cgat | please refer to our newest code

by CGATOxford Python Version: v0.3.3 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | cgat Summary

cgat is a Python library. cgat has no bugs, it has no vulnerabilities, it has build file available and it has low support. However cgat has a Non-SPDX License. You can download it from GitHub.

Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps

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Quality

Security

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Support

cgat has a low active ecosystem.

It has 118 star(s) with 66 fork(s). There are 38 watchers for this library.

It had no major release in the last 12 months.

There are 6 open issues and 187 have been closed. On average issues are closed in 345 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of cgat is v0.3.3

Quality

cgat has no bugs reported.

Security

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

License

cgat has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

cgat releases are available to install and integrate.

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

Top functions reviewed by kandi - BETA

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

Build Allelele objects .
Start the worker .
Run edge r .
Join tables .
Run DESeq .
Reconciliate a gene .
Plot phenotypes .
Convert a sparse matrix to a matrix .
Run edge r .
Given a list of exons and a sequence return the position of the codon .

Get all kandi verified functions for this library.

cgat Key Features

No Key Features are available at this moment for cgat.

cgat Examples and Code Snippets

No Code Snippets are available at this moment for cgat.

Community Discussions

Trending Discussions on cgat

How to control the number of loops with user input?

How do I separate the pattern counts with R?

How do you validate that an input string only contains a set of letters?

Tatsu Parsing Performance

QUESTION

How to control the number of loops with user input?

Asked 2020-Oct-27 at 06:06

My question is: how I can define an input code that the user can be entered for example 3, 5, 6, or any number to get an output with 3 letters, 5 letters and etc(according to user input).

Output for this code is:

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ANSWER

Answered 2020-Oct-25 at 17:27

I think you can put the logic of the inner-most loop in a function and then call that function based on the input. Alternatively, you can try to solve the same problem with recursion, wherein the user-input would define the recursion depth. Initialize a global variable depth and set that to 0. In the first line of the function, increment depth with 1 and every time the function will be called, it's value will be increased. In the base case, set a condition for the depth variable and the input variable to be equal, as soon as the depth variable == the input variable, the recursion will stop.

Source https://stackoverflow.com/questions/64526182

QUESTION

How do I separate the pattern counts with R?

Asked 2019-Feb-04 at 15:10

via a program I have received the following pattern count.

Counter({'CCCC': 22115, 'TTTT': 22043, 'AAAA': 22037, 'GGGG': 21930, 'AAAC': 154, 'TTAT': 152, 'CCCA': 152, 'CCTC': 152, 'GGGC': 151, 'TTTG': 150, 'GTGG': 149, 'GCCC': 148, 'CCGC': 145, 'CGGG': 145, 'TGGG': 144, 'AGAA': 144, 'TTGT': 144, 'GAAA': 142, 'CCCG': 142, 'CCCT': 142, 'TCCC': 141, 'CAAA': 139, 'ATTT': 137, 'CGCC': 134, 'GGTG': 133, 'GAGG': 133, 'TTTA': 132, 'CTTT': 131, 'TCTT': 131, 'ACCC': 130, 'AGGG': 130, 'GGAG': 129, 'AACA': 129, 'TAAA': 129, 'TATT': 128, 'TTTC': 128, 'AAGA': 127, 'GGGA': 126, 'ACAA': 126, 'TTCT': 125, 'CTCC': 124, 'GCGG': 124, 'ATAA': 123, 'GGCG': 120, 'CACC': 119, 'AAAT': 118, 'AATA': 117, 'AAAG': 114, 'GTTT': 114, 'TGTT': 112, 'GGGT': 112, 'CCAC': 110, 'CGCG': 45, 'AACC': 43, 'TTAA': 41, 'CTCT': 41, 'GGCC': 41, 'ACTC': 40, 'CTTC': 40, 'GCCG': 39, 'ATTA': 39, 'ACCT': 39, 'TGCG': 39, 'ATAT': 39, 'TCTC': 38, 'ACGG': 38, 'TATA': 37, 'ATCA': 37, 'CGGC': 37, 'CGAG': 36, 'AGAG': 36, 'GACA': 35, 'GTTG': 35, 'TGAG': 35, 'TGGT': 35, 'CCAA': 35, 'TTGG': 34, 'GTGT': 34, 'GCGC': 34, 'CACA': 34, 'GTAA': 34, 'GTAG': 34, 'TCCA': 34, 'TCCT': 34, 'AAGG': 34, 'GAGA': 34, 'GCTT': 34, 'GTGC': 33, 'CTAT': 33, 'TTGC': 33, 'CGGA': 33, 'AGGA': 32, 'GACG': 32, 'AATT': 32, 'CAAC': 32, 'CTGC': 32, 'CTAC': 32, 'ACGA': 32, 'CGAC': 32, 'CCGG': 32, 'TCTG': 32, 'GGAA': 32, 'GGAT': 32, 'TGCT': 32, 'TTAG': 32, 'GCTG': 32, 'GAGT': 31, 'AGGC': 31, 'TTCC': 31, 'ATGA': 31, 'TTCA': 31, 'CCAT': 31, 'AAGT': 31, 'GAGC': 31, 'GTAT': 31, 'CGAA': 31, 'TCAT': 31, 'ATTC': 31, 'TGTG': 30, 'AGTT': 30, 'ATCC': 30, 'AGCA': 30, 'GTCT': 30, 'TGTC': 30, 'TCAC': 30, 'CACT': 30, 'ACTA': 30, 'TAAT': 30, 'CCGT': 30, 'CCTA': 29, 'TCGG': 29, 'GGTA': 29, 'TATG': 29, 'AACG': 29, 'CACG': 29, 'GATT': 29, 'ATCT': 29, 'TGGC': 29, 'AGCC': 29, 'TATC': 29, 'GCTC': 29, 'GGCT': 29, 'TCTA': 29, 'AACT': 28, 'CCTT': 28, 'CTTA': 28, 'TGTA': 28, 'TAGT': 28, 'AGTG': 28, 'CCGA': 27, 'AATG': 27, 'CCTG': 27, 'CTGT': 27, 'AGTC': 27, 'GTCC': 27, 'GGTT': 27, 'ACAC': 26, 'TACC': 26, 'CATC': 26, 'CATA': 26, 'GTGA': 26, 'TGAA': 26, 'GGTC': 26, 'CTTG': 26, 'GCAC': 26, 'GGCA': 26, 'CGTC': 26, 'CTGG': 26, 'TAAG': 26, 'TCGT': 26, 'TGAT': 25, 'CAGA': 25, 'GAAC': 25, 'ACCA': 25, 'TTAC': 25, 'CATT': 25, 'AGAT': 25, 'CGGT': 25, 'ATTG': 25, 'TTGA': 25, 'GATA': 24, 'GGAC': 24, 'AAGC': 24, 'GTCA': 24, 'CAAT': 24, 'GCAG': 24, 'ACAT': 24, 'TGCC': 24, 'ATAG': 24, 'CGTG': 24, 'CGCA': 24, 'TAGG': 23, 'ACCG': 23, 'TTCG': 23, 'AGCG': 23, 'GTTC': 23, 'ACTT': 23, 'CGTT': 23, 'AGAC': 23, 'GCAT': 22, 'TCCG': 22, 'TAAC': 22, 'ACGC': 22, 'CAGC': 22, 'GACC': 22, 'CATG': 22, 'TCGA': 22, 'TAGA': 22, 'GCAA': 22, 'CTCG': 22, 'TACT': 22, 'AATC': 21, 'CGCT': 21, 'GAAT': 21, 'GCGT': 21, 'AGTA': 21, 'GCCA': 21, 'ATGG': 21, 'TCAA': 21, 'CTCA': 21, 'TGGA': 20, 'GAAG': 20, 'GATC': 20, 'TGCA': 20, 'GCCT': 19, 'GTCG': 19, 'CAAG': 19, 'TCGC': 19, 'CTGA': 19, 'GATG': 19, 'CTAA': 19, 'GCGA': 19, 'ATAC': 18, 'GTTA': 18, 'GCTA': 18, 'AGGT': 18, 'CCAG': 18, 'ACAG': 18, 'CTAG': 17, 'CGTA': 17, 'ACGT': 17, 'TACA': 17, 'AGCT': 16, 'CAGG': 16, 'ATGT': 16, 'ATCG': 16, 'ATGC': 15, 'TGAC': 14, 'TAGC': 14, 'ACTG': 14, 'TCAG': 14, 'CGAT': 14, 'TACG': 13, 'CAGT': 11, 'GTAC': 10, 'GACT': 9})

I want to convert it now as a list, so that in the first column "AAAA" there are all corresponding values and so also for all combinations. Does anyone have an idea how to program this well?

This is how I read the data into R:

daten <- read.table("/PATTERN.txt", header = FALSE, sep = "\t");

So far I've tried direct reading, but somehow it doesn't really work. It should look like this:

AAAA CCCC

1 22128 22127

Thank you very much!

...

ANSWER

Answered 2019-Feb-04 at 13:57

This answer may help you in this particular case, but you should insist that whoever produced that result to export in such a way that can be easily imported with every programming language. Here you have a string representation of a python object which is definitely not a good way for exchanging data.

However, you can try this:

Source https://stackoverflow.com/questions/54517258

QUESTION

How do you validate that an input string only contains a set of letters?

Asked 2018-Jun-16 at 20:43

I'm attempting to write a function that takes in a string of any number of characters, and validates that the string contains only a predefined set of characters (none to many of each of those four characters).

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ANSWER

Answered 2018-Jun-16 at 20:02

You could use a regex pattern such as /^[CAGT]*$/ and the test() method to check each string.

[] will match any character within that set and * means 0 or more of those characters. So this essentially says from the start: ^ to the end $ there must be 0 or more of C or A or G or Ts.

Source https://stackoverflow.com/questions/50891198

QUESTION

Tatsu Parsing Performance

Asked 2018-Mar-03 at 15:34

I've implemented a grammar in Tatsu for parsing a description of a quantum program Quipper ASCII (link). The parser works but is slow for the files I'm looking at (about 10kB-1MB size, see the resources directory). It takes approximately 10-30 seconds to parse some files. The grammar is very straightforward and it should be possible to parse these files fairly quickly. One thing I've tried is adding cuts wherever possible to make sure there is no unneeded backtracking. The grammar is specified as

...

ANSWER

Answered 2018-Mar-03 at 15:34

The problem may be the @@whitespace definition, because it matches the empty string.

You could try:

Source https://stackoverflow.com/questions/49016536

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

Vulnerabilities

No vulnerabilities reported

Install cgat

You can download it from GitHub.
You can use cgat 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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