usage; sys.exit(1) + except: print(usage, file=sys.stderr); sys.exit(1) elif (i==2): try: P = string.atoi(sys.argv[i]) - except: print >> sys.stderr, usage; sys.exit(1) + except: print(usage, file=sys.stderr); sys.exit(1) elif (i==3): try: n = string.atoi(sys.argv[i]) - except: print >> sys.stderr, usage; sys.exit(1) + except: print(usage, file=sys.stderr); sys.exit(1) elif (i==4): try: N = string.atoi(sys.argv[i]) - except: print >> sys.stderr, usage; sys.exit(1) + except: print(usage, file=sys.stderr); sys.exit(1) else: - print >> sys.stderr, usage; sys.exit(1) + print(usage, file=sys.stderr); sys.exit(1) i += 1 # compute cumulative hypergeometric p-value @@ -262,7 +262,7 @@ pvalue = sprint_logx(log_pvalue, 3, "%6.3fe%-5.0f") #pvalue2 = sprint_logx(log_less, 3, "%6.3fe%-5.0f") #print >> sys.stdout, pvalue, pvalue2, p, P, n, N - print >> sys.stdout, pvalue, p, P, n, N + print(pvalue, p, P, n, N, file=sys.stdout) sys.exit(0) --- ./scripts/sequence.py (original) +++ ./scripts/sequence.py (refactored) @@ -1,6 +1,6 @@ #!@WHICHPYTHON@ -from __future__ import with_statement + import copy, string, sys import alphabet @@ -40,7 +40,7 @@ alpha = alphabet.getBySeq(self.data) if alpha == None: raise RuntimeError("Could not identify alphabet from sequence") - elif isinstance(alpha, basestring): + elif isinstance(alpha, str): alphaname = alpha alpha = alphabet.getByName(alphaname) if alpha == None: @@ -98,7 +98,7 @@ def nice(self): """ A short description of the sequence """ - print self.getName(), ":", self.getLen() + print(self.getName(), ":", self.getLen()) def readStrings(filename): """ Read one or more lines of text from a file--for example an alignment. @@ -131,8 +131,8 @@ else: seqnew = Sequence(seqdata, alpha, seqname, seqinfo) seqlist.append(seqnew) - except RuntimeError, e: - print >> sys.stderr, "Warning: "+seqname+" is invalid (ignored): ", e + except RuntimeError as e: + print("Warning: "+seqname+" is invalid (ignored): ", e, file=sys.stderr) seqinfo = thisline[1:-1] # everything on the defline is "info" seqname = seqinfo.split()[0] # up to first space seqdata = [] @@ -149,8 +149,8 @@ else: seqnew = Sequence(seqdata, alpha, seqname, seqinfo) seqlist.append(seqnew) - except RuntimeError, e: - print >> sys.stderr, "Warning: " + seqname + " is invalid (ignored): ", e + except RuntimeError as e: + print("Warning: " + seqname + " is invalid (ignored): ", e, file=sys.stderr) else: raise RuntimeError("No sequences on FASTA format found in this file") fh.close() @@ -177,7 +177,7 @@ if isinstance(seq, Sequence): _writeOneFASTA(seq, fh) else: - print >> sys.stderr, "Warning: could not write " + seq.getName() + " (ignored)." + print("Warning: could not write " + seq.getName() + " (ignored).", file=sys.stderr) fh.flush() fh.close() @@ -592,10 +592,10 @@ pwm = PWM(alpha) pwm.setFromAlignment(aln) for row in pwm.pretty(): - print row + print(row) for s in seqs: - print s.getName(), s.getLen(), s.getAlphabet().getSymbols() + print(s.getName(), s.getLen(), s.getAlphabet().getSymbols()) for m in regexp.match( s ): - print "pos: %d pat: %s %4.2f" % (m[0], m[1], m[2]) + print("pos: %d pat: %s %4.2f" % (m[0], m[1], m[2])) for m in pwm.match( s ): - print "pos: %d pat: %s %4.2f" % (m[0], m[1], m[2]) + print("pos: %d pat: %s %4.2f" % (m[0], m[1], m[2]))