BioPythonUtils
==============

[BioPython](http://biopython.org) Utilities for [Sublime Text 3](http://www.sublimetext.com/3).

### Install

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

The [BioPython](http://biopython.org) 1.68 code is bundled with this package, you do not need to install it.

### Configure

Add your email address and [BLAST](http://blast.ncbi.nlm.nih.gov/Blast.cgi) 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](http://www.ncbi.nlm.nih.gov)
using [EUtils](http://www.ncbi.nlm.nih.gov/books/NBK25500).

### 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.