Problem with insertions

[genevievebo]

I'm trying to get a translation for an insertion. Using the default SNPFiltering, I do not see the insertion in the sequence. I think it's not added to the sequence (it's is present in the db) and/or is treated as a SequenceSNP. Everything works great for snp.

I tried creating my own filter to support the insertion as explained in #33, but I get this error :

File "/u/boucherg/.virtualenvs/pyGeno_git/pyGeno/pyGeno/SNP.py", line 64, in __getattribute__ return Raba.__getattribute__(self, k) File "build/bdist.linux-x86_64/egg/rabaDB/Raba.py", line 648, in __getattribute__ TypeError: attribute name must be string, not 'int'

I'm not sure what I'm doing wrong. Here is the code and the snspset entry.

chromosomeNumber uniqueId start end ref alleles quality caller
5 1 170837542 170837543 - TCTT 0 custom

from pyGeno.Genome import *
 from pyGeno.importation.SNPs import * 
 from pyGeno.SNPFiltering import SNPFilter

 class MyFilter(SNPFilter) :
   	def __init__(self) :
   		SNPFilter.__init__(self)
   	def filter(self, chromosome, snp_custom) :
   		from pyGeno.SNPFiltering import  SequenceInsert, SequenceSNP, SequenceDel
   		for s in snp_custom:
   			if s.alleles != '-' and s.ref != '-':
   				return SequenceSNP(s.alleles)
   			elif s.alleles == '-':
   				return SequenceDel(len(s.ref))
   			elif s.ref == '-':
   				return SequenceInsert(s.alleles)

   if 'snp_custom' in getSNPSetsList() : 
   	deleteSNPs('snp_custom')

   importSNPs("snps_tmp")
   genome = Genome(name = 'GRCh37.75', SNPs='snp_custom', SNPFilter = MyFilter())
   gene = genome.get(Gene, name='NPM1')[0]
   tr = gene.get(Transcript, name='NPM1-001')[0]
   tr.sequence

[package_infos]
description = SNPs for testing purposes
maintainer = The Maintainer
maintainer_contact = maintainer [at] email.ca
version = 1

[set_infos]
species = human
name = snp_custom
type = agnosticsnp
source = Where do these snps come from?

[snps]
filename = snps.txt

[genevievebo]

I found the problem in my code. Since I only have one snp, I can not iterate over it. The filtering function should be :

class MyFilter(SNPFilter) :
	def __init__(self) :
		SNPFilter.__init__(self)
	def filter(self, chromosome, snp_custom) :	
		from pyGeno.SNPFiltering import  SequenceInsert, SequenceSNP, SequenceDel
		snp_custom = [snp_custom]
		for s in snp_custom :
			s.alleles = str(s.alleles)
			if s.alleles != '-' and s.ref != '-':
				return SequenceSNP(s.alleles)
			elif s.alt == '-':
				return SequenceDel(lenght=len(s.ref), ref=s.ref, bases=s.alleles)
			elif s.ref == '-':
				return SequenceInsert(bases=s.alleles, ref=s.ref)

However, I'm still have a lot of trouble getting the sequence.

[tariqdaouda]

What kind of trouble?

[genevievebo]

How do I retrieve the transcript sequence with the insertion?

[tariqdaouda]

As you did with:

genome = Genome(name = 'GRCh37.75', SNPs='snp_custom', SNPFilter = MyFilter())
tr = genome.get(Transcript, name='NPM1-001')[0]  #you can go for the transcript directly

tr.sequence

If the polymorphism passes the filter it should be present in the sequence.