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Bio​Python​Utils

by bosborne ST3

BioPython utilities for Sublime Text 3

Details

  • 2017.12.18.15.00.45
  • github.​com
  • github.​com
  • 7 years ago
  • 2 weeks ago
  • 11 years ago

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  • Total 2K
  • Win 1K
  • Mac 463
  • Linux 500
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Readme

Source
raw.​githubusercontent.​com

BioPythonUtils

BioPython Utilities for Sublime Text 3.

Install

Install BioPythonUtils using Package Control. If you don't have Package Control see https://sublime.wbond.net.

The BioPython 1.68 code is bundled with this package, you do not need to install it.

Configure

Add your email address and BLAST defaults to your Settings file.

{
    "email_for_eutils": "bio@bioteam.net",
    "entrez_retmax": 1000,
    "remote_blast_app": "blastp",
    "remote_blast_db": "nr",
    "remote_blast_format": "Text"
}

The email address is required if you want to download from NCBI using EUtils.

Commands

First select the relevant text, then run a command in the Tools -> BioPythonUtils menu.

  • “Translate”
  • “Get Sequences by Search”
  • “Get Sequences by Id”
  • “Get Sequences by Taxon”
  • “Remote BLAST”
  • “Genbank To Fasta”

“Translate”

Translates the selected text, which can be 1 or more entries in Fasta format or 1 or more entries of plain text. For example: ~~~~

2 atgctatcaatcgcgattctgcttctgctaatagcagagggctcctctcaaaattacaca ggaaatcctgtgatatgcctggggcaccatgctgtgtccaatgggacaatggtgaaaacc 1 atgctatcaatcacgattctgttcctgctcatagcagagggctcctctcagaattacaca gggaatcctgtgatatgcctgggacatcatgctgtatccaatgggacaatggtgaaaacc

or:

atgctatcaatcacgattctgttcctgctcatagcagagggctcctctcagaattacaca gggaatcctgtgatatgcctgggacatcatgctgtatccaatgggacaatggtgaaaacc

atgctgtcaatcacgattctgttggtgctcatagcagagggctcctctcagaattacacg gggagtcctgtgatatgcctgggacatcatgctgtatccaatgggacaatggtgaaaacg

Translation starts at the first codon and continues to the last, regardless of stop codons.

#### "Get Sequences by Search"

Queries [NCBI Nucleotide](https://www.ncbi.nlm.nih.gov/nucleotide/) using [Entrez](https://www.ncbi.nlm.nih.gov/books/NBK184582/)
search service and the selected text and downloads the sequence results in GenBank format.
For example:

human[ORGN] AND AKT1[GENE]

The default maximum number of records downloaded is 20, if you want more than 20 set
the value in your "Settings - User" file ("entrez_retmax").

#### "Get Sequences by Id"

Downloads sequence from [NCBI](http://www.ncbi.nlm.nih.gov) using the selected ids. Ids can be delimited by commas,
returns, or space. For example:

KC781785 2

or:

2 KC781786

or:

284218, 203807

#### "Get Sequences by Taxon"

Downloads a taxon as GenBank format entries from [NCBI](http://www.ncbi.nlm.nih.gov) using the selected
[NCBI Taxonomy](http://www.ncbi.nlm.nih.gov/taxonomy) ids. Ids can be delimited by commas, returns, or space.

#### "Remote BLAST"

Sends the selected Fasta format or "plain" sequence(s) to the [BLAST server at NCBI](http://blast.ncbi.nlm.nih.gov/Blast.cgi) and retrieves the results. You can set the application, database, and result format using the Command Palette. You can also set some default values in your "Settings - User" file ("remote_blast_app", "remote_blast_format"). Note that the available databases change depending on the BLAST application.

#### "Genbank To Fasta"

Creates Fasta format records from the selection, 1 or more GenBank format records.

### Issues

The interaction between the plugin and various services at NCBI are synchronized, so Sublime Text is
unusable while the queries ("Get Sequences*", "Remote BLAST") are running.