import networkx as nx
import seaborn
import skbio as sb
import matplotlib.pyplot as plt
import csv
%matplotlib inlineG = nx.read_weighted_edgelist('/Users/jasonblues/Desktop/Project_files/edges.txt',create_using=nx.MultiGraph())
G.nodes()
G.edges(data=True)[('3L0A3_003', 'GL890970', {'weight': 23573.0}),
('GL890970', '3L0A3_004', {'weight': 27976.0}),
('GL890970', '3L0A3_004', {'weight': 9649.0}),
('GL890970', 'JHB0A2_004', {'weight': 14295.0}),
('GL890970', 'PAL0A1_003', {'weight': 15458.0}),
('GL890970', 'PAL0A1_004', {'weight': 5363.0}),
('GL890970', 'PAL0A1_004', {'weight': 6607.0}),
('GL890970', 'PAL0A1_005', {'weight': 5234.0}),
('3L0A3_004', 'PNG0A4_003', {'weight': 18086.0}),
('3L0A3_004', 'PAL0A1_016', {'weight': 12123.0}),
('3L0A3_006', 'GL890941', {'weight': 8206.0}),
('GL890941', 'JHB0A2_008', {'weight': 7591.0}),
('3L0A3_007', 'GL890825', {'weight': 19014.0}),
('3L0A3_007', 'PAL0A1_007', {'weight': 8514.0}),
('GL890825', '3L0A3_031', {'weight': 9674.0}),
('GL890825', 'JHB0A2_009', {'weight': 5785.0}),
('3L0A3_008', 'GL890820', {'weight': 6485.0}),
('3L0A3_008', 'JHB0A2_011', {'weight': 16368.0}),
('GL890820', 'ASI1E3_001', {'weight': 6840.0}),
('3L0A3_010', 'GL890823', {'weight': 6848.0}),
('3L0A3_010', 'PAL0A1_012', {'weight': 12675.0}),
('3L0A3_010', 'JHB0A2_016', {'weight': 5620.0}),
('3L0A3_010', 'ASI1E3_006', {'weight': 7518.0}),
('3L0A3_010', 'PAL1D4_019', {'weight': 5619.0}),
('GL890823', '3L0A3_011', {'weight': 32073.0}),
('3L0A3_013', 'BGC0001001', {'weight': 5202.0}),
('BGC0001001', 'ASI1E3_021', {'weight': 8496.0}),
('BGC0001001', 'ASI1E3_028', {'weight': 10849.0}),
('BGC0001001', 'JHB0A2_023', {'weight': 12143.0}),
('BGC0001001', 'JHB0A2_036', {'weight': 15639.0}),
('BGC0001001', 'JHB0A2_036', {'weight': 20785.0}),
('BGC0001001', 'PAL0A1_035', {'weight': 31147.0}),
('BGC0001001', 'PAL1D4_023', {'weight': 10307.0}),
('BGC0001001', 'PNG3F7_024', {'weight': 8739.0}),
('3L0A3_015', 'GL890930', {'weight': 9893.0}),
('3L0A3_015', 'PNG3F7_006', {'weight': 6696.0}),
('GL890930', 'ASI1E3_032', {'weight': 9646.0}),
('GL890930', 'JHB0A2_026', {'weight': 8153.0}),
('GL890930', 'PAL0A1_024', {'weight': 7266.0}),
('GL890930', 'PNG0A4_020', {'weight': 7217.0}),
('3L0A3_017', 'CP003284', {'weight': 7239.0}),
('3L0A3_017', 'BGC0000302', {'weight': 7239.0}),
('3L0A3_021', 'GL890969', {'weight': 23545.0}),
('GL890969', 'JHB0A2_035', {'weight': 6786.0}),
('3L0A3_024', 'GL890827', {'weight': 12975.0}),
('3L0A3_024', 'PAL0A1_038', {'weight': 6507.0}),
('GL890827', 'JHB0A2_039', {'weight': 11875.0}),
('3L0A3_030', 'GL890840', {'weight': 7169.0}),
('3L0A3_030', 'GL890840', {'weight': 13804.0}),
('GL890840', 'ASI1E3_012', {'weight': 23025.0}),
('GL890840', 'JHB0A2_007', {'weight': 25350.0}),
('GL890840', 'PAL0A1_043', {'weight': 6841.0}),
('GL890840', 'PAL0A1_043', {'weight': 7034.0}),
('GL890840', 'PAL1D4_014', {'weight': 12357.0}),
('ASI1E3_001', 'JHB0A2_011', {'weight': 14426.0}),
('ASI1E3_002', 'CM002803', {'weight': 6651.0}),
('ASI1E3_002', 'PAL0A1_019', {'weight': 47192.0}),
('CM002803', 'JHB0A2_022', {'weight': 6758.0}),
('CM002803', 'PAL1D4_021', {'weight': 5610.0}),
('ASI1E3_018', 'CP001037', {'weight': 6134.0}),
('ASI1E3_018', 'PNG0A4_005', {'weight': 27426.0}),
('CP001037', 'ASI1E3_028', {'weight': 7156.0}),
('CP001037', 'ASX1E4_019', {'weight': 9209.0}),
('ASI1E3_021', 'GL890975', {'weight': 7187.0}),
('ASI1E3_021', 'GL890975', {'weight': 11792.0}),
('ASI1E3_021', 'BGC0000976', {'weight': 13061.0}),
('ASI1E3_021', 'AY652953', {'weight': 13059.0}),
('ASI1E3_021', 'CP000393', {'weight': 5295.0}),
('GL890975', 'ASI1E3_028', {'weight': 15001.0}),
('GL890975', 'JHB0A2_023', {'weight': 17530.0}),
('GL890975', 'JHB0A2_036', {'weight': 23999.0}),
('GL890975', 'PAL0A1_035', {'weight': 66760.0}),
('GL890975', 'PAL1D4_023', {'weight': 22687.0}),
('GL890975', 'PNG3F7_024', {'weight': 10499.0}),
('BGC0000976', 'ASI1E3_028', {'weight': 15001.0}),
('BGC0000976', 'JHB0A2_023', {'weight': 19344.0}),
('BGC0000976', 'JHB0A2_036', {'weight': 25949.0}),
('BGC0000976', 'PAL0A1_035', {'weight': 73116.0}),
('BGC0000976', 'PAL1D4_023', {'weight': 24616.0}),
('BGC0000976', 'PNG3F7_024', {'weight': 12822.0}),
('AY652953', 'ASI1E3_028', {'weight': 15001.0}),
('AY652953', 'JHB0A2_023', {'weight': 6782.0}),
('AY652953', 'JHB0A2_023', {'weight': 20068.0}),
('AY652953', 'JHB0A2_036', {'weight': 25943.0}),
('AY652953', 'PAL0A1_035', {'weight': 73989.0}),
('AY652953', 'PAL1D4_023', {'weight': 24612.0}),
('AY652953', 'PNG3F7_024', {'weight': 12816.0}),
('ASI1E3_028', 'PNG3F7_011', {'weight': 10692.0}),
('ASI1E3_028', 'ISBH3F3_004', {'weight': 5503.0}),
('ASI1E3_028', 'PNG3F7_032', {'weight': 5063.0}),
('ASI1E3_028', 'PNG0A4_016', {'weight': 11384.0}),
('ASI1E3_032', 'PNG3F7_006', {'weight': 6709.0}),
('ASX1E4_001', 'HG966617', {'weight': 5050.0}),
('HG966617', 'ASX1E4_017', {'weight': 11157.0}),
('HG966617', 'ASX1E4_018', {'weight': 8215.0}),
('ASX1E4_019', 'CP003597', {'weight': 7217.0}),
('ASX1E4_019', 'CP003630', {'weight': 5284.0}),
('CP003630', 'CHN1D9_011', {'weight': 8506.0}),
('ASX1E4_025', 'JTCM01000002', {'weight': 11372.0}),
('JHB0A2_004', 'PNG3F7_005', {'weight': 10283.0}),
('JHB0A2_009', 'PAL0A1_007', {'weight': 18856.0}),
('JHB0A2_022', 'PAL0A1_019', {'weight': 24377.0}),
('JHB0A2_023', 'PNG0A4_016', {'weight': 19689.0}),
('JHB0A2_023', 'PNG0A4_005', {'weight': 12015.0}),
('JHB0A2_023', 'PNG3F7_011', {'weight': 13092.0}),
('JHB0A2_026', 'PNG3F7_006', {'weight': 6723.0}),
('JHB0A2_034', 'CP003642', {'weight': 5359.0}),
('JHB0A2_034', 'PAL0A1_033', {'weight': 24888.0}),
('CP003642', 'PAL0A1_037', {'weight': 11027.0}),
('CP003642', 'PAL1D4_037', {'weight': 7460.0}),
('JHB0A2_039', 'PAL0A1_038', {'weight': 9837.0}),
('PAL0A1_003', 'PNG3F7_016', {'weight': 22883.0}),
('PAL0A1_003', 'PNG3F7_016', {'weight': 7972.0}),
('PAL0A1_003', 'PNG0A4_002', {'weight': 6945.0}),
('PAL0A1_003', 'PNG0A4_002', {'weight': 8500.0}),
('PAL0A1_008', 'CP002059', {'weight': 5557.0}),
('CP002059', 'PAL1D4_004', {'weight': 4985.0}),
('CP002059', 'PNG0A4_006', {'weight': 5542.0}),
('PAL0A1_009', 'BGC0001000', {'weight': 9223.0}),
('PAL0A1_009', 'PAL0A1_033', {'weight': 7019.0}),
('BGC0001000', 'PNG0A4_007', {'weight': 9851.0}),
('BGC0001000', 'PNG3F7_002', {'weight': 9287.0}),
('PAL0A1_028', 'CP003590', {'weight': 9449.0}),
('PAL0A1_028', 'PNG3F7_011', {'weight': 14248.0}),
('PAL0A1_028', 'ISBH3F3_004', {'weight': 12024.0}),
('PAL0A1_028', 'ASI1E3_023', {'weight': 6011.0}),
('PAL0A1_028', 'ASI1E3_023', {'weight': 5819.0}),
('PAL0A1_037', 'BGC0000017', {'weight': 10690.0}),
('PAL0A1_037', 'CACA01000369', {'weight': 5308.0}),
('PAL0A1_037', 'KM245024', {'weight': 5187.0}),
('PAL0A1_037', 'KM245023', {'weight': 5186.0}),
('BGC0000017', 'PAL1D4_037', {'weight': 7292.0}),
('PAL1D4_005', 'AAUW01000004', {'weight': 7217.0}),
('PAL1D4_005', 'AXCE01000034', {'weight': 7287.0}),
('PAL1D4_005', 'AXBY01000005', {'weight': 7287.0}),
('PAL1D4_005', 'CP002568', {'weight': 5420.0}),
('PAL1D4_005', 'GL476320', {'weight': 5662.0}),
('PAL1D4_008', 'BGC0001161', {'weight': 5883.0}),
('PAL1D4_008', 'BGC0001163', {'weight': 5716.0}),
('PAL1D4_008', 'BGC0001162', {'weight': 5707.0}),
('PAL1D4_008', 'PAL0A1_007', {'weight': 17409.0}),
('BGC0001161', 'PNG0A4_019', {'weight': 6279.0}),
('BGC0001163', 'PNG0A4_019', {'weight': 5688.0}),
('BGC0001162', 'PNG0A4_019', {'weight': 5649.0}),
('PAL1D4_018', 'BGC0000043', {'weight': 6335.0}),
('PAL1D4_021', 'PAL0A1_019', {'weight': 17171.0}),
('PAL1D4_023', 'PNG3F7_011', {'weight': 16735.0}),
('PAL1D4_023', 'PNG0A4_005', {'weight': 11289.0}),
('PAL1D4_023', 'PNG3F7_010', {'weight': 6998.0}),
('PAL1D4_023', 'PNG0A4_016', {'weight': 9244.0}),
('PAL1D4_023', 'ISBH3F3_004', {'weight': 7234.0}),
('PAL1D4_027', 'AY974560', {'weight': 6800.0}),
('PAP1D6_008', 'AANB01000007', {'weight': 6489.0}),
('PAP1D6_008', 'JAMD01000001', {'weight': 6154.0}),
('PAP1D6_008', 'GG703520', {'weight': 6475.0}),
('PAP1D6_008', 'JWLF01000002', {'weight': 6383.0}),
('PAP1D6_008', 'JWLH01000003', {'weight': 6380.0}),
('PAP1D6_008', 'JWLE01000001', {'weight': 6374.0}),
('PNG0A4_019', 'PAL0A1_007', {'weight': 5857.0}),
('PNG0A4_020', 'PNG3F7_006', {'weight': 8669.0}),
('PNG3F7_024', 'PNG0A4_016', {'weight': 20416.0}),
('PNG3F7_024', 'PNG0A4_016', {'weight': 5139.0}),
('3L0A3_002', 'JHB0A2_001', {'weight': 18938.0}),
('JHB0A2_001', 'JHB0A2_001', {'weight': 30814.0}),
('PNG0A4_003', 'JHB0A2_019', {'weight': 5175.0}),
('PNG0A4_003', 'PNG0A4_003', {'weight': 43537.0}),
('PAL0A1_016', 'ASI1E3_007', {'weight': 17479.0}),
('PAL0A1_016', 'JHB0A2_017', {'weight': 11520.0}),
('PAL0A1_016', 'JHB0A2_017', {'weight': 25776.0}),
('PAL0A1_016', 'JHB0A2_019', {'weight': 7978.0}),
('PAL0A1_016', 'PAL0A1_014', {'weight': 23514.0}),
('PAL0A1_016', 'PAL0A1_016', {'weight': 54795.0}),
('PAL0A1_016', 'PAL1D4_024', {'weight': 15889.0}),
('PAL0A1_016', 'PAL1D4_033', {'weight': 5579.0}),
('PAL0A1_016', 'PAL1D4_033', {'weight': 6401.0}),
('PAL0A1_016', 'PNG3F7_003', {'weight': 6308.0}),
('PAL0A1_007', 'ASI1E3_020', {'weight': 9377.0}),
('PAL0A1_007', 'PAL0A1_007', {'weight': 22325.0}),
('PAL0A1_007', 'PNG3F7_014', {'weight': 18508.0}),
('JHB0A2_011', 'JHB0A2_011', {'weight': 22095.0}),
('PAL0A1_012', 'PAL0A1_012', {'weight': 41951.0}),
('PAL0A1_012', 'PAL1D4_019', {'weight': 6321.0}),
('PAL0A1_012', 'PNG0A4_012', {'weight': 12752.0}),
('JHB0A2_016', 'ASI1E3_006', {'weight': 5043.0}),
('ASI1E3_006', 'ASI1E3_006', {'weight': 5279.0}),
('PNG3F7_006', 'PAL1D4_017', {'weight': 7267.0}),
('PNG3F7_006', 'PAL1D4_017', {'weight': 7267.0}),
('PNG3F7_006', 'PNG3F7_006', {'weight': 11154.0}),
('3L0A3_016', '3L0A3_016', {'weight': 12848.0}),
('3L0A3_016', 'PNG3F7_020', {'weight': 9799.0}),
('3L0A3_016', 'PNG3F7_020', {'weight': 9736.0}),
('3L0A3_016', 'PAL0A1_025', {'weight': 8847.0}),
('3L0A3_016', 'JHB0A2_029', {'weight': 8733.0}),
('3L0A3_016', 'ASI1E3_033', {'weight': 7507.0}),
('3L0A3_016', 'PNG0A4_021', {'weight': 8140.0}),
('PNG3F7_020', 'PAL0A1_025', {'weight': 6498.0}),
('PNG3F7_020', 'PAL0A1_025', {'weight': 10092.0}),
('PNG3F7_020', 'PNG0A4_021', {'weight': 8664.0}),
('PNG3F7_020', 'PNG0A4_021', {'weight': 8917.0}),
('PNG3F7_020', 'PNG3F7_020', {'weight': 12072.0}),
('PNG3F7_020', 'ASI1E3_033', {'weight': 7529.0}),
('PNG3F7_020', 'JHB0A2_029', {'weight': 8600.0}),
('PAL0A1_025', 'PAL0A1_025', {'weight': 6046.0}),
('PAL0A1_025', 'PNG0A4_021', {'weight': 7650.0}),
('JHB0A2_029', 'JHB0A2_029', {'weight': 6141.0}),
('3L0A3_018', '3L0A3_018', {'weight': 8614.0}),
('3L0A3_018', 'PNG0A4_022', {'weight': 8278.0}),
('3L0A3_018', 'PNG0A4_022', {'weight': 8278.0}),
('3L0A3_018', 'PAL0A1_027', {'weight': 8268.0}),
('3L0A3_018', 'PAL0A1_027', {'weight': 8268.0}),
('3L0A3_018', 'PAL1D4_003', {'weight': 8149.0}),
('3L0A3_018', 'JHB0A2_028', {'weight': 7389.0}),
('3L0A3_018', 'JHB0A2_028', {'weight': 7389.0}),
('PNG0A4_022', 'JHB0A2_028', {'weight': 7346.0}),
('PNG0A4_022', 'JHB0A2_028', {'weight': 7346.0}),
('PNG0A4_022', 'PAL0A1_027', {'weight': 8389.0}),
('PNG0A4_022', 'PAL0A1_027', {'weight': 8389.0}),
('PNG0A4_022', 'PNG0A4_022', {'weight': 8603.0}),
('PNG0A4_022', 'PAL1D4_003', {'weight': 8269.0}),
('PAL0A1_027', 'JHB0A2_028', {'weight': 7302.0}),
('PAL0A1_027', 'JHB0A2_028', {'weight': 7302.0}),
('PAL0A1_027', 'PAL0A1_027', {'weight': 8746.0}),
('PAL0A1_027', 'PAL1D4_003', {'weight': 8479.0}),
('PAL1D4_003', 'JHB0A2_028', {'weight': 7192.0}),
('JHB0A2_028', 'JHB0A2_028', {'weight': 8621.0}),
('3L0A3_019', '3L0A3_019', {'weight': 8828.0}),
('3L0A3_019', 'PAL0A1_031', {'weight': 10453.0}),
('3L0A3_019', 'PAL0A1_031', {'weight': 8276.0}),
('3L0A3_019', 'PAL1D4_026', {'weight': 7717.0}),
('3L0A3_019', 'PAL1D4_026', {'weight': 6130.0}),
('3L0A3_019', 'JHB0A2_032', {'weight': 7034.0}),
('3L0A3_019', 'PNG0A4_025', {'weight': 10912.0}),
('PAL0A1_031', 'JHB0A2_032', {'weight': 8853.0}),
('PAL0A1_031', 'PAL1D4_026', {'weight': 8868.0}),
('PAL0A1_031', 'PAL1D4_026', {'weight': 7409.0}),
('PAL0A1_031', 'PAL1D4_026', {'weight': 8677.0}),
('PAL0A1_031', 'PAL0A1_031', {'weight': 10875.0}),
('PAL0A1_031', 'PNG0A4_025', {'weight': 8121.0}),
('PAL1D4_026', 'JHB0A2_032', {'weight': 6170.0}),
('PAL1D4_026', 'JHB0A2_032', {'weight': 5039.0}),
('PAL1D4_026', 'PAL1D4_026', {'weight': 6101.0}),
('PAL1D4_026', 'PAL1D4_026', {'weight': 7562.0}),
('PAL1D4_026', 'PNG0A4_025', {'weight': 6171.0}),
('3L0A3_020', '3L0A3_020', {'weight': 10675.0}),
('3L0A3_020', 'PAL1D4_010', {'weight': 5598.0}),
('3L0A3_020', 'PAL1D4_010', {'weight': 5598.0}),
('3L0A3_020', 'PAL0A1_032', {'weight': 5597.0}),
('PAL1D4_010', 'CHN1D9_012', {'weight': 7188.0}),
('PAL1D4_010', 'PAL1D4_010', {'weight': 7149.0}),
('PAL1D4_010', 'PAL0A1_032', {'weight': 7094.0}),
('3L0A3_023', '3L0A3_023', {'weight': 24886.0}),
('3L0A3_023', 'PAL0A1_036', {'weight': 15631.0}),
('3L0A3_023', 'PAL0A1_036', {'weight': 15683.0}),
('3L0A3_023', 'ASI1E3_017', {'weight': 14643.0}),
('3L0A3_023', 'ASI1E3_017', {'weight': 14767.0}),
('PAL0A1_036', 'ASI1E3_017', {'weight': 20618.0}),
('PAL0A1_036', 'ASI1E3_017', {'weight': 20548.0}),
('PAL0A1_036', 'PAL0A1_036', {'weight': 26655.0}),
('PAL0A1_036', 'PAL1D4_020', {'weight': 16436.0}),
('PAL0A1_036', 'PAL1D4_020', {'weight': 5168.0}),
('ASI1E3_017', 'ASI1E3_017', {'weight': 28838.0}),
('PAL0A1_038', 'PAL0A1_038', {'weight': 12085.0}),
('3L0A3_025', 'PAL0A1_034', {'weight': 10705.0}),
('PAL0A1_034', 'PAL0A1_034', {'weight': 5920.0}),
('PAL0A1_034', 'PAL0A1_034', {'weight': 18073.0}),
('PAL0A1_034', 'PAL1D4_009', {'weight': 8551.0}),
('PAL0A1_034', 'PAL1D4_009', {'weight': 15153.0}),
('3L0A3_026', '3L0A3_026', {'weight': 26943.0}),
('3L0A3_026', 'ASI1E3_019', {'weight': 5112.0}),
('3L0A3_026', 'PNG3F7_005', {'weight': 5065.0}),
('3L0A3_026', 'PNG3F7_005', {'weight': 5635.0}),
('3L0A3_027', '3L0A3_027', {'weight': 7169.0}),
('PAL0A1_019', 'PAL0A1_019', {'weight': 57770.0}),
('PAL0A1_019', 'PAL0A1_022', {'weight': 5347.0}),
('PAL0A1_019', 'PNG3F7_013', {'weight': 5312.0}),
('ASI1E3_007', 'PAP1D6_003', {'weight': 23328.0}),
('ASI1E3_007', 'PAL0A1_014', {'weight': 19952.0}),
('PAP1D6_003', 'JHB0A2_017', {'weight': 10726.0}),
('PAP1D6_003', 'PAL0A1_014', {'weight': 20499.0}),
('PAP1D6_003', 'PAP1D6_003', {'weight': 12249.0}),
('PAL0A1_014', 'JHB0A2_017', {'weight': 14413.0}),
('PAL0A1_014', 'PAL0A1_014', {'weight': 34872.0}),
('PAL0A1_014', 'PAL1D4_033', {'weight': 5575.0}),
('PAL0A1_014', 'PAL1D4_033', {'weight': 7380.0}),
('ASI1E3_008', 'PAL0A1_010', {'weight': 10763.0}),
('ASI1E3_008', 'PAL0A1_010', {'weight': 12638.0}),
('ASI1E3_008', 'ISBH3F3_001', {'weight': 6500.0}),
('ASI1E3_008', 'ISBH3F3_001', {'weight': 6866.0}),
('ASI1E3_008', 'PNG0A4_009', {'weight': 11520.0}),
('ASI1E3_008', 'JHB0A2_014', {'weight': 11669.0}),
('PAL0A1_010', 'JHB0A2_014', {'weight': 21974.0}),
('PAL0A1_010', 'JHB0A2_014', {'weight': 21977.0}),
('PAL0A1_010', 'PAL0A1_010', {'weight': 29368.0}),
('PAL0A1_010', 'PNG0A4_009', {'weight': 20716.0}),
('PAL0A1_010', 'PNG0A4_009', {'weight': 20837.0}),
('ISBH3F3_001', 'ISBH3F3_001', {'weight': 22639.0}),
('PNG0A4_009', 'PNG0A4_009', {'weight': 27866.0}),
('JHB0A2_014', 'JHB0A2_014', {'weight': 29256.0}),
('ASI1E3_009', 'ASI1E3_009', {'weight': 14710.0}),
('ASI1E3_010', 'PNG3F7_004', {'weight': 5224.0}),
('PNG3F7_004', 'PNG3F7_004', {'weight': 11783.0}),
('ASI1E3_013', 'ASI1E3_013', {'weight': 23490.0}),
('ASI1E3_013', 'JHB0A2_020', {'weight': 14180.0}),
('ASI1E3_013', 'JHB0A2_020', {'weight': 14134.0}),
('ASI1E3_013', 'PAL0A1_018', {'weight': 11475.0}),
('JHB0A2_020', 'JHB0A2_020', {'weight': 24359.0}),
('PAL0A1_018', 'PAL0A1_018', {'weight': 22100.0}),
('PAL0A1_018', 'PAL1D4_022', {'weight': 12239.0}),
('ASI1E3_014', 'ASI1E3_014', {'weight': 19608.0}),
('ASI1E3_016', 'ASI1E3_016', {'weight': 7403.0}),
('PNG0A4_005', 'JHB0A2_006', {'weight': 14396.0}),
('PNG0A4_005', 'PNG0A4_005', {'weight': 9925.0}),
('ASI1E3_019', 'NAK4C8_005', {'weight': 7629.0}),
('ASI1E3_019', 'NAK4C8_005', {'weight': 5017.0}),
('ASI1E3_019', 'NAK4C8_005', {'weight': 14151.0}),
('NAK4C8_005', 'CHN1D9_003', {'weight': 15262.0}),
('NAK4C8_005', 'NAK4C8_005', {'weight': 28182.0}),
('ASI1E3_022', 'ASI1E3_022', {'weight': 23146.0}),
('ASI1E3_023', 'ASI1E3_023', {'weight': 22546.0}),
('ASI1E3_024', 'ASI1E3_024', {'weight': 7864.0}),
('PNG3F7_011', 'CHN1D9_004', {'weight': 9965.0}),
('PNG3F7_011', 'PNG3F7_011', {'weight': 30886.0}),
('ISBH3F3_004', 'ISBH3F3_004', {'weight': 60537.0}),
('PNG0A4_016', 'PNG0A4_016', {'weight': 48988.0}),
('ASI1E3_030', 'JHB0A2_024', {'weight': 6269.0}),
('ASI1E3_030', 'PAL0A1_022', {'weight': 4998.0}),
('JHB0A2_024', 'JHB0A2_024', {'weight': 9349.0}),
('JHB0A2_024', 'PAL0A1_022', {'weight': 4998.0}),
('PAL0A1_022', 'PAL0A1_022', {'weight': 10290.0}),
('PAL0A1_022', 'PNG3F7_013', {'weight': 5582.0}),
('PAL0A1_022', 'PNG3F7_013', {'weight': 5562.0}),
('ASI1E3_031', 'ASI1E3_031', {'weight': 9715.0}),
('ASI1E3_034', 'ASI1E3_034', {'weight': 20492.0}),
('ASX1E4_002', 'ASX1E4_002', {'weight': 11586.0}),
('ASX1E4_003', 'PNG3F7_003', {'weight': 5651.0}),
('PNG3F7_003', 'NAK4C8_004', {'weight': 13460.0}),
('PNG3F7_003', 'PAL1D4_015', {'weight': 10426.0}),
('PNG3F7_003', 'PNG3F7_003', {'weight': 6821.0}),
('PNG3F7_003', 'PNG0A4_013', {'weight': 6604.0}),
('ASX1E4_004', 'ASX1E4_004', {'weight': 22559.0}),
('ASX1E4_005', 'ASX1E4_005', {'weight': 9619.0}),
('ASX1E4_007', 'ASX1E4_007', {'weight': 11896.0}),
('ASX1E4_008', 'ASX1E4_008', {'weight': 32525.0}),
('ASX1E4_009', 'ASX1E4_009', {'weight': 12366.0}),
('ASX1E4_010', 'ASX1E4_010', {'weight': 26479.0}),
('ASX1E4_011', 'ASX1E4_011', {'weight': 13526.0}),
('ASX1E4_013', 'CHN1D9_001', {'weight': 13092.0}),
('CHN1D9_001', 'CHN1D9_001', {'weight': 24332.0}),
('ASX1E4_014', 'ASX1E4_014', {'weight': 27411.0}),
('ASX1E4_015', 'ASX1E4_015', {'weight': 12760.0}),
('ASX1E4_016', 'ASX1E4_016', {'weight': 5936.0}),
('ASX1E4_020', 'ASX1E4_020', {'weight': 13516.0}),
('ASX1E4_021', 'ASX1E4_021', {'weight': 5232.0}),
('ASX1E4_022', 'ASX1E4_022', {'weight': 11698.0}),
('ASX1E4_023', 'ASX1E4_023', {'weight': 12189.0}),
('ASX1E4_024', 'STM4C5_004', {'weight': 18374.0}),
('STM4C5_004', 'PAB3F5_003', {'weight': 11665.0}),
('STM4C5_004', 'STM4C5_004', {'weight': 16758.0}),
('ASX1E4_026', 'ASX1E4_026', {'weight': 17707.0}),
('ASX1E4_027', 'ASX1E4_027', {'weight': 11459.0}),
('ASX1E4_028', 'ASX1E4_028', {'weight': 8505.0}),
('ASX1E4_029', 'ASX1E4_029', {'weight': 8903.0}),
('ASX1E4_030', 'ASX1E4_030', {'weight': 6061.0}),
('CHN1D9_002', 'ISBH3F3_003', {'weight': 28248.0}),
('ISBH3F3_003', 'ISBH3F3_003', {'weight': 18670.0}),
('CHN1D9_005', 'CHN1D9_005', {'weight': 17920.0}),
('CHN1D9_009', 'CHN1D9_009', {'weight': 17307.0}),
('CHN1D9_010', 'CHN1D9_010', {'weight': 7770.0}),
('CHN1D9_013', 'CHN1D9_013', {'weight': 10319.0}),
('CHN1D9_014', 'CHN1D9_014', {'weight': 12649.0}),
('CHN1D9_015', 'CHN1D9_015', {'weight': 11575.0}),
('CHN1D9_016', 'CHN1D9_016', {'weight': 10869.0}),
('ISBH3F3_002', 'STM4C5_003', {'weight': 5350.0}),
('STM4C5_003', 'NAK4C8_002', {'weight': 13596.0}),
('STM4C5_003', 'NAK4C8_002', {'weight': 13197.0}),
('STM4C5_003', 'STM4C5_003', {'weight': 21128.0}),
('ISBH3F3_005', 'ISBH3F3_005', {'weight': 18833.0}),
('ISBH3F3_006', 'ISBH3F3_006', {'weight': 18726.0}),
('ISBH3F3_007', 'ISBH3F3_007', {'weight': 26800.0}),
('ISBH3F3_009', 'ISBH3F3_009', {'weight': 18878.0}),
('ISBH3F3_010', 'ISBH3F3_010', {'weight': 9410.0}),
('ISBH3F3_011', 'ISBH3F3_011', {'weight': 16343.0}),
('ISBH3F3_013', 'PAL1D4_016', {'weight': 7455.0}),
('PAL1D4_016', 'PAB3F5_008', {'weight': 9876.0}),
('PAL1D4_016', 'PAL1D4_016', {'weight': 7219.0}),
('PAL1D4_016', 'PAL0A1_020', {'weight': 6177.0}),
('JHB0A2_003', 'JHB0A2_003', {'weight': 24533.0}),
('PNG3F7_005', 'PNG3F7_005', {'weight': 5060.0}),
('PNG3F7_005', 'PNG3F7_005', {'weight': 7439.0}),
('JHB0A2_005', 'JHB0A2_005', {'weight': 13396.0}),
('JHB0A2_006', 'PAL1D4_028', {'weight': 5002.0}),
('PAL1D4_028', 'PAL0A1_006', {'weight': 5577.0}),
('PAL1D4_028', 'PAL1D4_028', {'weight': 10824.0}),
('JHB0A2_019', 'JHB0A2_019', {'weight': 8890.0}),
('JHB0A2_019', 'JHB0A2_019', {'weight': 9166.0}),
('JHB0A2_019', 'PNG3F7_016', {'weight': 10062.0}),
('PNG3F7_016', 'PNG3F7_016', {'weight': 38864.0}),
('PNG3F7_016', 'PNG0A4_002', {'weight': 17622.0}),
('JHB0A2_021', 'JHB0A2_021', {'weight': 16260.0}),
('JHB0A2_025', 'JHB0A2_025', {'weight': 9892.0}),
('JHB0A2_027', 'JHB0A2_027', {'weight': 10494.0}),
('JHB0A2_027', 'PAL0A1_026', {'weight': 7016.0}),
('JHB0A2_027', 'PAL0A1_026', {'weight': 7018.0}),
('PAL0A1_026', 'PAL0A1_026', {'weight': 10395.0}),
('JHB0A2_030', 'JHB0A2_030', {'weight': 14827.0}),
('JHB0A2_030', 'PAL0A1_029', {'weight': 11230.0}),
('JHB0A2_030', 'PAL0A1_029', {'weight': 11292.0}),
('PAL0A1_029', 'PAL0A1_029', {'weight': 16037.0}),
('JHB0A2_031', 'JHB0A2_031', {'weight': 22218.0}),
('JHB0A2_033', 'JHB0A2_033', {'weight': 23720.0}),
('PAL0A1_033', 'PAL0A1_033', {'weight': 77222.0}),
('PAL0A1_033', 'PNG0A4_026', {'weight': 20705.0}),
('PAL0A1_033', 'PNG0A4_026', {'weight': 25394.0}),
('PAL0A1_033', 'PAL1D4_011', {'weight': 10688.0}),
('JHB0A2_038', 'JHB0A2_038', {'weight': 22865.0}),
('NAK4C8_002', 'NAK4C8_002', {'weight': 37399.0}),
('NAK4C8_003', 'NAK4C8_003', {'weight': 12952.0}),
('NAK4C8_006', 'NAK4C8_006', {'weight': 7314.0}),
('PAB3F5_001', 'PAB3F5_001', {'weight': 29092.0}),
('PAB3F5_004', 'PAB3F5_004', {'weight': 27134.0}),
('PAB3F5_005', 'PAB3F5_005', {'weight': 17347.0}),
('PAB3F5_006', 'PAB3F5_006', {'weight': 7258.0}),
('PAB3F5_007', 'PNG3F7_025', {'weight': 6984.0}),
('PNG3F7_025', 'PNG3F7_025', {'weight': 11152.0}),
('PAB3F5_009', 'PNG3F7_027', {'weight': 7745.0}),
('PNG3F7_027', 'PNG3F7_027', {'weight': 5207.0}),
('PNG3F7_027', 'PNG0A4_004', {'weight': 5072.0}),
('PAB3F5_011', 'PAB3F5_011', {'weight': 6321.0}),
('PAL0A1_001', 'PAL0A1_001', {'weight': 19898.0}),
('PAL0A1_001', 'PAL1D4_032', {'weight': 7602.0}),
('PAL0A1_002', 'PAL0A1_002', {'weight': 5085.0}),
('PNG0A4_002', 'PNG0A4_002', {'weight': 27277.0}),
('PAL0A1_011', 'PAL0A1_011', {'weight': 28687.0}),
('PAL0A1_011', 'PNG0A4_011', {'weight': 17054.0}),
('PAL0A1_011', 'PNG0A4_011', {'weight': 17033.0}),
('PAL0A1_011', 'PAL1D4_007', {'weight': 7273.0}),
('PNG0A4_011', 'PNG0A4_011', {'weight': 22196.0}),
('PNG0A4_011', 'PNG3F7_021', {'weight': 14568.0}),
('PNG0A4_011', 'PNG3F7_021', {'weight': 14527.0}),
('PAL0A1_013', 'PAL0A1_013', {'weight': 5188.0}),
('PAL0A1_013', 'PAL0A1_013', {'weight': 29400.0}),
('PAL0A1_013', 'PAL1D4_015', {'weight': 7282.0}),
('PAL0A1_013', 'PAL1D4_015', {'weight': 17194.0}),
('PAL0A1_017', 'PAL0A1_017', {'weight': 28829.0}),
('PAL0A1_017', 'PAL1D4_034', {'weight': 5053.0}),
('PAL0A1_020', 'PAL0A1_020', {'weight': 24027.0}),
('PNG3F7_013', 'PNG3F7_013', {'weight': 8211.0}),
('PAL0A1_023', 'PAL0A1_023', {'weight': 11479.0}),
('PAL0A1_023', 'PNG0A4_018', {'weight': 6357.0}),
('PAL0A1_023', 'PNG3F7_017', {'weight': 5504.0}),
('PAL0A1_030', 'PAL0A1_030', {'weight': 10805.0}),
('PAL0A1_030', 'PNG3F7_009', {'weight': 8653.0}),
('PAL0A1_030', 'PNG3F7_009', {'weight': 8568.0}),
('PAL0A1_030', 'PAL1D4_036', {'weight': 5620.0}),
('PAL0A1_030', 'PAL1D4_036', {'weight': 5610.0}),
('PNG3F7_009', 'PAL1D4_036', {'weight': 5330.0}),
('PNG3F7_009', 'PAL1D4_036', {'weight': 5341.0}),
('PNG3F7_009', 'PAP1D6_005', {'weight': 24867.0}),
('PNG3F7_009', 'PNG3F7_009', {'weight': 12856.0}),
('PAL1D4_036', 'PAL1D4_036', {'weight': 5503.0}),
('PNG0A4_025', 'PNG0A4_025', {'weight': 18350.0}),
('PNG0A4_026', 'PNG0A4_026', {'weight': 25788.0}),
('PAL1D4_009', 'PAL1D4_009', {'weight': 16058.0}),
('PAL1D4_020', 'PAL1D4_020', {'weight': 5289.0}),
('PAL0A1_039', 'PAL0A1_039', {'weight': 10101.0}),
('PAL0A1_040', 'PAL0A1_040', {'weight': 10326.0}),
('PAL1D4_001', 'PAL1D4_001', {'weight': 32542.0}),
('PAL1D4_006', 'PAL1D4_006', {'weight': 9321.0}),
('PAL1D4_007', 'PAL1D4_007', {'weight': 7273.0}),
('PAL1D4_011', 'PAL1D4_011', {'weight': 7507.0}),
('PAL1D4_011', 'PNG3F7_019', {'weight': 5152.0}),
('PAL1D4_013', 'PAL1D4_013', {'weight': 12588.0}),
('PAL1D4_015', 'PAL1D4_015', {'weight': 7419.0}),
('PAL1D4_015', 'PAL1D4_015', {'weight': 16259.0}),
('PAL1D4_017', 'PAL1D4_017', {'weight': 7716.0}),
('PAL1D4_022', 'PAL1D4_022', {'weight': 13156.0}),
('PNG3F7_010', 'PNG3F7_010', {'weight': 16902.0}),
('PAL1D4_024', 'PAL1D4_024', {'weight': 12083.0}),
('PAL1D4_025', 'PAL1D4_025', {'weight': 6372.0}),
('PAL1D4_025', 'PAL1D4_025', {'weight': 6115.0}),
('PAL1D4_031', 'PAL1D4_031', {'weight': 8879.0}),
('PAL1D4_031', 'PNG0A4_015', {'weight': 6374.0}),
('PAL1D4_031', 'PNG0A4_015', {'weight': 6374.0}),
('PAL1D4_031', 'PNG3F7_018', {'weight': 6315.0}),
('PNG0A4_015', 'PNG0A4_015', {'weight': 12061.0}),
('PNG0A4_015', 'PNG3F7_018', {'weight': 7187.0}),
('PNG3F7_018', 'PNG3F7_018', {'weight': 10205.0}),
('PAL1D4_032', 'PAL1D4_032', {'weight': 7600.0}),
('PAL1D4_033', 'PAL1D4_033', {'weight': 5593.0}),
('PAL1D4_033', 'PAL1D4_033', {'weight': 6934.0}),
('PAL1D4_034', 'PAP1D6_013', {'weight': 5049.0}),
('PAP1D6_013', 'PAP1D6_013', {'weight': 6797.0}),
('PAP1D6_002', 'PAP1D6_002', {'weight': 11669.0}),
('PAP1D6_004', 'PAP1D6_004', {'weight': 25650.0}),
('PAP1D6_006', 'PAP1D6_006', {'weight': 9427.0}),
('PAP1D6_007', 'PAP1D6_007', {'weight': 11070.0}),
('PAP1D6_010', 'PAP1D6_010', {'weight': 16316.0}),
('PAP1D6_012', 'PAP1D6_012', {'weight': 12484.0}),
('PAP1D6_014', 'PAP1D6_014', {'weight': 7051.0}),
('PAP1D6_015', 'PAP1D6_015', {'weight': 6036.0}),
('PNG0A4_001', 'PNG0A4_001', {'weight': 5135.0}),
('PNG0A4_004', 'PNG0A4_004', {'weight': 20731.0}),
('PNG0A4_008', 'PNG0A4_008', {'weight': 23273.0}),
('PNG0A4_010', 'PNG0A4_010', {'weight': 8356.0}),
('PNG3F7_021', 'PNG3F7_021', {'weight': 19350.0}),
('PNG0A4_013', 'PNG0A4_013', {'weight': 29758.0}),
('PNG0A4_017', 'PNG0A4_017', {'weight': 9148.0}),
('PNG0A4_018', 'PNG0A4_018', {'weight': 10016.0}),
('PNG0A4_018', 'PNG3F7_017', {'weight': 5436.0}),
('PNG0A4_021', 'PNG0A4_021', {'weight': 11455.0}),
('PNG0A4_023', 'PNG0A4_023', {'weight': 36963.0}),
('PNG0A4_024', 'PNG0A4_024', {'weight': 21270.0}),
('PNG0A4_028', 'PNG0A4_028', {'weight': 25804.0}),
('PNG0A4_029', 'PNG0A4_029', {'weight': 5271.0}),
('PNG0A4_031', 'PNG0A4_031', {'weight': 5928.0}),
('PNG3F7_008', 'PNG3F7_008', {'weight': 5427.0}),
('PNG3F7_012', 'PNG3F7_012', {'weight': 8196.0}),
('PNG3F7_015', 'PNG3F7_015', {'weight': 11268.0}),
('PNG3F7_017', 'PNG3F7_017', {'weight': 9249.0}),
('PNG3F7_022', 'PNG3F7_022', {'weight': 8579.0}),
('PNG3F7_026', 'PNG3F7_026', {'weight': 11848.0}),
('STM4C5_001', 'STM4C5_001', {'weight': 43879.0}),
('STM4C5_002', 'STM4C5_002', {'weight': 12144.0}),
('STM4C5_005', 'STM4C5_005', {'weight': 13696.0}),
('STM4C5_007', 'STM4C5_007', {'weight': 7302.0}),
('STM4C5_008', 'STM4C5_008', {'weight': 6422.0}),
('STM4C5_009', 'STM4C5_009', {'weight': 12208.0}),
('STM4C5_010', 'STM4C5_010', {'weight': 7481.0}),
('STM4C5_012', 'STM4C5_012', {'weight': 5290.0})]
nx.draw(G)
plt.draw()
plt.show()/Users/jasonblues/anaconda/lib/python3.6/site-packages/networkx/drawing/nx_pylab.py:126: MatplotlibDeprecationWarning: pyplot.hold is deprecated.
Future behavior will be consistent with the long-time default:
plot commands add elements without first clearing the
Axes and/or Figure.
b = plt.ishold()
/Users/jasonblues/anaconda/lib/python3.6/site-packages/networkx/drawing/nx_pylab.py:138: MatplotlibDeprecationWarning: pyplot.hold is deprecated.
Future behavior will be consistent with the long-time default:
plot commands add elements without first clearing the
Axes and/or Figure.
plt.hold(b)
/Users/jasonblues/anaconda/lib/python3.6/site-packages/matplotlib/__init__.py:917: UserWarning: axes.hold is deprecated. Please remove it from your matplotlibrc and/or style files.
warnings.warn(self.msg_depr_set % key)
/Users/jasonblues/anaconda/lib/python3.6/site-packages/matplotlib/rcsetup.py:152: UserWarning: axes.hold is deprecated, will be removed in 3.0
warnings.warn("axes.hold is deprecated, will be removed in 3.0")
families = list(nx.connected_component_subgraphs(G))nx.draw(families[4])
plt.draw()
plt.show()
families[4].nodes()/Users/jasonblues/anaconda/lib/python3.6/site-packages/networkx/drawing/nx_pylab.py:126: MatplotlibDeprecationWarning: pyplot.hold is deprecated.
Future behavior will be consistent with the long-time default:
plot commands add elements without first clearing the
Axes and/or Figure.
b = plt.ishold()
/Users/jasonblues/anaconda/lib/python3.6/site-packages/networkx/drawing/nx_pylab.py:138: MatplotlibDeprecationWarning: pyplot.hold is deprecated.
Future behavior will be consistent with the long-time default:
plot commands add elements without first clearing the
Axes and/or Figure.
plt.hold(b)
/Users/jasonblues/anaconda/lib/python3.6/site-packages/matplotlib/__init__.py:917: UserWarning: axes.hold is deprecated. Please remove it from your matplotlibrc and/or style files.
warnings.warn(self.msg_depr_set % key)
/Users/jasonblues/anaconda/lib/python3.6/site-packages/matplotlib/rcsetup.py:152: UserWarning: axes.hold is deprecated, will be removed in 3.0
warnings.warn("axes.hold is deprecated, will be removed in 3.0")
['3L0A3_011',
'ASI1E3_006',
'GL890823',
'PAL1D4_019',
'PNG0A4_012',
'JHB0A2_016',
'3L0A3_010',
'PAL0A1_012']
print(len(families))137
families[60].nodes()['ISBH3F3_003', 'CHN1D9_002']
toremove=[]
for family in families:
if len(family.nodes()) == 1:
toremove.append(family)
len(toremove)
92
for fm in toremove:
families.remove(fm)
len(families)45
bgcs={}
with open('/Users/jasonblues/Desktop/Project_files/bgcs.txt','r') as nodes:
for node in nodes:
infopair = node.split('\t')
bgcs[infopair[0]] = infopair[1]
print(infopair[1])
# if infopair[1] in Strains:
# Strains[infopair[1]].append(infopair[0])
# else:
# li = [infopair[0]]
# Strains[infopair[1]] = li
nodes.close()Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
Ga0081465_101 Moorea producens-heterotrophic bacteria co-culture from Cura?ao Moorea producens 3L (One linear chromosome and 78 unmapped contigs) : Ga0081465_101
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Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
Ga0081187_11 Moorea producens-heterotrophic bacteria co-culture from Jamaica Moorea producens JHB 22AUG96-1 (Final Draft of Linear Chromosome and 2 Linear Plasmid Scaffolds) : Ga0081187_11
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Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
Chromosome_contig_1_Moorea_producens_PAL_15AUG08-1
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Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
Ga0081470_101 Moorea bouillonii-heterotrophic bacteria co-culture from Papua New Guinea Moorea bouillonii PNG 19MAY05-8 (One linear chromosome and 12 unmapped contigs) : Ga0081470_101
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Nostoc sp. ATCC 53789
Nostoc sp. ATCC 53789
Lyngbya majuscula
Planktothrix agardhii NIVA-CYA 116
Arabidopsis thaliana
Moorea producens 3L
Moorea producens JHB
Moorea bouillonii PNG5-198
Cylindrospermum alatosporum CCALA 988
Streptomyces nodosus subsp. asukaensis
Lyngbya majuscula
Moorea producens 3L
Planktothrix agardhii NIVA-CYA 126
Anabaena sp. 90
Candidatus Entotheonella sp. (ex. Theonella swinhoei)
Planktothrix agardhii NIVA-CYA 126/8
Anabaena sp. 90
Heliobacillus mobilis
Heliophilum fasciatum
Microcystis aeruginosa NIES-98
Lyngbya majuscula
Nostoc sp. 152
Nostoc sp. CAVN2
Cylindrospermum licheniforme UTEX B 2014
Methylobacter marinus
Sporosarcina pasteurii
Methylomicrobium kenyense
Methylophaga alcalica
Methylomicrobium alcaliphilum
Methylomicrobium alcaliphilum 20Z
Cylindrospermopsis raciborskii AWT205
Aphanizomenon sp. 10E6
Planktothrix agardhii NIES-596
Trichodesmium erythraeum IMS101
Microcystis aeruginosa PCC 7005
uncultured Prochloron sp. 06037A
Sphingomonas sp. PB304
Sorangium cellulosum
Chondromyces crocatus
Streptoalloteichus sp. ATCC 53650
Sorangium cellulosum
Nostoc punctiforme PCC 73102
Lyngbya majuscula
Sorangium cellulosum
Sorangium cellulosum
Sorangium cellulosum So0157-2
Sorangium cellulosum
Moorea producens 19L
Methylophaga thalassica
Actinomadura kijaniata
Microcystis aeruginosa K-139
Microcystis sp. NIVA-CYA 172/5
Stigmatella aurantiaca Sg a15
Nocardiopsis sp. TFS65-07
Bacillus cereus ATCC 14579
Algoriphagus sp. KK10202C
Nostoc sp. 'Peltigera membranacea cyanobiont'
Chondromyces crocatus
Stigmatella aurantiaca
Anabaena variabilis ATCC 29413
[Oscillatoria] sp. PCC 6506
Rhodobacter sphaeroides
Streptomyces halstedii
Escherichia coli
Anabaena sp. Syke748
Streptomyces sp. KCTC 0041BP
Streptomyces bikiniensis
Streptomyces sp. A1(2016)
strain_list = []
for f in families:
nl = f.nodes()
for bgc in nl:
if bgc.find('_') != -1:
nomen = bgc.split('_')
if nomen[0] in strain_list:
print("in here already")
else:
strain_list.append(nomen[0])
print(nomen[0])JHB0A2
ASI1E3
in here already
PAL1D4
NAK4C8
3L0A3
PNG0A4
in here already
PNG3F7
PAL0A1
PAP1D6
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
ASX1E4
in here already
in here already
CHN1D9
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
ISBH3F3
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
PAB3F5
STM4C5
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
in here already
len(strain_list)14
p_axis = []
for strain in strain_list:
otu = []
for fami in families:
edges = fami.edges(data=True)
idnt = 0
avg = 1
for edge in edges:
if edge[0].split('_')[0] == strain:
idnt = idnt + int(edge[2]['weight'])
otu.append(int(idnt/avg))
p_axis.append(otu)
import numpy as np
print(np.matrix(p_axis))[[105069 0 24641 22095 5620 144662 14876 0 6786 9837
25350 46753 0 0 0 0 0 0 0 0
30814 6141 8621 20062 0 0 0 84876 0 52673
0 0 0 0 0 24528 37349 0 0 0
0 0 0 0 0]
[ 92668 0 9377 14426 17840 111959 0 0 0 0
0 6651 0 0 0 0 0 0 0 0
0 15036 0 0 0 28838 0 48287 0 23490
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0]
[ 97699 0 28832 0 11940 81358 7716 0 0 0
0 0 0 0 12659 0 32873 0 0 0
0 0 15341 44788 14337 5289 39762 0 0 25395
0 0 0 0 23272 0 0 0 0 15202
14546 0 0 27404 15194]
[ 43444 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 64192 0 0 0 0 0 0
0 0 0 0 0]
[118350 0 37202 22853 44748 0 0 7239 23545 6507
0 0 0 0 0 0 0 0 0 0
18938 21581 23392 59350 21871 54296 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0]
[138814 0 0 0 12752 100735 0 0 0 0
0 0 0 0 25788 0 0 0 0 0
0 27245 64898 18350 0 0 0 69419 0 0
0 0 0 0 0 0 0 0 25803 0
56283 0 10016 0 31996]
[152250 0 0 0 0 95903 47762 0 0 0
0 19355 0 0 0 0 0 0 0 0
0 74378 0 0 0 0 0 0 17007 0
0 0 0 0 0 0 0 11152 5207 0
48445 0 20189 12856 10205]
[199064 0 46690 0 41951 92838 0 0 0 12085
0 153078 0 0 181793 0 0 0 0 0
0 14893 48365 18996 12691 120739 34698 29368 0 33575
0 0 0 0 24027 10395 16037 0 0 19898
28687 33882 17836 28026 0]
[ 32748 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 31875
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 11846 0 24867 0]
[ 0 0 0 0 0 0 0 0 0 0
0 0 5050 11372 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 18374 0 0 0 0 0 0 0 0
0 0 0 0 0]
[ 0 0 0 0 0 9965 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
37424 0 0 0 0 0 0 0 0 0
0 0 0 0 0]
[ 0 0 0 0 0 85298 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 22639 0 0
0 0 46918 5350 7455 0 0 0 0 0
0 0 0 0 0]
[ 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 11665 0 0 0 0 0 6984 7745 0
0 0 0 0 0]
[ 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 16758 0 21128 0 0 0 0 0 0
0 0 0 0 0]]
for la in strain_list:
print(la)JHB0A2
ASI1E3
PAL1D4
NAK4C8
3L0A3
PNG0A4
PNG3F7
PAL0A1
PAP1D6
ASX1E4
CHN1D9
ISBH3F3
PAB3F5
STM4C5
from skbio.diversity import beta_diversity
bc_dm = beta_diversity("braycurtis", p_axis, strain_list)
print(bc_dm)14x14 distance matrix
IDs:
'JHB0A2', 'ASI1E3', 'PAL1D4', 'NAK4C8', '3L0A3', 'PNG0A4', 'PNG3F7', 'PAL0A1', ...
Data:
[[ 0. 0.38687321 0.54217974 0.88837458 0.60290989 0.4988155
0.5928271 0.56845265 0.9151704 1. 0.97224783 0.74252069
1. 1. ]
[ 0.38687321 0. 0.49188997 0.81754191 0.56983212 0.43307832
0.52391595 0.60210782 0.86061953 1. 0.95208685 0.59742425
1. 1. ]
[ 0.54217974 0.49188997 0. 0.86013846 0.55165751 0.51248419
0.56359718 0.50921147 0.81261678 1. 0.9644739 0.73927109
1. 1. ]
[ 0.88837458 0.81754191 0.86013846 0. 0.84689555 0.87402698
0.86038612 0.93453522 0.68658002 1. 1. 0.96113274
1. 0.70962466]
[ 0.60290989 0.56983212 0.55165751 0.84689555 0. 0.62681303
0.71283865 0.60907279 0.88329461 1. 1. 1. 1.
1. ]
[ 0.4988155 0.43307832 0.51248419 0.87402698 0.62681303 0.
0.38761388 0.5339197 0.90416645 1. 0.96833935 0.71207548
0.97454367 1. ]
[ 0.5928271 0.52391595 0.56359718 0.86038612 0.71283865 0.38761388
0. 0.60939757 0.85194588 1. 0.96454355 0.7499945
0.95494019 1. ]
[ 0.56845265 0.60210782 0.50921147 0.93453522 0.60907279 0.5339197
0.60939757 0. 0.89483159 1. 0.98426994 0.83364185
1. 1. ]
[ 0.9151704 0.86061953 0.81261678 0.68658002 0.88329461 0.90416645
0.85194588 0.89483159 0. 1. 1. 1. 1.
1. ]
[ 1. 1. 1. 1. 1. 1. 1.
1. 1. 0. 1. 1. 0.61872855
0.53886795]
[ 0.97224783 0.95208685 0.9644739 1. 1. 0.96833935
0.96454355 0.98426994 1. 1. 0. 0.90732345
1. 1. ]
[ 0.74252069 0.59742425 0.73927109 0.96113274 1. 0.71207548
0.7499945 0.83364185 1. 1. 0.90732345 0. 1.
0.94794353]
[ 1. 1. 1. 1. 1. 0.97454367
0.95494019 1. 1. 0.61872855 1. 1. 0.
0.63705663]
[ 1. 1. 1. 0.70962466 1. 1. 1.
1. 1. 0.53886795 1. 0.94794353 0.63705663
0. ]]
from skbio.stats.ordination import pcoa
bc_pc = pcoa(bc_dm)import pandas as pdsample_md = [('PAL0A1', ['Moorea']),('PAL1D4', ['Moorea']),('JHB0A2', ['Moorea']),('NAK4C8', ['Okeania']),('3L0A3', ['Moorea']),('ASI1E3', ['Moorea']),('ASX1E4', ['Leptolyngbya']),('PNG3F7', ['Moorea']),('PNG0A4', ['Moorea']),('CHN1D9', ['Kamptonema']),('PAP1D6', ['No 16S']),('ISBH3F3', ['Leptolyngbya']),('PAB3F5', ['Scytolyngbya']),('STM4C5', ['Leptolyngbya'])]
sample_md = pd.DataFrame.from_items(sample_md, columns=['Species'], orient='index')sample_md| Species | |
|---|---|
| PAL0A1 | Moorea |
| PAL1D4 | Moorea |
| JHB0A2 | Moorea |
| NAK4C8 | Okeania |
| 3L0A3 | Moorea |
| ASI1E3 | Moorea |
| ASX1E4 | Leptolyngbya |
| PNG3F7 | Moorea |
| PNG0A4 | Moorea |
| CHN1D9 | Kamptonema |
| PAP1D6 | No 16S |
| ISBH3F3 | Leptolyngbya |
| PAB3F5 | Scytolyngbya |
| STM4C5 | Leptolyngbya |
fig = bc_pc.plot(sample_md, 'Species',
... axis_labels=('PC 1', 'PC 2', 'PC 3'),
... title='Samples colored by species', cmap='jet', s=50)
toShow = bc_dm.data
ligand = bc_dm.ids
g = pd.DataFrame(toShow,ligand,ligand)
x = seaborn.clustermap(g)
plt.setp(x.ax_heatmap.get_yticklabels(), rotation=0) # For y axis
plt.setp(x.ax_heatmap.get_xticklabels(), rotation=90) # For x axis/Users/jasonblues/anaconda/lib/python3.6/site-packages/matplotlib/cbook.py:136: MatplotlibDeprecationWarning: The axisbg attribute was deprecated in version 2.0. Use facecolor instead.
warnings.warn(message, mplDeprecation, stacklevel=1)
[None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None]
l= pd.DataFrame(np.matrix(p_axis),ligand)
m = seaborn.clustermap(l)
plt.setp(m.ax_heatmap.get_yticklabels(), rotation=0) /Users/jasonblues/anaconda/lib/python3.6/site-packages/matplotlib/cbook.py:136: MatplotlibDeprecationWarning: The axisbg attribute was deprecated in version 2.0. Use facecolor instead.
warnings.warn(message, mplDeprecation, stacklevel=1)
[None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None]
