tiptoft | Predict plasmids from uncorrected long read data | Genomics library

by andrewjpage Python Version: 1.0.2 License: GPL-3.0

X-Ray Key Features Code Snippets(3)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | tiptoft Summary

tiptoft is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. tiptoft has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install tiptoft' or download it from GitHub, PyPI.

Given some raw uncorrected long reads, such as those from PacBio or Oxford Nanopore, predict which plasmid should be present. Assemblies of long read data can often miss out on plasmids, particularly if they are very small or have a copy number which is too high/low when compared to the chromosome. This software gives you an indication of which plasmids to expect, flagging potential issues with an assembly.

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Support

tiptoft has a low active ecosystem.

It has 24 star(s) with 8 fork(s). There are 3 watchers for this library.

It had no major release in the last 12 months.

There are 0 open issues and 17 have been closed. On average issues are closed in 18 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of tiptoft is 1.0.2

Quality

tiptoft has 0 bugs and 0 code smells.

Security

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

tiptoft code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

tiptoft is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

tiptoft releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

tiptoft saves you 614 person hours of effort in developing the same functionality from scratch.

It has 1429 lines of code, 88 functions and 18 files.

It has medium code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

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

Run analysis
Count all k -mers in a plasmid FASTA file
Calculate the coverage of a sequence
Read through FASTQ file and map alleles
Run refgenes

Get all kandi verified functions for this library.

tiptoft Key Features

No Key Features are available at this moment for tiptoft.

tiptoft Examples and Code Snippets

Usage,tiptoft script

Python

Lines of Code : 42

License : Strong Copyleft (GPL-3.0)

Copy

usage: tiptoft [options] input.fastq

plasmid incompatibility group prediction from uncorrected long reads

positional arguments:
  input_fastq           Input FASTQ file (optionally gzipped)

optional arguments:
  -h, --help            show this hel

Usage,tiptoft_database_downloader script

Python

Lines of Code : 12

License : Strong Copyleft (GPL-3.0)

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usage: tiptoft_database_downloader [options] output_prefix

Download PlasmidFinder database

positional arguments:
  output_prefix  Output prefix

optional arguments:
  -h, --help     show this help message and exit
  --verbose, -v  Turn on debugging

Output

Python

Lines of Code : 10

License : Strong Copyleft (GPL-3.0)

Copy

GENE	COMPLETENESS	%COVERAGE	ACCESSION	DATABASE	PRODUCT
rep7.1	Full	100	AB037671	plasmidfinder	rep7.1_repC(Cassette)_AB037671
rep7.5	Partial	99	AF378372	plasmidfinder	rep7.5_CDS1(pKC5b)_AF378372
rep7.6	Partial	94	SAU38656	plasmidfinder	rep7.6_ORF(pKH1

Community Discussions

Trending Discussions on Genomics

search for regex match between two files using python

Is there a way to permute inside using to variables in bash?

BigQuery Regex to extract string between two substrings

how to stop letter repeating itself python

Split multiallelic to biallelic in vcf by plink 1.9 and its variant name

Delete specific letter in a FASTA sequence

How to get the words within the first single quote in r using regex?

Does Apache Spark 3 support GPU usage for Spark RDDs?

Aggregating and summing columns across 1500 files by matching IDs in R (or bash)

Usage of compression IO functions in apache arrow

QUESTION

search for regex match between two files using python

Asked 2022-Apr-09 at 00:49

I´m working with two text files that look like this: File 1

...

ANSWER

Answered 2022-Apr-09 at 00:49

Perhaps you are after this?

Source https://stackoverflow.com/questions/71789818

QUESTION

Is there a way to permute inside using to variables in bash?

Asked 2021-Dec-09 at 23:50

I'm using the software plink2 (https://www.cog-genomics.org/plink/2.0/) and I'm trying to iterate over 3 variables.

This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file.

The idea is to iterate over the input files and then over exclude files to generate single outputfiles.

Input files: Highland.ped - Midland.ped - Lowland.ped
Exclude-map files: HighlandMidland.txt - HighlandLowland.txt - MidlandLowland.txt
Output files: HighlandMidland - HighlandLowland - MidlandHighland - MidlandLowland - LowlandHighland - LowlandMidland

The general code is:

...

ANSWER

Answered 2021-Dec-09 at 23:50

Honestly, I think your current code is quite clear; but if you really want to write this as a loop, here's one possibility:

Source https://stackoverflow.com/questions/70298074

QUESTION

BigQuery Regex to extract string between two substrings

Asked 2021-Dec-09 at 01:11

From this example string:

...

ANSWER

Answered 2021-Dec-09 at 01:11

use regexp_extract(col, r"&q;Stockcode&q;:([^/$]*?),&q;.*")

if applied to sample data in your question - output is

Source https://stackoverflow.com/questions/70283253

QUESTION

how to stop letter repeating itself python

Asked 2021-Nov-25 at 18:33

I am making a code which takes in jumble word and returns a unjumbled word , the data.json contains a list and here take a word one-by-one and check if it contains all the characters of the word and later checking if the length is same , but the problem is when i enter a word as helol then the l is checked twice and giving me some other outputs including the main one(hello). i know why does it happen but i cant get a fix to it

...

ANSWER

Answered 2021-Nov-25 at 18:33

As I understand it you are trying to identify all possible matches for the jumbled string in your list. You could sort the letters in the jumbled word and match the resulting list against sorted lists of the words in your data file.

Source https://stackoverflow.com/questions/70112201

QUESTION

Split multiallelic to biallelic in vcf by plink 1.9 and its variant name

Asked 2021-Nov-17 at 13:56

I am trying to use plink1.9 to split multiallelic into biallelic. The input is that

...

ANSWER

Answered 2021-Nov-17 at 09:45

I used bcftools to complete the task.

https://github.com/samtools/bcftools/issues/1193

Source https://stackoverflow.com/questions/70001737

QUESTION

Delete specific letter in a FASTA sequence

Asked 2021-Oct-12 at 21:00

I have a FASTA file that has about 300000 sequences but some of the sequences are like these

...

ANSWER

Answered 2021-Oct-12 at 20:28

You can match your non-X containing FASTA entries with the regex >.+\n[^X]+\n. This checks for a substring starting with > having a first line of anything (the FASTA header), which is followed by characters not containing an X until you reach a line break.

For example:

Source https://stackoverflow.com/questions/69545912

QUESTION

How to get the words within the first single quote in r using regex?

Asked 2021-Oct-04 at 22:27

For example, I have two strings:

...

ANSWER

Answered 2021-Oct-04 at 22:27

For your example your pattern would be:

Source https://stackoverflow.com/questions/69442717

QUESTION

Does Apache Spark 3 support GPU usage for Spark RDDs?

Asked 2021-Sep-23 at 05:53

I am currently trying to run genomic analyses pipelines using Hail(library for genomics analyses written in python and Scala). Recently, Apache Spark 3 was released and it supported GPU usage.

I tried spark-rapids library start an on-premise slurm cluster with gpu nodes. I was able to initialise the cluster. However, when I tried running hail tasks, the executors keep getting killed.

On querying in Hail forum, I got the response that

That’s a GPU code generator for Spark-SQL, and Hail doesn’t use any Spark-SQL interfaces, only the RDD interfaces.

So, does Spark3 not support GPU usage for RDD interfaces?

...

ANSWER

Answered 2021-Sep-23 at 05:53

As of now, spark-rapids doesn't support GPU usage for RDD interfaces.

Source: Link

Apache Spark 3.0+ lets users provide a plugin that can replace the backend for SQL and DataFrame operations. This requires no API changes from the user. The plugin will replace SQL operations it supports with GPU accelerated versions. If an operation is not supported it will fall back to using the Spark CPU version. Note that the plugin cannot accelerate operations that manipulate RDDs directly.

Here, an answer from spark-rapids team

Source: Link

We do not support running the RDD API on GPUs at this time. We only support the SQL/Dataframe API, and even then only a subset of the operators. This is because we are translating individual Catalyst operators into GPU enabled equivalent operators. I would love to be able to support the RDD API, but that would require us to be able to take arbitrary java, scala, and python code and run it on the GPU. We are investigating ways to try to accomplish some of this, but right now it is very difficult to do. That is especially true for libraries like Hail, which use python as an API, but the data analysis is done in C/C++.

Source https://stackoverflow.com/questions/69273205

QUESTION

Aggregating and summing columns across 1500 files by matching IDs in R (or bash)

Asked 2021-Sep-07 at 13:09

I have 1500 files with the same format (the .scount file format from PLINK2 https://www.cog-genomics.org/plink/2.0/formats#scount), an example is below:

...

ANSWER

Answered 2021-Sep-07 at 11:10

a tidyverse solution

Source https://stackoverflow.com/questions/69086946

QUESTION

Usage of compression IO functions in apache arrow

Asked 2021-Jun-02 at 18:58

I have been implementing a suite of RecordBatchReaders for a genomics toolset. The standard unit of work is a RecordBatch. I ended up implementing a lot of my own compression and IO tools instead of using the existing utilities in the arrow cpp platform because I was confused about them. Are there any clear examples of using the existing compression and file IO utilities to simply get a file stream that inflates standard zlib data? Also, an object diagram for the cpp platform would be helpful in ramping up.

...

ANSWER

Answered 2021-Jun-02 at 18:58

Here is an example program that inflates a compressed zlib file and reads it as CSV.

Source https://stackoverflow.com/questions/67799265

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

Vulnerabilities

No vulnerabilities reported

Install tiptoft

The only dependancies are Python3 and a compiler (gcc, clang,...) and this should work on Linux or OSX. Cython needs to be installed in advance. Assuming you have Python 3.4+ and pip installed, just run:.