GAG | Generates an NCBI .tbl file of annotations on a genome | Genomics library
kandi X-RAY | GAG Summary
kandi X-RAY | GAG Summary
A command line program to read, modify, annotate and output genomic data. Can write files to .gff3 or to the NCBI's .tbl format. Perfect if you're trying to submit a genome to NCBI. For usage, type 'python gag.py'. See documentation at Please cite the following: when using GAG for your research.
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Top functions reviewed by kandi - BETA
- Perform the gag
- Add a genome from a file
- Read an annotation file
- Apply a filter
- Update a GFF file based on trimlist
- Checks if two indices are within the range
- Check if intervals overlap
- Updates an agp file
- Return a dictionary of information about the CDS
- Return a dictionary containing the partial info for each gene
- Return a string representation of this gene
- Calculate statistics on the genome
- Adjust the indices by n
- Return the index of the first exon
- Parses a string into a list of regions
- Returns the length of the longest exon
- Returns the total length of the exon
- Returns the total number ofags in the mRNA
- Produce a table of nucleotides
- Convert cds to table
- Create start and stop coordinates for all mrna
- Add the annotations from the given annotations
- Remove features from bad list
- Return the length of the segment
- Convert to protein sequence
- Convert the mrna sequence to a cds file
GAG Key Features
GAG Examples and Code Snippets
Community Discussions
Trending Discussions on GAG
QUESTION
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 17:11It always return after first if check. It should be:
QUESTION
If one has a dict like the following:
...ANSWER
Answered 2021-Apr-25 at 21:38No there isn't. Instead, use an alternative form to you dictionary, it's ok to have duplicate values so:
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 am using the Python regex module for approximate string matching. I have a DNA sequence which I would like to search for a specific pattern, while allowing for at most 1 substitution: {s<=1}. In the DNA sequence, multiple patterns are acceptable. For example, the first three characters can either be 'GAG' or 'GAT', and the same principle holds true for the rest of the DNA sequence.
I made an example below, where I want to use regex search on a 9 character long string. To my understanding, the pattern should match the string without any subtitution.
However, regex gives me a match with a fuzzy count of 1 for substitutions (see below). I do not understand this, as the sequence matches the pattern.
...ANSWER
Answered 2021-Apr-11 at 15:55From the regex module documentation:
By default, fuzzy matching searches for the first match that meets the given constraints.
In your case, the first match is obtained using GAG and performing one substitution (since GAG is tried before GAT). You can use the BESTMATCH flag to look for the best match instead:
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 have two dataframes
df1
...ANSWER
Answered 2021-Mar-31 at 22:25QUESTION
I switched from React to Vue and for me there are some incomprehensible nuances I want to create a drop-down menu, but I have some incomprehensible things related to this who is familiar with React knows that you can create a certain property with a boolean value inside a state or using hooks then when clicking on the buttons, use setState and manage with it,
I understand that you can implement something like this in Vue JS, but I am confused by one question, how can you create a certain property in Vue JS? is it possible to instantiate by type let app = new Vue({el: '#app',}); for each component? Because I don't understand how to create a property for example showDropDown without using new Vue ({})?
My code at the moment looks like this
...ANSWER
Answered 2021-Mar-30 at 22:50Using the Options API, you can create local reactive state in Vue components by declaring them in data:
QUESTION
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 18:27To 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:
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 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)
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No vulnerabilities reported
Install GAG
You can use GAG 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.
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