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Can't seem to figure out how to put all of the lists items from a loop into 1 list
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Can't seem to figure out how to put all of the lists items from a loop into 1 list
Cosmosso
Programmer named Tim
Posts: 11
Threads: 3
Joined: Dec 2019
Reputation: 0
#1
Feb-21-2020, 01:40 PM (This post was last modified: Feb-21-2020, 02:52 PM by Cosmosso.)
So I have this code:
Btw it uses BioPython

from Bio import SeqIO
import collections as C
import requests as R
import itertools

proteins2 = list(SeqIO.parse("2-proteins-tryout.gb","gb"))
#print(proteins2)

for protein in proteins2:
    #print(protein)
    for f in protein.features:
        if f.type == "BLAST":
            if "db_xref" in f.qualifiers:
                idss = f.qualifiers["db_xref"]
                print(idss)
                
            #Read file
            for idd in idss:
                
                fullProtein = SeqIO.read(f'{idd}.xml','uniprot-xml')
                #print(fullProtein)
        
                goTerms = []
                for ref in fullProtein.dbxrefs:
                    if ref.startswith('GO:'):
                        goTerm = ref[3:]
                        goTerms.append(goTerm)
                print(goTerms)
                
                allTerms = []
                for terms in goTerms:
                     allTerms.append(terms)
                print(allTerms)
For now it does what I want and gives me this results:

Quote:['P52326', 'P26480', 'P52327', 'P0A2E3', 'P00579', 'O24744', 'P32001', 'P57163', 'Q89B10', 'Q83BB6', 'Q9PDM9', 'Q87DT7', 'Q8PG33', 'P43766', 'Q8P4H2', 'P52325', 'P33452', 'Q59753', 'Q2K619', 'P52324', 'D5AQI9', 'P17531', 'P0CZ15', 'Q1RKH7', 'Q92FZ8', 'Q4UJT1', 'P33451', 'Q68VQ5']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005829', 'GO:0009408', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0006352', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987', 'GO:0030435']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005829', 'GO:0009408', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0006352', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987', 'GO:0030435']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987']
['Q9RR29', 'D4GU70', 'P08075', 'A6VG23', 'A6UP85', 'A4FX98', 'Q58501', 'Q6LYB5', 'A6UUQ4', 'Q975F9', 'Q9Y725', 'Q6FRY2', 'P0C5I2', 'O93827', 'Q8BTZ7', 'Q9Y5P6', 'Q752H4', 'P41940', 'Q6BN12', 'O74624', 'Q2YDJ9', 'A2VD83', 'Q4U3E8']
['GO:0008879', 'GO:0017000', 'GO:0046872']
['GO:0006486', 'GO:0016779', 'GO:0045232', 'GO:0046872']
['GO:0008879', 'GO:0019872', 'GO:0046872']
['GO:0003977', 'GO:0006048', 'GO:0019134']
['GO:0003977', 'GO:0006048', 'GO:0019134']
['GO:0003977', 'GO:0006048', 'GO:0019134']
['GO:0003977', 'GO:0006048', 'GO:0019134']
['GO:0003977', 'GO:0006048', 'GO:0019134']
['GO:0003977', 'GO:0006048', 'GO:0019134']
['GO:0000166', 'GO:0003977', 'GO:0003983', 'GO:0006048', 'GO:0008879', 'GO:0019134']
['GO:0000032', 'GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0006486', 'GO:0007049', 'GO:0009298']
['GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0007049', 'GO:0009298']
['GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0009298']
['GO:0000032', 'GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0005886', 'GO:0007049', 'GO:0009298', 'GO:0009986', 'GO:0030445']
['GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0005739', 'GO:0009298']
['GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0009298']
['GO:0000032', 'GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0006486', 'GO:0007049', 'GO:0009272', 'GO:0009298', 'GO:0051286']
['GO:0000032', 'GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0006486', 'GO:0007049', 'GO:0009298']
['GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0007049', 'GO:0009272', 'GO:0009298', 'GO:0051286']
['GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0007049', 'GO:0009298']
['GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0009298']
['GO:0004475', 'GO:0005525', 'GO:0009298']
['GO:0004475', 'GO:0005525', 'GO:0005737', 'GO:0007049', 'GO:0009298', 'GO:0070590']
['P14738', 'Q2FE03', 'Q6G6H3', 'A7X6I5', 'Q6GDU5', 'Q2YW62', 'A0A0H2XKG3']
['GO:0001968', 'GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020', 'GO:0070051', 'GO:0098630']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['P08320', 'P39347', 'P37317', 'P37326', 'P32053', 'P76542']
['GO:0003677', 'GO:0006310', 'GO:0015074', 'GO:0016740', 'GO:0016787', 'GO:0044826', 'GO:0046718', 'GO:0075713']
['GO:0003677', 'GO:0006310', 'GO:0015074', 'GO:0044826', 'GO:0046718', 'GO:0075713']
['GO:0003677', 'GO:0006310', 'GO:0015074', 'GO:0016740', 'GO:0016787', 'GO:0044826', 'GO:0046718', 'GO:0075713']
['GO:0006310', 'GO:0015074', 'GO:0032359', 'GO:0042802', 'GO:0043565', 'GO:0044826', 'GO:0046718', 'GO:0075713']
['GO:0003677', 'GO:0008979', 'GO:0032359', 'GO:0044826', 'GO:0046718']
['GO:0003677', 'GO:0006310', 'GO:0015074', 'GO:0044826', 'GO:0046718', 'GO:0075713']
['P69451', 'Q8XDR6', 'P63521', 'Q8ZES9', 'P46450', 'P94547', 'O07610', 'Q0DV32', 'P41636', 'Q42982', 'Q54P79', 'Q54P77', 'P14912', 'P14913', 'O24146', 'Q54P78']
['GO:0003996', 'GO:0004467', 'GO:0005504', 'GO:0005524', 'GO:0005737', 'GO:0005829', 'GO:0006629', 'GO:0006631', 'GO:0006635', 'GO:0006637', 'GO:0008654', 'GO:0009411', 'GO:0009898', 'GO:0015908', 'GO:0070538', 'GO:0102391']
['GO:0003996', 'GO:0004467', 'GO:0005524', 'GO:0016020', 'GO:0102391']
['GO:0003996', 'GO:0004467', 'GO:0005524', 'GO:0016020', 'GO:0102391']
['GO:0003996', 'GO:0004467', 'GO:0005524', 'GO:0016020', 'GO:0102391']
['GO:0003996', 'GO:0004467', 'GO:0005524', 'GO:0016020', 'GO:0102391']
['GO:0003996', 'GO:0004467', 'GO:0005524', 'GO:0102391']
['GO:0003996', 'GO:0004467', 'GO:0005524', 'GO:0006635', 'GO:0102391']
['GO:0004321', 'GO:0005524', 'GO:0005777', 'GO:0009695', 'GO:0016874']
['GO:0005524', 'GO:0009698', 'GO:0016207']
['GO:0005524', 'GO:0009698', 'GO:0010584', 'GO:0016207']
['GO:0005524', 'GO:0009698', 'GO:0016207']
['GO:0005524', 'GO:0009698', 'GO:0016207']
['GO:0005524', 'GO:0009698', 'GO:0016207']
['GO:0005524', 'GO:0009698', 'GO:0016207']
['GO:0005524', 'GO:0009698', 'GO:0016207']
['GO:0005524', 'GO:0009698', 'GO:0016207']

Everything that starts without GO: are just IDs xml {idd}.xml files and every fle has those GO: numbers. Basically (looking at the begging): for this ID 'P52326' we get this ['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987'], for the other ID 'P26480' we get the other GO: numbers ['GO:0001123', 'GO:0003677', 'GO:0003700', 'GO:0005737', 'GO:0016987'] and so.

What I am try to do is I want to put every GO: numbers into one list. So lets say this whole thing:
Quote:['GO:0001968', 'GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020', 'GO:0070051', 'GO:0098630']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
['GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']

Into a list, like so:
['GO:0001968', 'GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020', 'GO:0070051', 'GO:0098630','GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020','GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020','GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020','GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020','GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020','GO:0005576', 'GO:0005618', 'GO:0007155', 'GO:0009405', 'GO:0016020']
so I try to iterate it and put into in a list:

allTerms = []
for terms in goTerms:
   allTerms.append(terms )
print(allTerms)
But it just gives me the same results as goTerms variable does.

I need the list, is because I need to find the duplicate GO: numbers in all of the ID's xml files. Like for example these IDs (or xml file) ['P52326', 'P26480', 'P52327', 'P0A2E3', 'P00579', 'O24744', 'P32001', 'P57163', 'Q89B10', 'Q83BB6', 'Q9PDM9', 'Q87DT7', 'Q8PG33', 'P43766', 'Q8P4H2', 'P52325', 'P33452', 'Q59753', 'Q2K619', 'P52324', 'D5AQI9', 'P17531', 'P0CZ15', 'Q1RKH7', 'Q92FZ8', 'Q4UJT1', 'P33451', 'Q68VQ5'] need to find the GO: numbers that are the same.
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Gribouillis

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Posts: 4,485
Threads: 68
Joined: Jan 2018
Reputation: 330
#2
Feb-21-2020, 01:43 PM
Use the extend() method or list comprehension
allTerms = []
for terms in goTerms:
   allTerms.extend(terms )
print(allTerms)
or
allTerms = [t for terms in goTerms for t in terms]
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Cosmosso
Programmer named Tim
Posts: 11
Threads: 3
Joined: Dec 2019
Reputation: 0
#3
Feb-21-2020, 02:18 PM (This post was last modified: Feb-21-2020, 02:18 PM by Cosmosso.)
(Feb-21-2020, 01:43 PM)Gribouillis Wrote: Use the extend() method or list comprehension
allTerms = []
for terms in goTerms:
   allTerms.extend(terms )
print(allTerms)
or
allTerms = [t for terms in goTerms for t in terms]

It gives me this instead (its a snip it):
Quote:['G', 'O', ':', '0', '0', '0', '1', '1', '2', '3', 'G', 'O', ':', '0', '0', '0', '3', '6', '7', '7', 'G', 'O', ':', '0', '0', '0', '3', '7', '0', '0', 'G', 'O', ':', '0', '0', '0', '5', '7', '3', '7', 'G', 'O', ':', '0', '0', '1', '6', '9', '8', '7']
['G', 'O', ':', '0', '0', '0', '1', '1', '2', '3', 'G', 'O', ':', '0', '0', '0', '3', '6', '7', '7', 'G', 'O', ':', '0', '0', '0', '3', '7', '0', '0', 'G', 'O', ':', '0', '0', '0', '5', '7', '3', '7', 'G', 'O', ':', '0', '0', '1', '6', '9', '8', '7']
['G', 'O', ':', '0', '0', '0', '1', '1', '2', '3', 'G', 'O', ':', '0', '0', '0', '3', '6', '7', '7', 'G', 'O', ':', '0', '0', '0', '3', '7', '0', '0', 'G', 'O', ':', '0', '0', '0', '5', '7', '3', '7', 'G', 'O', ':', '0', '0', '1', '6', '9', '8', '7']
['G', 'O', ':', '0', '0', '0', '1', '1', '2', '3', 'G', 'O', ':', '0', '0', '0', '3', '6', '7', '7', 'G', 'O', ':', '0', '0', '0', '3', '7', '0', '0', 'G', 'O', ':', '0', '0', '0', '5', '7', '3', '7', 'G', 'O', ':', '0', '0', '1', '6', '9', '8', '7']
['G', 'O', ':', '0', '0', '0', '1', '1', '2', '3', 'G', 'O', ':', '0', '0', '0', '3', '6', '7', '7', 'G', 'O', ':', '0', '0', '0', '3', '7', '0', '0', 'G', 'O', ':', '0', '0', '0', '5', '8', '2', '9', 'G', 'O', ':', '0', '0', '0', '9', '4', '0', '8', 'G', 'O', ':', '0', '0', '1', '6', '9', '8', '7']
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Gribouillis

Super Moderators
Posts: 4,485
Threads: 68
Joined: Jan 2018
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#4
Feb-21-2020, 02:26 PM
I thought goTerms was a list of lists. What is it exactly?
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Cosmosso
Programmer named Tim
Posts: 11
Threads: 3
Joined: Dec 2019
Reputation: 0
#5
Feb-21-2020, 02:40 PM
(Feb-21-2020, 02:26 PM)Gribouillis Wrote: I thought goTerms was a list of lists. What is it exactly?

Its a list of GO numbers for every ID in a list (['P52326', 'P26480', 'P52327', 'P0A2E3', 'P00579', 'O24744', 'P32001', 'P57163', 'Q89B10', 'Q83BB6', 'Q9PDM9', 'Q87DT7', 'Q8PG33', 'P43766', 'Q8P4H2', 'P52325', 'P33452', 'Q59753', 'Q2K619', 'P52324', 'D5AQI9', 'P17531', 'P0CZ15', 'Q1RKH7', 'Q92FZ8', 'Q4UJT1', 'P33451', 'Q68VQ5'])

I also checked the type:
print(type(goTerms))
<class 'list'>
<class 'list'>
<class 'list'>
....
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