for chrom in Chromosomes: ChromosomeSizes.append(Chromosomes[chrom].size()) print Chromosomes[chrom].size() ChromosomeSizes.sort() ChromosomeSizes.reverse() ChromosomeSizes = np.array(ChromosomeSizes) largest_size = ChromosomeSizes.max() 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}, {'$set': { 'number': chrom } } ) if largest_size == Chromosomes[chrom].size(): largest_chrom = chrom if smallest_size == Chromosomes[chrom].size():
numInsertions = 0 numDeletions = 0 numIDDI = 0 for pos in indel[chr].keys(): if any([indel[chr][pos][GENOTYPE] == x for x in ['I', 'II']]): numInsertions += 1 elif any([indel[chr][pos][GENOTYPE] == x for x in ['D', 'DD']]): numDeletions += 1 elif any([indel[chr][pos][GENOTYPE] == x for x in ['ID', 'DI']]): numIDDI += 1 if chr == '23': chrom = 'X' elif chr == '24': chrom = 'Y' elif chr == '25': chrom = 'MT' else: chrom = chr ChromosomeCollection.update_one( {'_id': chr}, {'$set': { # 'totalIndels': totalIndels, # 'numIDDI': numIDDI, # 'numInsertions': numInsertions, # 'numDeletions': numDeletions 'value': chrom } } )