Created
October 19, 2011 13:50
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Get SNPs for gene from our Illumina data
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| from yeastgenome import samsnp | |
| from yeastgenome import yeastgff as yff | |
| from yeastgenome import yeastsnp | |
| from yeastgenome import gff, gffsnp as gs | |
| flist = gff.parse_GFFfeatures('./yeast-genome-Feb2011/saccharomyces_cerevisiae.gff') | |
| gdict = gff.fasta_asdict('../yeast-genome-feb2011/saccharomyces_cerevisiae.gff') | |
| bwa70 = samsnp.parse_samsnp('./PMY070/bwa.Feb2011/final.pileup') | |
| yeastsnp.change_ref2gff(bwa70) | |
| byc70 = gs.snps_bychrom(bwa70) | |
| HO = gff.get_gene(flist, 'HO') | |
| HOsnps = gs.snps_in_feature(HO,byc70) | |
| print HOsnps # no SNPs in HO | |
| upHO1k = gff.upstream_of(HO, 1000, gdict) | |
| downHO1k = gff.downstream_of(HO, 1000, gdict) | |
| upsnps = gs.snps_in_feature(upHO1k, byc70) | |
| print upsnps | |
| downsnps = gs.snps_in_feature(downHO1k, byc70) | |
| print downsnps |
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