Nested dictionary - python

Question

I have three large lists and I want to create a nested dictionary as so:

dic={"gene":{"isoform1":positions1,"isoform2":positions2}, "gene2":{"isoform1:positions1, "isoform2":positions2...etc}

I was able to get the isoforms and positions into one dictionary as so:

Dictionary = dict(zip(Isoform, ExonPos))

However, I don't know how to add the gene name as the key to the dictionary of Isoform and ExonPos

Also, is there a way to use a list as the values to a key?

Kind of like this:

Dictionary = {key:[1,2,3,4,5], key2:[3,5,4]}

Here are my sample lists:

Genes = ['A2M', 'ACADM', 'ACADS', 'ACADVL', 'ACAT1', 'ACVRL1', 'PSEN1', 'ADA', 'SGCA', 'ADRB2', 'ADSL', 'AGA', 'AGT', 'AGXT', 'ALAD', 'ALAS2', 'ABCD1', 'ALDOA', 'ALDOB']

Isoforms = ['NM_000014', 'NM_000016', 'NM_000017', 'NM_000018', 'NM_000019', 'NM_000020', 'NM_000021', 'NM_000022', 'NM_000023', 'NM_000024', 'NM_000026', 'NM_000027', 'NM_000029', 'NM_000030', 'NM_000031', 'NM_000032', 'NM_000033', 'NM_000034']

ExonPos = ['9220303,9220778,9221335,9222340,9223083,9224954,9225248,9227155,9229351,9229941,9230296,9231839,9232234,9232689,9241795,9242497,9242951,9243796,9246060,9247568,9248134,9251202,9251976,9253739,9254042,9256834,9258831,9259086,9260119,9261916,9262462,9262909,9264754,9264972,9265955,9268359,', '76190031,76194085,76198328,76198537,76199212,76200475,76205664,76211490,76215103,76216135,76226806,76228376,', '121163570,121164828,121174788,121175158,121175639,121176082,121176335,121176622,121176942,121177098,', '7123149,7123440,7123782,7123922,7124084,7124242,7124856,7125270,7125495,7125985,7126451,7126962,7127131,7127286,7127464,7127639,7127798,7127960,7128127,7128275,', '107992257,108002633,108004546,108004947,108005868,108009624,108010791,108012331,108013163,108014709,108016928,108017996,', '52301201,52306253,52306882,52307342,52307757,52308222,52309008,52309819,52312768,52314542,', '73603142,73614502,73614674,73637504,73640273,73653560,73659351,73664738,73673093,73678476,73683833,73685841,', '43248162,43248939,43249658,43251228,43251469,43251647,43252842,43254209,43255096,43257687,43264867,43280215,', '48243365,48244728,48244942,48245307,48245734,48246452,48247503,48248000,48252617,48253072,', '148206155,', '40742503,40745835,40749076,40750251,40754867,40755263,40756405,40757276,40757491,40758984,40760279,40760883,40762439,']

The lists are of different lengths, I'm not sure how isoforms match to genes, genes match to exonpos and isoforms to exonpos. — Matt Davidson
– Matt Davidson, Commented Apr 16, 2015 at 14:35
How are you determining which Gene pairs with which Isoform or ExonPos? — ILostMySpoon
– ILostMySpoon, Commented Apr 16, 2015 at 14:37
ILostMySpoon, your comment made me realize I did something incorrectly. Thank you — cosmictypist
– cosmictypist, Commented Apr 16, 2015 at 14:43

dawg · Accepted Answer · 2015-04-16 14:59:51Z

You can use a dict comprehension:

>>> dic={gene:{iso:exon.split(',')} for gene, iso, exon in zip(Genes, Isoforms, ExonPos)}
>>> dic
{'ACADVL': {'NM_000018': ['7123149', '7123440', '7123782', '7123922', '7124084', '7124242', '7124856', '7125270', '7125495', '7125985', '7126451', '7126962', '7127131', '7127286', '7127464', '7127639', '7127798', '7127960', '7128127', '7128275', '']}, 'PSEN1': {'NM_000021': ['73603142', '73614502', '73614674', '73637504', '73640273', '73653560', '73659351', '73664738', '73673093', '73678476', '73683833', '73685841', '']}, 'SGCA': {'NM_000023': ['48243365', '48244728', '48244942', '48245307', '48245734', '48246452', '48247503', '48248000', '48252617', '48253072', '']}, 'ACADM': {'NM_000016': ['76190031', '76194085', '76198328', '76198537', '76199212', '76200475', '76205664', '76211490', '76215103', '76216135', '76226806', '76228376', '']}, 'ACAT1': {'NM_000019': ['107992257', '108002633', '108004546', '108004947', '108005868', '108009624', '108010791', '108012331', '108013163', '108014709', '108016928', '108017996', '']}, 'ADRB2': {'NM_000024': ['148206155', '']}, 'ACADS': {'NM_000017': ['121163570', '121164828', '121174788', '121175158', '121175639', '121176082', '121176335', '121176622', '121176942', '121177098', '']}, 'ACVRL1': {'NM_000020': ['52301201', '52306253', '52306882', '52307342', '52307757', '52308222', '52309008', '52309819', '52312768', '52314542', '']}, 'ADA': {'NM_000022': ['43248162', '43248939', '43249658', '43251228', '43251469', '43251647', '43252842', '43254209', '43255096', '43257687', '43264867', '43280215', '']}, 'ADSL': {'NM_000026': ['40742503', '40745835', '40749076', '40750251', '40754867', '40755263', '40756405', '40757276', '40757491', '40758984', '40760279', '40760883', '40762439', '']}, 'A2M': {'NM_000014': ['9220303', '9220778', '9221335', '9222340', '9223083', '9224954', '9225248', '9227155', '9229351', '9229941', '9230296', '9231839', '9232234', '9232689', '9241795', '9242497', '9242951', '9243796', '9246060', '9247568', '9248134', '9251202', '9251976', '9253739', '9254042', '9256834', '9258831', '9259086', '9260119', '9261916', '9262462', '9262909', '9264754', '9264972', '9265955', '9268359', '']}}

Or, if you want a string vs a list:

>>> dic={gene:{iso:exon} for gene, iso, exon in zip(Genes, Isoforms, ExonPos)}
>>> dic
{'ACADVL': {'NM_000018': '7123149,7123440,7123782,7123922,7124084,7124242,7124856,7125270,7125495,7125985,7126451,7126962,7127131,7127286,7127464,7127639,7127798,7127960,7128127,7128275,'}, 'PSEN1': {'NM_000021': '73603142,73614502,73614674,73637504,73640273,73653560,73659351,73664738,73673093,73678476,73683833,73685841,'}, 'SGCA': {'NM_000023': '48243365,48244728,48244942,48245307,48245734,48246452,48247503,48248000,48252617,48253072,'}, 'ACADM': {'NM_000016': '76190031,76194085,76198328,76198537,76199212,76200475,76205664,76211490,76215103,76216135,76226806,76228376,'}, 'ACAT1': {'NM_000019': '107992257,108002633,108004546,108004947,108005868,108009624,108010791,108012331,108013163,108014709,108016928,108017996,'}, 'ADRB2': {'NM_000024': '148206155,'}, 'ACADS': {'NM_000017': '121163570,121164828,121174788,121175158,121175639,121176082,121176335,121176622,121176942,121177098,'}, 'ACVRL1': {'NM_000020': '52301201,52306253,52306882,52307342,52307757,52308222,52309008,52309819,52312768,52314542,'}, 'ADA': {'NM_000022': '43248162,43248939,43249658,43251228,43251469,43251647,43252842,43254209,43255096,43257687,43264867,43280215,'}, 'ADSL': {'NM_000026': '40742503,40745835,40749076,40750251,40754867,40755263,40756405,40757276,40757491,40758984,40760279,40760883,40762439,'}, 'A2M': {'NM_000014': '9220303,9220778,9221335,9222340,9223083,9224954,9225248,9227155,9229351,9229941,9230296,9231839,9232234,9232689,9241795,9242497,9242951,9243796,9246060,9247568,9248134,9251202,9251976,9253739,9254042,9256834,9258831,9259086,9260119,9261916,9262462,9262909,9264754,9264972,9265955,9268359,'}}

I just realized that this won't work if there are Isoforms that have the same gene name. Is there any way to overcome this?
If the isoforms are the same but with more than one list entry, what is the result you are looking for?

giaosudau · Accepted Answer · 2015-04-16 14:43:51Z

2

Just zip 2 times and here it is

Dictionary = dict(zip(Genes, [{i[0]: i[1:]} for i in zip(Isoforms, ExonPos)]))


print(Dictionary)

edited Apr 16, 2015 at 14:43

answered Apr 16, 2015 at 14:33

giaosudau

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Comments

Chiyaan Suraj · Accepted Answer · 2015-04-16 14:51:23Z

1

answering your 2nd question. yes you obviously have a dictionary with values as lists look at this

>>> dic = {}
>>> dic = {"key1":[1,2,3]}
>>> dic.update({"key2":[4,5,6]})
>>> dic['key3'] = [7,8,9]
>>> dic
{'key3': [7, 8, 9], 'key2': [4, 5, 6], 'key1': [1, 2, 3]}

answering your 1st question. Since you told that you already have got 2 other lists zipped in a way you want, In a very crude You just have to do something like this

newdictionary = {}
newdictionary.update({gene[index]:zippeddictionary[index]})

answered Apr 16, 2015 at 14:51

Chiyaan Suraj

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Comments

selurvedu · Accepted Answer · 2015-04-16 14:40:06Z

0

result = {}
for gene, iso, exon in zip(Genes, Isoforms, ExonPos):
    result[gene] = {iso: exon.split(',')}

If you don't need to convert comma-seperated list of values from string to list, then use exon instead of exon.split(',').

answered Apr 16, 2015 at 14:40

selurvedu

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