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QUESTION
I apologize if the question has been asked before, but I have been searching for days and could not find a solution in Python.
I have a large fasta file, containing headers and sequences.
...ANSWER
Answered 2021-Mar-03 at 19:03If the lines all have that same format, so that there are 6 space-separated fields before the sequences, then this is easy. You will have to store all of the unique values in memory.
QUESTION
I had no error. Always refresh cache and local memory.
Resources for Verifying Translations:
[NCBI Protein Translation Tool][1] (Validation)
[Text Compare][2] (Verification)
[Solution Inspiration][3]
300 DNA chars -> 100 protein chars.
...ANSWER
Answered 2021-Mar-31 at 09:38I think the issue is with you mixing up variable names - your translation code appends to protein
but you print output_protein
which I assume is actually created somewhere else in your code(?). Also, you first edit the variable dna_sequence
but iterate over dna
which I assume is also defined elsewhere and maybe doesn't match dna_sequence
.
After editing the variable names I can use your code to get the same translation as the NCBI tool.
QUESTION
I have a list of pandas data frames that I got applying the groupby function and I want to add to them a new column with the frequency of each kmer. I did that with a loop but I got a message warning that I need to use df.loc[index, col_names]. Here it is a link to one example of the csv file: https://drive.google.com/file/d/17vYbIEza7l-1mFnavGGO1QjCjPdhxG7C/view?usp=sharing
...ANSWER
Answered 2021-Apr-05 at 12:28It's an error related SettingWithCopyWarning. It's important — read up on it here. Usually you can avoid it with .loc
and by avoiding repeat-slicing, but in some cases where you have to slice repeatedly you can get around it by ending .copy()
to the end of the expression. You can learn when and why this is important via the link. For a more precise answer for how this is emerging from you'll code, you'll need to show us an MRCE of your code.
QUESTION
I get data from another page with
...ANSWER
Answered 2021-Apr-05 at 05:37You set the BindingContext of the Sdeduction instance to the check instance, and then navigates to the Sdeduction. It's the right way to pass data when navigating.
But when you check for Age as page load in Sdeduction() method, it always get 0 before the Sdeduction page set the BindingContext. You nned to load in OnAppearing() method.
MainPage:
xaml:
QUESTION
According to this article, we can see the following in the paper:
Can we treat the above X.509 grammar as this: the SEQUENCE and SET elements are non-terminals, while the rest are terminals. We could therefore also rewrite the grammar as follows:
...
ANSWER
Answered 2021-Mar-16 at 03:26Can we treat the above X.509 grammar as this: the
SEQUENCE
andSET
elements are non-terminals, while the rest are terminals?
I'd say that's basically a category error. But even if it were not, it's not a particularly useful model for what ASN.1 types are.
A terminal is an atomic unit with no grammatical structure. (At least, that's one intuition for a terminal. In Chomskyian context-free grammars, the definition is even simpler: it's a symbol which does not appear on the left-hand side of any production.) But many of the types in that extract do have definitions in the X.509 documents, so they certainly aren't terminals. Arguably, BIT STRING
is a terminal, since it's more or less a primitive ASN.1 type, but in concrete grammars in the BER and DER profiles, it's actually a non-terminal, too.
"ASN" is an abbreviation for "Abstract Syntax Notation"; avoiding the ambiguity of English noun phrases, it is a notation for writing abstract syntaxes. ASN.1 abstracts away from the concrete syntax. It's a way of focussing on the structural interrelationships inside a complex data object without getting bogged down in the real-world mechanics of parsing or generating sentences. In that sense, it's more or less the mirror image of a Chomskyian grammar; Chomsky's goal (in the famous paper which gave rise to the hierarchy) was to abstract away from the semantics, leaving only the mechanics of parsing and generating sentences. It's in this sense that I think the question here is a category error; it's attempting to unify two conceptual systems whose essence is to separate the concepts.
As a final note, I think you may be misunderstanding the ASN.1 concept of SEQUENCE
, which is different from a SEQUENCE OF
. A SEQUENCE
is, roughly speaking, an abstraction of something like a C struct
; it's a single composite type with named members. It's not a repetition. if you want to express the concept of an ordered list of objects of the same type, you use a SEQUENCE OF
, which is vaguely similar to a C array, although the length constraints can be a lot more flexible.
SET
and SET OF
are the same, except that they are unordered. I don't know of any language which implements anything resembling an ASN.1 SET
, and I'm not sure what advantage such a thing would have. But SET OF
types certainly exist in many languages, where they're usually called things like "unordered multiset". (Again, ASN.1 allows a the specification of complex constraints on particular SET OF
objects. A common use case is representing a mapping type as a SET OF
two-element SEQUENCE
s.
ASN.1 also has a CHOICE
composite type, which (like a C++ std::variant
) represents a single object of one of a specified list of types.
One of the interesting features of ASN.1 is that it allows recursive definitions (although it disallows infinite concrete objects, so the recursive element needs to be optional or inside a possibly empty SEQUENCE OF
/SET OF
composite. Recursive definitions at least open the possibility of non-regular grammars.
ASN.1 tools build serializers (generators) and deserializers (parsers) from a set of ASN.1 descriptions. There are a large variety of representation schemes which can be used, and most of them require a more complex syntax than might be apparent from the Abstract Syntax defined in ASN.1. For example, in BER sequence-of objects and character strings can be transparently represented either by preceding the elements with a precise length, or as a series of subsequence chunks followed by an "end-of-sequence" sentinel. Even integers are preceded by a length indicator, since an unconstrained ASN.1 integer does not have a size limit. (The ASN.1 definition can apply a constraint, and some representation schemes use this constraint to simplify the concrete representation.)
X.509 certificates are serialized using the DER representation, which was designed to eliminate encoding options. The intent of DER is to create a one-to-one mapping between each representable value and a bit-vector which can be transmitted. Some aspects of DER are very difficult (if not impossible) to write in a context-free grammar, starting with the requirement that variable-length bit vectors be preceded by their length. Even more complicated is the DER requirement for transmitting SET-OF
composites: the elements in the SET-OF
must be individual encoded, and then the encodings are output in lexicographic bit ordering.
The point of a canonical representation such as DER, by the way, is precisely to make it possibly to digitally sign a serialised datum.
In my opinion, ASN.1 is a fascinating and lamentably undervalued body of work. Although it seems unlikely that it will every enjoy a revival (but, then, who knows?), much less that there will ever be an ASN.2, the astonishing range of issues considered in the design of ASN.1 elucidates the complex task of reliably transmitting serialized data in a way that could have immensely benefited the design of other "simpler" serialization technologies.
QUESTION
As I was bored and wanted to practice my python, I thought I'd write a script that took some genetic code and converted it into the amino acid sequence. It looks through the code one letter at a time and when it sees a certain sequence, starts translating triplets of genetic code into their equivalent amino acid and strings them together until it reaches a triplet of genetic code that doesn't encode an amino acid. The script then goes back to where it started this translation, and restarts iterating through the code until it finds another start sequence.
The script works, up to a point. I started off using a while loop to iterate through the triplets of genetic code after a start sequence, but when it reaches the end of the genetic code, it goes out of range:
...ANSWER
Answered 2021-Feb-24 at 20:38You keep incrementing base
and incrementing l
but without checking if you've exceeded the length of the rna string. Changing the condition of your while loop to
QUESTION
I am currently in a C# boot camp. I am having trouble putting this together. The assignment is to create a console app for an insurance company that asks three questions.
- Age, which must be greater than 15,
- any speeding tickets, must be 3 or less, and
- DUI's, which must be answered "false". Then
- Qualified? with an answer of true / false.
I'm technically not supposed to use "if" statements in the code since we haven't covered "if" statements in the C# course yet so it should be a basic equation to check all 3 user inputs to print out one answer of true/false. I am having issues putting the equation together at the end that checks all three and outputs a true/false answer. This is my first post on here, so, my apologies if I'm not giving the proper info. Any help would be appreciated.
...ANSWER
Answered 2021-Feb-17 at 19:22You can test the conditions in a Boolean expression and write the result to the console directly.
QUESTION
bea3d
- list
50:EA:EC:0C:50:DF
- ID: " L084"
- brand: "BE"
- locate
- lat: "130.7273835"
- long: "10.776167"
- name
- shade
74:FA:FF:80:4D:E1
- ID: " GS58"
- brand: "TTA"
- locate
- lat: "130.7273835"
- long: "10.776167"
23:EA:FC:00:67:FD
- ID: " P09A"
- brand: "EE"
- locate
- lat: "130.7273835"
- long: "10.776167"
How to get only lat and long value in Kotlin from every key in my list? And how to convert these values to Double for use marker in the map?
...ANSWER
Answered 2021-Feb-02 at 13:08Assuming that "bea3d" is the root reference of your Firebase Realtime Database, to get the value of "lat" and "long" that exist underneath each node, please use the following lines of code:
QUESTION
i have a protein sequence:
...ANSWER
Answered 2021-Jan-04 at 19:54import itertools
list_codons = [('ATT', 'ATC', 'ATA'),
('GAA', 'GAG'),
('GAA', 'GAG'),
('GCT', 'GCC', 'GCA', 'GCG'),
('ACT', 'ACC', 'ACA', 'ACG'),
('CAT', 'CAC'),
('ATG',),
('ACT', 'ACC', 'ACA', 'ACG'),
('CCT', 'CCC', 'CCA', 'CCG'),
('TGT', 'TGC'),
('TAT', 'TAC'),
('GAA', 'GAG'),
('TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG'),
('CAT', 'CAC'),
('GGT', 'GGC', 'GGA', 'GGG'),
('TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG'),
('CGT', 'CGC', 'CGA', 'CGG', 'AGA', 'AGG'),
('TGG',),
('GTT', 'GTC', 'GTA', 'GTG'),
('CAA', 'CAG'),
('ATT', 'ATC', 'ATA'),
('CAA', 'CAG'),
('GAT', 'GAC'),
('TAT', 'TAC'),
('GCT', 'GCC', 'GCA', 'GCG'),
('ATT', 'ATC', 'ATA'),
('AAT', 'AAC'),
('GTT', 'GTC', 'GTA', 'GTG'),
('ATG',),
('CAA', 'CAG'),
('TGT', 'TGC'),
('TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG')]
counter = 0; max_proc = 1000000; list_seq = []
for x in itertools.product(*list_codons):
counter += 1
if counter % max_proc == 0:
#Do your stuff by slice and clear the list
list_seq = []
list_seq.append(x)
print (counter)
print (x)
QUESTION
ANSWER
Answered 2020-Nov-03 at 16:37You can simply use pandas
:
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