ccg | Generate scaffolds/models for FastAPI and Tortoise ORM | Generator Utils library

by DakshMiglani Python Version: Current License: No License

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kandi X-RAY | ccg Summary

ccg is a Python library typically used in Generator, Generator Utils, Fastapi applications. ccg has no bugs, it has no vulnerabilities and it has low support. However ccg build file is not available. You can download it from GitHub.

ccg is a cli generator that generates boilerplate code. It currently only supports model generation for tortoise orm.

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ccg has a low active ecosystem.

It has 5 star(s) with 0 fork(s). There are 1 watchers for this library.

It had no major release in the last 6 months.

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It has a neutral sentiment in the developer community.

The latest version of ccg is current.

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ccg has no bugs reported.

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ccg has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

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ccg has no build file. You will be need to create the build yourself to build the component from source.

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Community Discussions

Trending Discussions on ccg

Finding the first occurence of several different strings in a longer string

Function converting mRNA to peptide sequence depending on the reading frame does not work correctly

make log operations between a dictionary and a list of dictionaries

DNA to Protein | translation incorrection

I have a list of df resulting by groupby and I need to add a new column with the frequency of kmers

Struggling to find the number of distinct amino acids

Extracting information using Awk

How can I stop my script going out of range?

ASP.NET Core MVC empty object from response

calculate all possible combinations of RNA codons for a protein sequence

QUESTION

Finding the first occurence of several different strings in a longer string

Asked 2021-May-17 at 18:00

Im currently working on a study project where I am to make a python program where I can enter a DNA sequence, get all the possible reading frames from it and then find any open reading frame. I can't use Biopython as we are to do this ourselves.

From the code I have written, I will get an output in the style of: ["TGC", "ATG", "ATA", "TGG", "AGG", "AGG", "CCG", TAA", "TAG", "TGA"]

What I want to do now is to define the start codon as "ATG" and get its index as well as define stop codons as ["TAA", "TAG", "TGA"] and if any of these three are found, the index of the first found is reported and the rest is ignored. And if no stop codon is found to return some string.

In addition to this, i want to be able to compare the "lengts" of up to 6 different input in the style mentioned above and chone the one which is the longest.

This is my first time posting here so appologies if the question is not well phrased and thanks for any help!

...

ANSWER

Answered 2021-May-17 at 18:00

Strings in longer string

I am not completely sure if this is what you want, but to find the first occurrence of strings in a longer string you can do like this for example

Source https://stackoverflow.com/questions/67571270

QUESTION

Function converting mRNA to peptide sequence depending on the reading frame does not work correctly

Asked 2021-May-08 at 17:11

I am trying to write a fuction that translates an mRNA sequence to a peptide sequence depending on the nucleotide from which we start counting codons (either the first nucleotide, the second or the third). I have a code for it, but when I print the three results (of the three peptides) I only get a sequence for the first peptide. The last two are blank. Any idea what the problem might be? And how could I return all three peptides by default?

...

ANSWER

Answered 2021-May-08 at 17:11

It always return after first if check. It should be:

Source https://stackoverflow.com/questions/67450015

QUESTION

make log operations between a dictionary and a list of dictionaries

Asked 2021-Apr-26 at 15:58

Hello I am looking to do find out this:

Assume I have this.

...

ANSWER

Answered 2021-Apr-26 at 15:58

If a and b are your inputs from question:

Source https://stackoverflow.com/questions/67269673

QUESTION

DNA to Protein | translation incorrection

Asked 2021-Apr-22 at 15:41

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 09:38

I 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.

Source https://stackoverflow.com/questions/66884855

QUESTION

I have a list of df resulting by groupby and I need to add a new column with the frequency of kmers

Asked 2021-Apr-05 at 12:28

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 12:28

It'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.

Source https://stackoverflow.com/questions/66936330

QUESTION

Struggling to find the number of distinct amino acids

Asked 2021-Mar-24 at 18:27

def amino_acids(mrna):
    aa_dict = {'CUU': 'Leu', 'UAG': '---', 'ACA': 'Thr', 'AAA': 'Lys', 'AUC': 'Ile',
 'AAC': 'Asn','AUA': 'Ile', 'AGG': 'Arg', 'CCU': 'Pro', 'ACU': 'Thr',
 'AGC': 'Ser','AAG': 'Lys', 'AGA': 'Arg', 'CAU': 'His', 'AAU': 'Asn',
 'AUU': 'Ile','CUG': 'Leu', 'CUA': 'Leu', 'CUC': 'Leu', 'CAC': 'His',
 'UGG': 'Trp','CAA': 'Gln', 'AGU': 'Ser', 'CCA': 'Pro', 'CCG': 'Pro',
 'CCC': 'Pro', 'UAU': 'Tyr', 'GGU': 'Gly', 'UGU': 'Cys', 'CGA': 'Arg',
 'CAG': 'Gln', 'UCU': 'Ser', 'GAU': 'Asp', 'CGG': 'Arg', 'UUU': 'Phe',
 'UGC': 'Cys', 'GGG': 'Gly', 'UGA':'---', 'GGA': 'Gly', 'UAA': '---',
 'ACG': 'Thr', 'UAC': 'Tyr', 'UUC': 'Phe', 'UCG': 'Ser', 'UUA': 'Leu',
 'UUG': 'Leu', 'UCC': 'Ser', 'ACC': 'Thr', 'UCA': 'Ser', 'GCA': 'Ala',
 'GUA': 'Val', 'GCC': 'Ala', 'GUC': 'Val', 'GGC':'Gly', 'GCG': 'Ala',
 'GUG': 'Val', 'GAG': 'Glu', 'GUU': 'Val', 'GCU': 'Ala', 'GAC': 'Asp',
 'CGU': 'Arg', 'GAA': 'Glu', 'AUG': 'Met', 'CGC': 'Arg'}
    
    mrna_list = [aa_dict[mrna[i:i + 3]] for i in range(0, len(mrna) - 1, 3)]
    count = 0
    while True:
        if mrna_list[count] == '---':
            
            mrna_list = mrna_list[:count]
            break
        else:
            count += 1
    conversion_result = tuple(mrna_list)
    return [conversion_result, count]

...

ANSWER

Answered 2021-Mar-24 at 18:27

To get only the unique elements of a list, you can usually just convert it to a set and back (at least, when it only contains simple things like strings or numbers). You can then find the number of unique elements by taking the length of that set:

Source https://stackoverflow.com/questions/66786981

QUESTION

Extracting information using Awk

Asked 2021-Mar-11 at 23:00

This post is related to my previous question about string splitting: Awk split string into words and numbers. Let's say we have a following string:

...

ANSWER

Answered 2021-Mar-05 at 17:55

% echo 1A5T4 | gawk 'BEGIN{ FS=""; }{ for (i=1;i<=NF;i++) { if($i>="A"){ s=s $i } else { for(j=1;j<=$i;j++)s=s "." }} print s }'
.A.....T....
% echo 1A2^CCG3T4 | gawk 'BEGIN{ FS=""; }{ for (i=1;i<=NF;i++) { if($i>="A"){ s=s $i } else { for(j=1;j<=$i;j++)s=s "." }} print s }'
.A..^CCG...T....
%

Source https://stackoverflow.com/questions/66496854

QUESTION

How can I stop my script going out of range?

Asked 2021-Feb-24 at 20:38

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 20:38

You 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

Source https://stackoverflow.com/questions/66358276

QUESTION

ASP.NET Core MVC empty object from response

Asked 2021-Jan-16 at 03:01

I'm having some trouble with this code, I have used something similar before and is working but it isn't on this one I don't know why. Each time I hit submit the object message comes empty, the only values that are submitted into the database are the ones that I add in the controller like the Date for example, I don't know much about ASP.NET to know why is it failing nor the correct terms to look for myself on google

Model

...

ANSWER

Answered 2021-Jan-16 at 01:30

I'm pretty sure uou need to make those fields into properties by adding get and set methods.

e.g.

Source https://stackoverflow.com/questions/65745262

QUESTION

calculate all possible combinations of RNA codons for a protein sequence

Asked 2021-Jan-04 at 22:50

i have a protein sequence:

...

ANSWER

Answered 2021-Jan-04 at 19:54

import 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)

Source https://stackoverflow.com/questions/65568728

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Vulnerabilities

No vulnerabilities reported

Install ccg

You can download it from GitHub.
You can use ccg like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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