# Check that the argument exists and is a file
if not os.path.isfile(DataFile):
print DataFile, 'does not exist or is not a file.'
exit(1)
# Read in the sequences as a dictionary. They are (nominally) not aligned.
Aligned=False
SeqDict, FirstSeqLength = ReadSequencesFromFile(DataFile, Aligned)
# We are expecting two sequences.
if len(SeqDict) != 2:
print 'Expected 2 sequences;', DataFile, 'contains', str(len(SeqDict)) +\
'.\nQuitting.'
exit(1)
SeqNames = SeqDict.keys()
Seqs = SeqDict.values()
# If the two sequences are the same length, there is no shuffling to do. Print
# them as they are.
if len(Seqs[0]) == len(Seqs[1]):
for SeqName, seq in SeqDict.items():
print '>'+SeqName
print seq
exit(0)
# Find which of the two sequences is the shorter one
if len(SeqDict[SeqNames[0]]) < len(SeqDict[SeqNames[1]]):
ShorterSeqName, ShorterSeq, LongerSeqName, LongerSeq = \
SeqNames[0], SeqDict[SeqNames[0]], SeqNames[1], SeqDict[SeqNames[1]]
else:
# Check this file is called from the command line with one argument if len(sys.argv[1:]) != 1: print 'Incorrect number of arguments given.' print 'Usage:\n', sys.argv[0], 'NameOfYourFastaFile.fasta' exit(1) DataFile = sys.argv[1] # Check that the argument exists and is a file if not os.path.isfile(DataFile): print DataFile, 'does not exist or is not a file.' exit(1) # Read in all the sequences as a dictionary AllSequences, SequenceLength = ReadSequencesFromFile(DataFile) SequenceNames = AllSequences.keys() sequences = AllSequences.values() NumSequences = len(AllSequences) DataFromAllPositions = [] SetOfAllBasesEncountered = [] # For brevity acgt = ['A','C','G','T'] AllExpectedBases = acgt + IUPACdict.keys() + GapChars TotalEntropy = 0
exit(1)
# Rename arguments for brevity / clarity.
MainAlnFile = args.MainAlignmentFile
PairedAlnFile = args.PairedAlignmentFile
ExciseUniqueInsertionsOfRefInMainAlignment = args.excise
# Check that the arguments exist and are files
for InputFile in [MainAlnFile, PairedAlnFile]:
if not os.path.isfile(InputFile):
print(InputFile, 'does not exist or is not a file.', file=sys.stderr)
exit(1)
# Read in the sequences from the main alignment file (into a dictionary)
MainAlnSeqDict, MainAlnSeqLength = ReadSequencesFromFile(MainAlnFile)
MainAlnSeqNames = MainAlnSeqDict.keys()
MainAlnSeqs = MainAlnSeqDict.values()
# Read in the sequences from the paired alignment file
PairedAlnSeqDict, PairedAlnSeqLength = ReadSequencesFromFile(PairedAlnFile)
# Check it has two sequences
if len(PairedAlnSeqDict) != 2:
print('File', PairedAlnFile, 'contains', len(PairedAlnSeqDict),\
'sequences; two were expected.\nQuitting.', file=sys.stderr)
exit(1)
Seq1name, Seq2name = PairedAlnSeqDict.keys()
# Check that one of the sequences is in the main alignment file (the 'Ref')
# and one is not (the 'SeqToAdd').
if Seq1name in MainAlnSeqNames:
