for i in range(len(groups_list)): group_hits = [] kv.make_id_list_fasta(groups_list[i], 'core') results = blast_vs_db('tmp.fna', 'blast_databases/other') hits_collection = kv.get_collection('hits') if results: for j in range(len(results)): group_hits.append(results[j]) hits_collection.insert_one({'group':(i+1), 'group_hits':group_hits}) if __name__ == '__main__': import sys kv.mongo_init('pacbio2') os.chdir('/Users/KBLaptop/computation/kvasir/data/output/pacbio2/') # kv.mongo_init(sys.argv[1]) # os.chdir('output/{}/'.format(sys.argv[1])) make_blast_db('core') make_blast_db('other') hits_reset() hgt_blast(perc_identity='90') hgt_blast(perc_identity='95') hgt_blast(perc_identity='99') blast_to_db(perc_identity='90') blast_to_db(perc_identity='95') blast_to_db(perc_identity='99') other_blast()
for i in range(len(ssu_df['strain'])): print ssu_df['strain'][i], ssu_df['16S'][i] if not pd.isnull(ssu_df['16S'][i]): gene_record = { 'species':ssu_df['strain'][i], 'location':{ 'contig':None, 'start':None, 'end':None, 'strand':None, }, 'annotation':'Small subunit ribosomal RNA', 'dna_seq':ssu_df['16S'][i], 'kvtag':None, 'type':'16S' } print "adding 16S gene!" kv.get_collection('16S').remove({'species':ssu_df['strain'][i]}) print kv.get_collection('16S').find_one({'species':ssu_df['strain'][i]}) kv.get_collection('16S').insert_one(gene_record) print kv.get_collection('16S').find_one({'species':ssu_df['strain'][i]}) def get_list_from_tree(newick_file): pass if __name__ == '__main__': os.chdir('/Users/KBLaptop/computation/kvasir/data/output/reorg/') kv.mongo_init('reorg')
fig = plt.figure() ypos = 1 for pair in list_of_species_pairs: if pair[0] == pairs[0][0]: ax = fig.add_axes([1,ypos,1,1]) output_loc_hist(pair[0], pair[1], ax) plot_url = py.plot_mpl(fig) print plot_url # plt.xlabel("Position") # plt.ylabel("percent identity") # plt.savefig('/Users/KBLaptop/Desktop/try.pdf') if __name__ == '__main__': kv.mongo_init('more_genomes') os.chdir('/Users/KBLaptop/computation/kvasir/data/output/more_genomes/') ls = kv.get_species_collections() print ls ls.remove('Arthrobacter_arilaitensis_Re117') pairs = [] for pair in combinations(ls, 2): pairs.append((pair[0], pair[1])) plot_many(pairs) # if os.path.isfile('{}_{}.pdf'.format(pair[0], pair[1])): # continue # try: # output_loc_hist(pair[0], pair[1]) # except RuntimeError:
#!/usr/bin/env python # by Kevin Bonham, PhD (2015) # for Dutton Lab, Harvard Center for Systems Biology, Cambridge MA # Unless otherwise indicated, licensed under GNU Public License (GPLv3) import sys import KvDataStructures as kv kv.mongo_init(sys.argv[1]) kv.reset_database(kv.db.name)