qiime | Official QIIME 1 software repository. QIIME 2 | Genomics library

by biocore Python Version: 1.9.1 License: GPL-2.0

X-Ray Key Features Code Snippets Community Discussions(7)Vulnerabilities Install Support

kandi X-RAY | qiime Summary

qiime is a Python library typically used in Artificial Intelligence, Genomics applications. qiime has build file available, it has a Strong Copyleft License and it has high support. However qiime has 140 bugs and it has 1 vulnerabilities. You can download it from GitHub.

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

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Quality

Security

License

Reuse

Support

qiime has a highly active ecosystem.

It has 272 star(s) with 263 fork(s). There are 58 watchers for this library.

It had no major release in the last 12 months.

There are 387 open issues and 996 have been closed. On average issues are closed in 331 days. There are 10 open pull requests and 0 closed requests.

It has a negative sentiment in the developer community.

The latest version of qiime is 1.9.1

Quality

qiime has 140 bugs (9 blocker, 0 critical, 27 major, 104 minor) and 1818 code smells.

Security

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

qiime code analysis shows 1 unresolved vulnerabilities (1 blocker, 0 critical, 0 major, 0 minor).

There are 119 security hotspots that need review.

License

qiime is licensed under the GPL-2.0 License. This license is Strong Copyleft.

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

Reuse

qiime releases are available to install and integrate.

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

qiime saves you 104474 person hours of effort in developing the same functionality from scratch.

It has 112289 lines of code, 3287 functions and 408 files.

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

Top functions reviewed by kandi - BETA

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

Select a subset of open reference reference OTU
Return the index page header
Format a link description
Generate index page
Run core diversity analysis
Generate summaries for each table
Run the alphararefaction
Run beta diversity_through
Select subset of reference OTU
Select a subset of OpenSelected reference OTU
Extract barcodes from fastq files
Make a distance box plot
Run summaries through a table
Run an alphararefaction
Run beta diversity through a table
Compute the similarity between two categories
Calculate the beta output for a single file
Calculate LEA sequence consensus sequences
Run the mntr correlation
Compares two taxa summaries
Preprocess a FASTA file
Process a fastq_single_read file
Run jacknn beta diversity
Run ampliconnoise
Generate paired_difference analysis
Runs pick_de_de
Wrapper around open_reference_tasks

Get all kandi verified functions for this library.

qiime Key Features

No Key Features are available at this moment for qiime.

qiime Examples and Code Snippets

No Code Snippets are available at this moment for qiime.

Community Discussions

Trending Discussions on qiime

A good way for pairwise t-test for many rows? (R)

How do I repeat codes with names changing at every block? (with R)

python bar chart plot of 16S bacterial abundance

How to use integers in subprocess.call

User input in subprocess.call

bash: python: .py: command not found

if then bash statement does not work with qiime commands

QUESTION

A good way for pairwise t-test for many rows? (R)

Asked 2020-Jul-10 at 23:21

I'm writing a code that, from a table of raw data (output of microbiome QIIME analysis), generates a t-test per group of all the rows. Every row has a bacteria and the values corresponding for every sample. The table can be huge, like 80 columns per 400 rows.

Group_phylum_data:

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ANSWER

Answered 2020-Jul-10 at 22:59

You can try this (Archaea_Other is zero, so no output is produced). I hope this helped.

Source https://stackoverflow.com/questions/62843237

QUESTION

How do I repeat codes with names changing at every block? (with R)

Asked 2020-Apr-23 at 16:12

I'm dealing with several outputs I obtain from QIIME, texts which I want to manipulate for obtaining boxplots. Every input is formatted in the same way, so the manipulation is always the same, but it changes the source name. For each input, I want to extract the last 5 rows, have a mean for each column/sample, associate the values to sample experimental labels (Group) taken from the mapfile and put them in the order I use for making a boxplot of all the 6 data obtained.

In bash, I do something like "for i in GG97 GG100 SILVA97 SILVA100 NCBI RDP; do cp ${i}/alpha/collated_alpha/chao1.txt alpha_tot/${i}_chao1.txt; done" to do a command various times changing the names in the code in an automatic way through ${i}.

I'm struggling to find a way to do the same with R. I thought creating a vector containing the names and then using a for cycle by moving the i with [1], [2] etc., but it doesn't work, it stops at the read.delim line not finding the file in the wd.

Here's the manipulation code I wrote. After the comment, it will repeat itself 6 times with the 6 databases I'm using (GG97 GG100 SILVA97 SILVA100 NCBI RDP).

PLUS, I repeat this process 4 times because I have 4 metrics to use (here I'm showing shannon, but I also have a copy of the code for chao1, observed_species and PD_whole_tree).

...

ANSWER

Answered 2020-Jan-09 at 12:11

You didn't provide a Minimal reproducible example, so this answer cannot guarantee correctness.

An important point to note is that you use rm(...), so this means some variables are only relevant within a certain scope. Therefore, encapsulate this scope into a function. This makes your code reusable and spares you the manual variable removal:

Source https://stackoverflow.com/questions/59661496

QUESTION

python bar chart plot of 16S bacterial abundance

Asked 2019-Nov-23 at 17:28

I have this kind of data (data.txt), a file in tab delimited text ):

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ANSWER

Answered 2019-Nov-23 at 17:28

There are many ways to solve this problem, here is a solution using pandasand bokeh:

Source https://stackoverflow.com/questions/49166822

QUESTION

How to use integers in subprocess.call

Asked 2018-Mar-12 at 23:18

I am writing a program that runs qiime. I need the program to recognize numbers that the user types on the command line, but I think that subprocess.call may not be able to tell that the numbers are integers.

What I have so far:

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ANSWER

Answered 2018-Mar-12 at 23:18

This is not really about integers/strings but actually about the parsing of the options with spaces.

In all the places where you have

Source https://stackoverflow.com/questions/49245859

QUESTION

User input in subprocess.call

Asked 2018-Mar-11 at 00:44

I am writing a program to automate some qiime2 commands. I want to incorporate user input.

So far, I have:

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ANSWER

Answered 2018-Mar-11 at 00:44

Don't use shell=True when the command you are executing is built from unsanitized user input. It can lead to the user being able to execute arbitrary commands, even if this is not wanted.

Also, pass the command as a list to subprocess.call to avoid issues with quoting.

Source https://stackoverflow.com/questions/49215384

QUESTION

bash: python: .py: command not found

Asked 2017-Nov-25 at 05:58

I am trying to run the following command in QIIME2 virtual machine, installed on macbook but the code is not working

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ANSWER

Answered 2017-Nov-25 at 05:58

To execute a Python script in this way, you need three things:

The file needs to have the executable bit set for you. To do this, try using: chmod u+x validate_mapping_file.py
The file needs to begin with a shebang, for example #!/usr/bin/env python3 which will tell the system to run the script using the python3 executable according to your environment
The file needs to be in one of the directories in your PATH environment variable. You can add the current directory using export PATH=$PWD:$PATH or use ./validate_mapping_file.py instead of just validate_mapping_file.py (thanks @Grisha)

Afterwards you should be able to execute the script the way you tried before.

Source https://stackoverflow.com/questions/47443988

QUESTION

if then bash statement does not work with qiime commands

Asked 2017-Oct-25 at 08:25

I just started to bash and I have been stuck for sometime on a simple if;then statement. I use bash to run QIIME commands which are written in python. These commands allow me to deal with microbial DNA. From the raw dataset from the sequencing I first have to first check if they match the format that QIIME can deal with before I can proceed to the rest of the commands.

...

ANSWER

Answered 2017-Oct-25 at 08:25

I think the code can be improved. What's wrong in your code is mostly the dollar operator used to call variables once you set them.

You are counting the rows inside temp.txt. A better version would be:

Source https://stackoverflow.com/questions/46906854

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

Vulnerabilities

No vulnerabilities reported

Install qiime

You can download it from GitHub.
You can use qiime 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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