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Biopython: return chain but with the new chain ID already

I have script which can extract selected chains from a structure into a new file. I do it for 400+ structures. Because chainIDs of my selected chains can differ in the structures, I parse .yaml files where I store the corresponding chainIDs. This script is working, everything is fine but the next step is to rename the chains to be the same in each file. I used edited code from here:this. Basically it worked as well, however the problem is that e.g. my new chainID of chain1 is the same as original chainID of chain2, and the error occurrs:Cannot change id from U to T. The id T is already used for a sibling of this entity. Actually, this happened for many variables and it'd be too complicated doing it manually.
I've got idea that this could be solved by renaming the chainIDs right in the moment when I'm extracting it. Is it possible using Biopython like that? Could'nt find anything similar to my problem.
Simplified code for one structure (in the original one is one more loop for iterating over 400+ structures and its .yaml files):
with open(yaml_file, "r") as file:
proteins = yaml.load(file, Loader=yaml.FullLoader)
chain1= proteins["1_chain"].split(",")[0] #just for illustration that I have to parse the original chainIDs
chain2= proteins["2_chain"].split(",")[0]
structure = parser.get_structure("xxx", "xxx.cif" )[0]
for model in structure:
for chain in model:
class ChainSelect(Select):
def accept_chain(self, chain):
if chain.get_id() == '{}'.format(chain1):
return True # I thought that somewhere in this part could be added command renaming the chain to "A"
if chain.get_id() == '{}'.format(chain2):
return True #here I'd rename it "B"
else:
return False
io = MMCIFIO()
io.set_structure(structure)
io.save("new.cif" , ChainSelect())
Is it possible to somehow expand "return" command in a way that it would return the chain with desired chainID (e.g. A)? Note that the original chain ID can differ in the structures (thus I have to use .format(chainX))
I don't have any other idea how I'd get rid of the error that my desired chainID is already in sibling entity.

Parsing JSON in Python (Reverse dictionary search)

I'm using Python and "requests" to practice the use of API. I've had success with basic requests and parsing, but having difficulty with list comprehension for a more complex project.
I requested from a server and got a dictionary. From there, I used:
participant_search = (match1_request['participantIdentities'])
To convert the values of the participantIdentities key to get the following data:
[{'player':
{'summonerName': 'Crescent Bladex',
'matchHistoryUri': '/v1/stats/player_history/NA1/226413119',
'summonerId': 63523774,
'profileIcon': 870},
'participantId': 1},
My goal here is to combine the summonerId and participantId to one list. Which is easy normally, but the order of ParticipantIdentities is randomized. So the player I want information on will sometimes be 1st on the list, and other times third.
So I can't use the var = list[0] like how I would normally do.
I have access to summonerId, so I'm thinking I can search the list the summonerId, then somehow collect all the information around it. For instance, if I knew 63523774 then I could find the key for it. From here, is it possible to find the parent list of the key?
Any guidance would be appreciated.
Edit (Clarification):
Here's the data I'm working with: http://pastebin.com/spHk8VP0
At line 1691 is where participant the nested dictionary 'participantIdentities' is. From here, there are 10 dictionaries. These 10 dictionaries include two nested dictionaries, "player" and "participantId".
My goal is to search these 10 dictionaries for the one dictionary that has the summonerId. The summonerId is something I already know before I make this request to the server.
So I'm looking for some sort of "search" method, that goes beyond "true/false". A search method that, if a value is found within an object, the entire dictionary (key:value) is given.

Not sure if I properly understood you, but would this work?
for i in range(len(match1_request['participantIdentities'])):
if(match1_request['participantIdentities'][i]['summonerid'] == '63523774':
# do whatever you want with it.
i becomes the index you're searching for.

ds = match1_request['participantIdentities']
result_ = [d for d in ds if d["player"]["summonerId"] == 12345]
result = result_[0] if result_ else {}
See if it works for you.

You can use a dict comprehension to build a dict wich uses summonerIds as keys:
players_list = response['participantIdentities']
{p['player']['summonerId']: p['participantId'] for p in players_list}

I think what you are asking for is: "How do I get the stats for a given a summoner?"
You'll need a mapping of participantId to summonerId.
For example, would it be helpful to know this?
summoner[1] = 63523774
summoner[2] = 44610089
...
If so, then:
# This is probably what you are asking for:
summoner = {ident['participantId']: ident['player']['summonerId']
for ident in match1_request['participantIdentities']}
# Then you can do this:
summoner_stats = {summoner[p['participantId']]: p['stats']
for p in match1_request['participants']}
# And to lookup a particular summoner's stats:
print summoner_stats[44610089]
(ref: raw data you pasted)

Parsing multiple occurrences of an item into a dictionary

Attempting to parse several separate image links from JSON data through python, but having some issues drilling down to the right level, due to what I believe is from having a list of strings.
For the majority of the items, I've had success with the below example, pulling back everything I need. Outside of this instance, everything is a 1:1 ratio of keys:values, but for this one, there are multiple values associated with one key.
resultsdict['item_name'] = item['attribute_key']
I've been adding it all to a resultsdict={}, but am only able to get to the below sample string when I print.
INPUT:
for item in data['Item']:
resultsdict['images'] = item['Variations']['Pictures']
OUTPUT (only relevant section):
'images': [{u'VariationSpecificPictureSet': [{u'PictureURL': [u'http//imagelink1'], u'VariationSpecificValue': u'color1'}, {u'PictureURL': [u'http//imagelink2'], u'VariationSpecificValue': u'color2'}, {u'PictureURL': [u'http//imagelink3'], u'VariationSpecificValue': u'color3'}, {u'PictureURL': [u'http//imagelink4'], u'VariationSpecificValue': u'color4'}]
I feel like I could add ['VariationPictureSet']['PictureURL'] at the end of my initial input, but that throws an error due to the indices not being integers, but strings.
Ideally, I would like to see the output as a simple comma-separated list of just the URLs, as follows:
OUTPUT:
'images': http//imagelink1, http//imagelink2, http//imagelink3, http//imagelink4

An answer to your comment that required a bit of code to it.
When using
for item in data['Item']:
resultsdict['images'] = item['Variations']['Pictures']
you get a list with one element, so I recommend using this
for item in data['Item']:
resultsdict['images'] = item['Variations']['Pictures'][0]
now you can use
for image in resultsdict['images']['VariationsSpecificPictureSet']:
print(image['PictureUR‌​L'])

Thanks for the help, #uzzee, it's appreciated. I kept tinkering with it and was able to pull the continuous string of all the image URLs with the following code.
resultsdict['images'] = sum([x['PictureURL'] for x in item['variations']['Pictures'][0]['VariationSpecificPictureSet']],[])
Without the sum it looks like this and pulls in the whole list of lists...
resultsdict['images'] = [x['PictureURL'] for x in item['variations']['Pictures'][0]['VariationSpecificPictureSet']]

Parsing data with pattern

I'm parsing some data with the pattern as follows:
tagA:
titleA
dataA1
dataA2
dataA3
...
tagB:
titleB
dataB1
dataB2
dataB3
...
tagC:
titleC
dataC1
dataC2
...
...
These tags are stored in a list list_of_tags, if I iterate through the list, I can get all the tags; also, if iterating through the tags, I can get the title and the data associated with the title.
The tags in my data are pretty much something like <div>, so they are not useful to me; what I'm trying to do is to construct a dictionary which uses titles as keys and datas as a list of values.
The constructed dictionary would look like:
{
titleA: [dataA1, dataA2, dataA3...],
titleB: [dataB1, dataB2, dataB3...],
...
}
Notice every tag only contains one title and some datas, and title always comes before data.
So here are my working codes:
Method 1:
result = {}
for tag in list_of_tags:
list_of_values = []
for idx, elem in enumerate(tag):
if not idx:
key = elem
else:
construct_list_of_values()
update_the_dictionary()
Actually, method 1 works fine and gives me my desired result; however, if I put that piece of codes in PyCharm, it warns me that "Local variable 'key' might be referenced before assignment" at the last line. Hence, I try another approach:
Method 2:
result = {tag[0]: tag[1:] for tag in list_of_tags}
Method 2 works fine if tags are lists, but I also want the code to work normally if tags are generators ('generator' object is not subscriptable will occur with method 2)
In order to work with generators, I come up with:
Method 3:
key_val_list = [(next(tag), list(tag)) for tag in list_of_tags]
result = dict(key_val_list)
Method 3 also works; but I cannot write this in dictionary comprehension ({next(tag): list(tag) for tag in list_of_tags} would give StopIteration exception because list(tag) will be evaluated first)
So, my question is, is there an elegant way for dealing with this pattern which could work no matter tags are lists or generators? (method 1 seems to work for both, but I don't know if I should ignore the warning PyCharms gives; the other two methods looks more concise, but one can only work on lists while the other can only work on generators)
Sorry for the long question, thanks for the patience!

I guess the reason why PyCharm is giving you a warning is that you are using key in update_the_dictionary, but key could be left unassigned if tag does not contain at least one element. You might have the knowledge that the title will always be in the list, but the static analyzer is not able to infer that from the context.
If you are using Python 3, you might want to try using PEP 3132 - Extended Iterable Unpacking. It should work for both lists and generators.
e.g.
title, *data = tag

Using Strings to Name Hash Keys?

I'm working through a book called "Head First Programming," and there's a particular part where I'm confused as to why they're doing this.
There doesn't appear to be any reasoning for it, nor any explanation anywhere in the text.
The issue in question is in using multiple-assignment to assign split data from a string into a hash (which doesn't make sense as to why they're using a hash, if you ask me, but that's a separate issue). Here's the example code:
line = "101;Johnny 'wave-boy' Jones;USA;8.32;Fish;21"
s = {}
(s['id'], s['name'], s['country'], s['average'], s['board'], s['age']) = line.split(";")
I understand that this will take the string line and split it up into each named part, but I don't understand why what I think are keys are being named by using a string, when just a few pages prior, they were named like any other variable, without single quotes.
The purpose of the individual parts is to be searched based on an individual element and then printed on screen. For example, being able to search by ID number and then return the entire thing.
The language in question is Python, if that makes any difference. This is rather confusing for me, since I'm trying to learn this stuff on my own.
My personal best guess is that it doesn't make any difference and that it was personal preference on part of the authors, but it bewilders me that they would suddenly change form like that without it having any meaning, and further bothers me that they don't explain it.
EDIT: So I tried printing the id key both with and without single quotes around the name, and it worked perfectly fine, either way. Therefore, I'd have to assume it's a matter of personal preference, but I still would like some info from someone who actually knows what they're doing as to whether it actually makes a difference, in the long run.
EDIT 2: Apparently, it doesn't make any sense as to how my Python interpreter is actually working with what I've given it, so I made a screen capture of it working https://www.youtube.com/watch?v=52GQJEeSwUA

I don't understand why what I think are keys are being named by using a string, when just a few pages prior, they were named like any other variable, without single quotes
The answer is right there. If there's no quote, mydict[s], then s is a variable, and you look up the key in the dict based on what the value of s is.
If it's a string, then you look up literally that key.
So, in your example s[name] won't work as that would try to access the variable name, which is probably not set.
EDIT: So I tried printing the id key both with and without single
quotes around the name, and it worked perfectly fine, either way.
That's just pure luck... There's a built-in function called id:
>>> id
<built-in function id>
Try another name, and you'll see that it won't work.

Actually, as it turns out, for dictionaries (Python's term for hashes) there is a semantic difference between having the quotes there and not.
For example:
s = {}
s['test'] = 1
s['othertest'] = 2
defines a dictionary called s with two keys, 'test' and 'othertest.' However, if I tried to do this instead:
s = {}
s[test] = 1
I'd get a NameError exception, because this would be looking for an undefined variable called test whose value would be used as the key.
If, then, I were to type this into the Python interpreter:
>>> s = {}
>>> s['test'] = 1
>>> s['othertest'] = 2
>>> test = 'othertest'
>>> print s[test]
2
>>> print s['test']
1
you'll see that using test as a key with no quotes uses the value of that variable to look up the associated entry in the dictionary s.
Edit: Now, the REALLY interesting question is why using s[id] gave you what you expected. The keyword "id" is actually a built-in function in Python that gives you a unique id for an object passed as its argument. What in the world the Python interpreter is doing with the expression s[id] is a total mystery to me.
Edit 2: Watching the OP's Youtube video, it's clear that he's staying consistent when assigning and reading the hash about using id or 'id', so there's no issue with the function id as a hash key somehow magically lining up with 'id' as a hash key. That had me kind of worried for a while.