smallest_size = ChromosomeSizes.min()
largest_chrom = ""
smallest_chrom = ""
printMsg("Chromosomes By Size")
index = 1
for size in ChromosomeSizes:
for chrom in Chromosomes:
if not ChromosomeCollection.find({'_id': chrom}):
ChromosomeCollection.insert({'_id': chrom})
if size == Chromosomes[chrom].size():
print "%d | Chr%s %s bp | %s #SNPs" % (index, chrom, Chromosomes[chrom].size(), Chromosomes[chrom].totalSNPs())
index += 1
ChromosomeCollection.update_one(
{'_id': chrom},
{'$set':
{
'number': chrom
}
}
)
if largest_size == Chromosomes[chrom].size():
largest_chrom = chrom
if smallest_size == Chromosomes[chrom].size():
smallest_chrom = chrom
print "LARGEST: Chromosome %s, %sbp" % (largest_chrom, largest_size)
print "SMALLEST: Chromosome %s, %sbp" % (smallest_chrom, smallest_size)
### (2) One list containing tuples of every SNP position and asssociated chromsome
AllChromosomes = []
for chrom in ChromosomePositions:
for i in ChromosomePositions[chrom]:
numInsertions = 0
numDeletions = 0
numIDDI = 0
for pos in indel[chr].keys():
if any([indel[chr][pos][GENOTYPE] == x for x in ['I', 'II']]):
numInsertions += 1
elif any([indel[chr][pos][GENOTYPE] == x for x in ['D', 'DD']]):
numDeletions += 1
elif any([indel[chr][pos][GENOTYPE] == x for x in ['ID', 'DI']]):
numIDDI += 1
if chr == '23':
chrom = 'X'
elif chr == '24':
chrom = 'Y'
elif chr == '25':
chrom = 'MT'
else:
chrom = chr
ChromosomeCollection.update_one(
{'_id': chr},
{'$set':
{
# 'totalIndels': totalIndels,
# 'numIDDI': numIDDI,
# 'numInsertions': numInsertions,
# 'numDeletions': numDeletions
'value': chrom
}
}
)
