seqkit | ultrafast toolkit for FASTA/Q file manipulation | Genomics library

 by   shenwei356 Go Version: v2.4.0 License: MIT

X-RayKey FeaturesCode SnippetsCommunity Discussions(8)VulnerabilitiesInstallSupport

kandi X-RAY | seqkit Summary

kandi X-RAY | seqkit Summary

seqkit is a Go library typically used in Artificial Intelligence, Genomics applications. seqkit has no bugs, it has no vulnerabilities, it has a Permissive License and it has medium support. You can download it from GitHub.

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
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            kandi-support Support

              seqkit has a medium active ecosystem.
              It has 1026 star(s) with 144 fork(s). There are 27 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 12 open issues and 340 have been closed. On average issues are closed in 113 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of seqkit is v2.4.0

            kandi-Quality Quality

              seqkit has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              seqkit is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              seqkit releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

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            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of seqkit
            Get all kandi verified functions for this library.

            seqkit Key Features

            No Key Features are available at this moment for seqkit.

            seqkit Examples and Code Snippets

            No Code Snippets are available at this moment for seqkit.

            Community Discussions

            Trending Discussions on seqkit

            Extract FASTA sequences (with version number) using sequence IDs (without version number) listed in txt file
            Snakemake tries to run rule, reason: Missing output files, but files are temporary
            Extract UNIQUE fasta sequences from a text file
            Add sequence lengths to headers in a fasta file
            Snakemake with specific combination of files as input
            replace names in fasta
            Run command on pair of files (different file types) with matching character string
            How to slice multiple fasta sequences to substrings with the length in a range in fasta format?

            QUESTION

            Extract FASTA sequences (with version number) using sequence IDs (without version number) listed in txt file
            Asked 2020-Nov-27 at 04:06

            I would like to extract specific sequences from myfile.fasta based on the ids listed in transcript_id.txt file. My main problem is that my transcript_id.txt file only lists transcripts ids while fasta file also has transcript versions and transcripts listed in transcript_id.txt can have multiple versions in fasta file. I have tried several approach (listed below) but couldn't get what I need.

            myfile.fasta

            ...

            ANSWER

            Answered 2020-Nov-25 at 15:47

            1st solution: Could you please try following. Written and tested with shown samples in GNU awk.

            Source https://stackoverflow.com/questions/65007580

            QUESTION

            Snakemake tries to run rule, reason: Missing output files, but files are temporary
            Asked 2020-Jul-17 at 08:40

            I have a series of rule leading into using vsearch, with the barebones shown here:

            ...

            ANSWER

            Answered 2020-Jul-17 at 08:40

            I would move seqkit fq2fa to its own rule producing the temp file nedded by vsearch. Like (not tested):

            Source https://stackoverflow.com/questions/62942329

            QUESTION

            Extract UNIQUE fasta sequences from a text file
            Asked 2020-Feb-21 at 23:06

            I have a TXT file:

            ...

            ANSWER

            Answered 2020-Feb-21 at 23:06

            Try with

            Source https://stackoverflow.com/questions/60303552

            QUESTION

            Add sequence lengths to headers in a fasta file
            Asked 2020-Jan-01 at 00:08

            I have a multifasta file and would like to add the sequence lengths to the headers by keeping the sequences.

            ...

            ANSWER

            Answered 2020-Jan-01 at 00:08

            When the line doesn't begin with >, accumulate the sequence data in a variable and add its length to a total variable. When the line begins with >, print the sequence that you were accumulating, and save the current line as the name of the next sequence. Finally, at the end of the file print the last sequence.

            Source https://stackoverflow.com/questions/59537796

            QUESTION

            Snakemake with specific combination of files as input
            Asked 2019-Dec-20 at 17:30

            Do you know how to run snakemake with specific combination of files? i.e. In this txt files I have list of sequence ID's:

            ...

            ANSWER

            Answered 2019-Dec-20 at 16:54

            Comma is missing in rule seqkit input.

            Source https://stackoverflow.com/questions/59425953

            QUESTION

            replace names in fasta
            Asked 2019-Aug-29 at 06:50

            I want to change the sequence names in a fasta file according a text file containing new names. I found several approaches but seqkit made a good impression, anyway I can´t get it running. Replace key with value by key-value file

            The fasta file seq.fa looks like

            ...

            ANSWER

            Answered 2019-Aug-28 at 17:43

            could you please try following.

            Source https://stackoverflow.com/questions/57697102

            QUESTION

            Run command on pair of files (different file types) with matching character string
            Asked 2019-Jan-05 at 16:56

            I have a list of files:

            ...

            ANSWER

            Answered 2019-Jan-05 at 08:11

            With bash's Parameter Expansion:

            Source https://stackoverflow.com/questions/54049861

            QUESTION

            How to slice multiple fasta sequences to substrings with the length in a range in fasta format?
            Asked 2019-Jan-05 at 11:39

            Given a file containing multiple protein sequences in fasta format with different lengthes, how to generate a fasta format protein fragments (substrings) with length i ( i is greater or equal to 5 but not more than the length of each protein,respectively) ?

            For example,the protein sequences file:

            ...

            ANSWER

            Answered 2019-Jan-05 at 11:39

            With Perl, please try:

            Source https://stackoverflow.com/questions/54048759

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

            Vulnerabilities

            No vulnerabilities reported

            Install seqkit

            Go to Download Page for more download options and changelogs, or install via conda:.

            Support

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