deSPI | fast classification of metagenomic sequences | Genomics library

 by   dfguan C++ Version: Current License: Apache-2.0

kandi X-RAY | deSPI Summary

kandi X-RAY | deSPI Summary

deSPI is a C++ library typically used in Artificial Intelligence, Genomics applications. deSPI has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

deSPI is a novel metagenomics reads classification tool which classifies reads by recognizing and analyzing short exact matches between reads and references with de Bruijin graph-based lightweight reference indexing. deSPI is mainly designed by Dr. Bo Liu and developed by Mr. Dengfeng Guan with the supervision of Prof. Yadong Wang in Center for Bioinformatics, Harbin Institute of Technology, China.
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              deSPI has a low active ecosystem.
              It has 10 star(s) with 5 fork(s). There are 2 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 1 open issues and 0 have been closed. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of deSPI is current.

            kandi-Quality Quality

              deSPI has 0 bugs and 0 code smells.

            kandi-Security Security

              deSPI has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              deSPI code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              deSPI is licensed under the Apache-2.0 License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              deSPI releases are not available. You will need to build from source code and install.
              Installation instructions are not available. Examples and code snippets are available.

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            deSPI Key Features

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            deSPI Examples and Code Snippets

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            Community Discussions

            QUESTION

            Count keywords and word stems in tweets
            Asked 2019-Nov-06 at 09:37

            I have a large dataframe consisting of tweets, and keyword dictionaries loaded as values that have words associated with morality (kw_Moral) and emotion (kw_Emo). In the past I have used the keyword dictionaries to subset a dataframe to get only the tweets that have one or more of the keywords present.

            For example, to create a subset with only those tweets that have emotional keywords, I loaded in my keyword dictionary...

            ...

            ANSWER

            Answered 2018-Dec-12 at 14:02

            Your requirement would seem to lend itself to a matrix type output, where, for example, the tweets are rows, and each term is a column, with the cell value being the number of occurrences. Here is a base R solution using gsub:

            Source https://stackoverflow.com/questions/53744358

            QUESTION

            Counting words and word stems in a large dataframe (RStudio)
            Asked 2019-Jan-09 at 11:12

            I have a large dataframe consisting of tweets, and a keyword dictionary loaded as a list that has words and word stems associated with emotion (kw_Emo). I need to find a way to count how many times any given word/word stem from kw_Emo is present each tweet. In kw_Emo, word stems are marked with an asterisk ( * ). For example, one word stem is ador*, meaning that I need to account for the presence of adorable, adore, adoring, or any pattern of letters that starts with ador….

            From a previous Stack Overflow discussion (see previous question on my profile), I was greatly helped with the following solution, but it only counts exact character matches (Ex. only ador, not adorable):

            1. Load relevant package.

              library(stringr)

            2. Identify and remove the * from word stems in kw_Emo.

              for (x in 1:length(kw_Emo)) { if (grepl("[*]", kw_Emo[x]) == TRUE) { kw_Emo[x] <- substr(kw_Emo[x],1,nchar(kw_Emo[x])-1) } }

            3. Create new columns, one for each word/word stem from kw_Emo, with default value 0.

              for (x in 1:length(keywords)) { dataframe[, keywords[x]] <- 0}

            4. Split each Tweet to a vector of words, see if the keyword is equal to any, add +1 to the appropriate word/word stems' column.

              for (x in 1:nrow(dataframe)) { partials <- data.frame(str_split(dataframe[x,2], " "), stringsAsFactors=FALSE) partials <- partials[partials[] != ""] for(y in 1:length(partials)) { for (z in 1:length(keywords)) { if (keywords[z] == partials[y]) { dataframe[x, keywords[z]] <- dataframe[x, keywords[z]] + 1 } } } }

            Is there a way to alter this solution to account for word stems? I'm wondering if it's possible to first use a stringr pattern to replace occurrences of a word stem with the exact characters, and then use this exact match solution. For instance, something like stringr::str_replace_all(x, "ador[a-z]+", "ador"). But I'm unsure how to do this with my large dictionary and numerous word stems. Maybe the loop removing [*], which essentially identifies all word stems, can be adapted somehow?

            Here is a reproducible sample of my dataframe, called TestTweets with the text to be analysed in a column called clean_text:

            dput(droplevels(head(TestTweets, 20)))

            ...

            ANSWER

            Answered 2019-Jan-08 at 12:17

            So first of all I would get rid of some of the for loops:

            Source https://stackoverflow.com/questions/54089957

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

            Vulnerabilities

            No vulnerabilities reported

            Install deSPI

            You can download it from GitHub.

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            For advising, bug reporting and requiring help, please contact dfguan@hit.edu.cn.
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