def ReadReferenceFromFile(File):
'''Read in all sequences in the reference file; check there is only one.'''
AllSequences, ReferenceLength = ReadSequencesFromFile(File,False)
if len(AllSequences) != 1:
print('Found', len(AllSequences), 'sequences in', ReferenceFile+\
'; expected 1.\nQuitting.', file=sys.stderr)
exit(1)
return AllSequences.items(), ReferenceLength
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:
ShorterSeqName, ShorterSeq, LongerSeqName, LongerSeq = \
SeqNames[1], SeqDict[SeqNames[1]], SeqNames[0], SeqDict[SeqNames[0]]
LenLongerSeq = len(LongerSeq)
deficit = LenLongerSeq - len(ShorterSeq)
SortedList = [['start_of_'+primer,value] for primer,value in \
StartPrimerPositions.items()] + [['end_of_'+primer,value] for primer,value in \
EndPrimerPositions.items()]
SortedList = sorted(SortedList, key=lambda item: item[1])
if args.AlignmentCoords:
print(' '.join(str(value) for key, value in SortedList))
exit(0)
# Now convert those primer positions, which were with respect to the alignment,
# into positions with respect to each reference.
# For each primer, sorted left to right, count how many bases to the left
# (ignoring gaps). Only count once through the genome, stopping and restarting
# when we get to each primer.
PositionsDict = {}
for SeqName, seq in SeqDict.items():
PositionsWRTseq = []
LastPositionWRTalignment = 0
PositionWRTseq = 0
for [name, PrimerPosition] in SortedList:
for base in seq[LastPositionWRTalignment:PrimerPosition]:
if not base in GapChars:
PositionWRTseq += 1
PositionsWRTseq.append(PositionWRTseq)
LastPositionWRTalignment = PrimerPosition
# Replace any zeroes by ones (i.e. map positions off to the left onto the
# first position for this sequence).
for i in range(0, len(PositionsWRTseq)):
if PositionsWRTseq[i] == 0:
PositionsWRTseq[i] = 1
# alignment has a gap there in which case we just skip. b) If it's not a
# GapChar, and is a unique insertion (i.e. at that position in the main
# alignment only that sequence has a base), we want to excise that base from
# SeqToAdd. c) If it's neither a GapChar nor a unique insertion, we use that
# base from SeqToAdd.
SeqToAdd_WithGaps = ''
ReferenceWithoutInsertions = ''
PositionInSeqToAdd = 0
PositionInFinalAln = 0
TranslationRecord = '"position w.r.t. final alignment","position w.r.t. ref","base"'
for MainPosition, BaseInMainRef in enumerate(RefSeqFromMain):
if BaseInMainRef == GapChar:
EveryBaseHereIsAGap = False
if ExciseUniqueInsertionsOfRefInMainAlignment:
EveryBaseHereIsAGap = True
for SeqName, seq in MainAlnSeqDict.items():
if SeqName == RefSeqName:
continue
elif seq[MainPosition] != GapChar:
EveryBaseHereIsAGap = False
break
if EveryBaseHereIsAGap:
continue
SeqToAdd_WithGaps += GapChar
ReferenceWithoutInsertions += GapChar
PositionInFinalAln += 1
TranslationRecord += '\n' + str(PositionInFinalAln) + ',-,-'
else:
SeqBase = SeqToAdd[PositionInSeqToAdd]
RefInMainHasUniqueInsertion = False
if ExciseUniqueInsertionsOfRefInMainAlignment:
