bioinformatics | Quick ugly bioinformatics scripts in Python | Genomics library

by brendan-rius Python Version: Current License: No License

X-Ray Key Features Code Snippets(1)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | bioinformatics Summary

bioinformatics is a Python library typically used in Artificial Intelligence, Genomics applications. bioinformatics has no bugs, it has no vulnerabilities and it has low support. However bioinformatics build file is not available. You can download it from GitHub.

This repository contains Python script I wrote while leraning about bioinformatics. These scripts are ofter ugly and not optimized, because just written as POC or for quick testing.

Support

Quality

Security

License

Reuse

Support

bioinformatics has a low active ecosystem.

It has 5 star(s) with 2 fork(s). There are 1 watchers for this library.

It had no major release in the last 6 months.

bioinformatics has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of bioinformatics is current.

Quality

bioinformatics has no bugs reported.

Security

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

License

bioinformatics does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

bioinformatics releases are not available. You will need to build from source code and install.

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

Top functions reviewed by kandi - BETA

kandi has reviewed bioinformatics and discovered the below as its top functions. This is intended to give you an instant insight into bioinformatics implemented functionality, and help decide if they suit your requirements.

Count the number of words in a genome
Computes hamming distance between two sequences
Get the neighbors of a kmer
Count hamming distance
Reverse complements
Return the immediate neighbors of a kmer
Return a copy of the genotype
Return a mutated genotype genotype
Return a shallow copy of the object
Return the median string for kmers in a DNA sequence
R Returns a generator of all k - mers
Compute hamming distance between two sequences
Generator for kers
Finds a sequence of kumps in the sequence
Find the frequency of k - mer in a sequence
R Return a set of kumps that start with k
Return the frequency of kmer in a sequence
Count occurrences of pattern in text
Removes kmer from text at position
Return a copy of the object
Find the minimum skew of the genome
Compute the probability for a given number of characters
Reverse complements
Return all pattern matching the given sequence
Find the kmers in text
Enumeration of motifs
Get the neighbors of a given kmer

Get all kandi verified functions for this library.

bioinformatics Key Features

No Key Features are available at this moment for bioinformatics.

bioinformatics Examples and Code Snippets

Citing TPOT

pypi

Lines of Code : 38

License : No License

Copy

@article{le2020scaling,
  title={Scaling tree-based automated machine learning to biomedical big data with a feature set selector},
  author={Le, Trang T and Fu, Weixuan and Moore, Jason H},
  journal={Bioinformatics},
  volume={36},
  number={1},

Community Discussions

Trending Discussions on bioinformatics

Conversion table replace all elements in other file

snakemake - define input for aggregate rule without wildcards

Python: build consensus sequence

Modified knapsack problem gets stuck in infinite loop

How to source R file and run it at the same time in R script

How to send imputed data from R script to another script

script to remove lines that have same string at the end of the line and save the remaining lines in another file in another format

Ideas to complete a script to search in two files and extract a section of data

Multiple captures within a string

Suffix Tree check existence of P pattern before k position

QUESTION

Conversion table replace all elements in other file

Asked 2021-Jun-11 at 12:10

I am trying to convert all ICD codes in a tab separated file to Phecodes (based on a ICD-Phecode conversion table tab separated file) for a biology bioinformatics project. I found a good starting point with the code from the below stackoverflow post:

...

ANSWER

Answered 2021-Jun-07 at 14:28

The loop has to be outside of the condition. Ie. you want to check for each column, not only for $1 in a. Consider a more readable multiline format.

Source https://stackoverflow.com/questions/67873367

QUESTION

snakemake - define input for aggregate rule without wildcards

Asked 2021-Jun-08 at 15:40

I am writing a snakemake to produce Sars-Cov-2 variants from Nanopore sequencing. The pipeline that I am writing is based on the artic network, so I am using artic guppyplex and artic minion.

The snakemake that I wrote has the following steps:

zip all the fastq files for all barcodes (rule zipFq)
perform read filtering with guppyplex (rule guppyplex)
call the artic minion pipeline (rule minion)
move the stderr and stdout from qsub to a folder under the working directory (rule mvQsubLogs)

Below is the snakemake that I wrote so far, which works

...

ANSWER

Answered 2021-Jun-08 at 15:40

The rule that fails is rule guppyplex, which looks for an input in the form of {FASTQ_PATH}/{{barcode}}.

Looks like the wildcard {barcode} is filled with barcode49/barcode49.consensus.fasta, which happened because of two reasons I think:

First (and most important): The workflow does not find a better way to produce the final output. In rule catFasta, you give an input file which is never described as an output in your workflow. The rule minion has the directory as an output, but not the file, and it is not perfectly clear for the workflow where to produce this input file.

It therefore infers that the {barcode} wildcard somehow has to contain this .consensus.fasta that it has never seen before. This wildcard is then handed over to the top, where the workflow crashes since it cannot find a matching input file.

Second: This initialisation of the wildcard with sth. you don't want is only possible since you did not constrain the wildcard properly. You can for example forbid the wildcard to contain a . (see wildcard_constraints here)

However, the main problem is that catFasta does not find the desired input. I'd suggest changing the output of minion to "nanopolish/{barcode}/{barcode}.consensus.fasta", since the you already take the OUTDIR from the params, that should not hurt your rule here.

Edit: Dummy test example:

Source https://stackoverflow.com/questions/67805295

QUESTION

Python: build consensus sequence

Asked 2021-Jun-06 at 08:09

I want to build a consensus sequence from several sequences in python and I'm looking for the most efficient / most pythonic way to achieve this.

I have a list of strings like this:

...

ANSWER

Answered 2021-Jun-06 at 08:09

If you already have the position frequency matrix, you could process it as a pandas DataFrame. I chose to orient it such that the alphabet is the index (note the transpose call at the end):

Source https://stackoverflow.com/questions/67837882

QUESTION

Modified knapsack problem gets stuck in infinite loop

Asked 2021-Jun-03 at 11:40

I've been trying to implement a modified knapsack problem algorithm regarding bioinformatics.

What I have so far is, in my opinion, pretty close to the solution, but the program gets stuck at a certain point.

I have a list of nodes which have mass (of a certain amino-acid), index, and list of nodes that they can get to.

NODE:

...

ANSWER

Answered 2021-Jun-03 at 11:40

While trying to debug the code, the problem seemed to be in the whole concept of the attribute next in the Node class.

When I printed out all of the Nodes' next lists, I found multiple occurences of the same Node, for example [2,2,2,3,8,...] so when I converted the list to set it didn't get stuck anymore.

Hope this helps someone in the future.

Source https://stackoverflow.com/questions/67805191

QUESTION

How to source R file and run it at the same time in R script

Asked 2021-May-31 at 21:50

I am trying to make source and run r script in another r script at the same time

...

ANSWER

Answered 2021-May-31 at 21:50

You can use rstudio jobs to avoid locking the console

Source https://stackoverflow.com/questions/67780508

QUESTION

How to send imputed data from R script to another script

Asked 2021-May-31 at 19:12

I have make a script that imputes the missing data (NA) in the file but i want to send this imputed data to another R.script from this script my_code:

...

ANSWER

Answered 2021-May-31 at 19:12

We could source the first script to second script by placing the below line at the top of the second script

Source https://stackoverflow.com/questions/67778888

QUESTION

script to remove lines that have same string at the end of the line and save the remaining lines in another file in another format

Asked 2021-May-30 at 18:12

my file looks like that:

...

ANSWER

Answered 2021-May-30 at 17:38

I haven't tested this but try adding the following statement after line_items = line.split('\t')

Source https://stackoverflow.com/questions/67763930

QUESTION

Ideas to complete a script to search in two files and extract a section of data

Asked 2021-May-22 at 14:41

I have been doing a script that takes two files to extract a specific part of the data to make a new file. If you want to see the complete file, here's a GitHub link: enter link description here

File one (report file) is a type of file that reports me when a value is >=0.5 (column N°6 is the value that interests me). This file is something like this (this is only a part):

...

ANSWER

Answered 2021-May-21 at 18:59

Untested (since you did not post a MRE), but this should work:

Source https://stackoverflow.com/questions/67640684

QUESTION

Multiple captures within a string

Asked 2021-May-14 at 00:24

Haven't found a Q/A on SO that quite answers this situation. I have implemented solutions from some to get as far as I have.

I'm parsing the header (metadata) part of VCF files. Each line has the format:

##TAG=

I have a regex that parses the multiple k-v pairs inside the <>, but I can't seem to add in the <> and have it still "work."

...

ANSWER

Answered 2021-May-14 at 00:24

With PyPi regex:

Source https://stackoverflow.com/questions/67527640

QUESTION

Suffix Tree check existence of P pattern before k position

Asked 2021-May-04 at 15:53

I need to design an algorithm that given a T string of n length, after a process O(n), for every string P of m length and a k value between 1 to n, to checks in O(m) time, if P appears on T before k position, only using Suffix Tree.

Unfortunately there are not any good bioinformatics books with fair examples and practical methodologies. Dan Gusfield book does not offer a solution manual.

...

ANSWER

Answered 2021-May-04 at 15:53

Preprocessing: after constructing the suffix tree, use DFS to label each node with the minimum index of the suffixes that appear in its descendants.

Query: descend in the suffix tree on the links indicated by P, threshold the node value constructed above.

Source https://stackoverflow.com/questions/67382921

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install bioinformatics

You can download it from GitHub.
You can use bioinformatics 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 .

Find more information at: