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add indel #46

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add indel #46

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15 changes: 13 additions & 2 deletions pyGeno/Chromosome.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,12 +72,23 @@ def getSequenceData(self, slic) :
if sequenceModifier.__class__ is SF.SequenceDel :
seqPos = seqPos + sequenceModifier.offset
#To avoid to change the length of the sequence who can create some bug or side effect
data[seqPos:(seqPos + sequenceModifier.length)] = [''] * sequenceModifier.length
if (sequenceModifier.indel == 0):
data[seqPos:(seqPos + sequenceModifier.length)] = [''] * sequenceModifier.length
else: # indel
data[seqPos] = sequenceModifier.bases
seqPos += 1
data[seqPos:(seqPos + sequenceModifier.indel)] = [''] * sequenceModifier.indel

elif sequenceModifier.__class__ is SF.SequenceSNP :
data[seqPos] = sequenceModifier.alleles
elif sequenceModifier.__class__ is SF.SequenceInsert :
seqPos = seqPos + sequenceModifier.offset
data[seqPos] = "%s%s" % (data[seqPos], sequenceModifier.bases)
if (sequenceModifier.indel == 0):
data[seqPos] = "%s%s" % (data[seqPos], sequenceModifier.bases)
else: # indel
data[seqPos] = sequenceModifier.bases
seqPos += 1
data[(seqPos):(seqPos + sequenceModifier.indel)] = [''] * sequenceModifier.indel
else :
raise TypeError("sequenceModifier on chromosome: %s starting at: %s is of unknown type: %s" % (self.chromosome.number, snp.start, sequenceModifier.__class__))

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13 changes: 9 additions & 4 deletions pyGeno/SNPFiltering.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,16 +29,18 @@ def __init__(self, bases, sources = {}, ref = '-') :
Sequence_modifiers.__init__(self, sources)
self.bases = bases
self.offset = 0
self.indel = 0

# Allow to use format like C/CCTGGAA(dbSNP) or CCT/CCTGGAA(samtools)
if ref != '-':
if ref == bases[:len(ref)]:
self.offset = len(ref)
self.bases = self.bases[self.offset:]
#-1 because if the insertion are after the last nuc we go out of table
#-1 because if the insertion are after the last nuc we go out of table
self.offset -= 1
else:
raise NotImplemented("This format of Insetion is not accepted. Please change your format, or implement your format in pyGeno.")
# Allow indel like GG/GAG
else:
self.indel = len(ref) - 1


class SequenceDel(Sequence_modifiers) :
Expand All @@ -47,15 +49,18 @@ def __init__(self, length, sources = {}, ref = None, alt = '-') :
Sequence_modifiers.__init__(self, sources)
self.length = length
self.offset = 0
self.indel = 0

# Allow to use format like CCTGGAA/C(dbSNP) or CCTGGAA/CCT(samtools)
if alt != '-':
if ref is not None:
if alt == ref[:len(alt)]:
self.offset = len(alt)
self.length = self.length - len(alt)
# Allow indel like CATA/CAA
else:
raise NotImplemented("This format of Deletion is not accepted. Please change your format, or implement your format in pyGeno.")
self.bases = alt
self.indel = len(ref) - 1
else:
raise Exception("You need to add a ref sequence in your call of SequenceDel. Or implement your format in pyGeno.")

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