#+TITLE: micronota

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micronota is an open-source, BSD-licensed package to annotate microbial genomes and metagenomes.

As Python 3 matures and majority python packages support Python 3, the scientific Python community is in favor of dropping Python 2 compatibility. Thus, micronota will only support Python 3. This will allow micronota to have few dependency and avoid maintenance of Python 2 legacy code.

* Introduction

  micronota can annotate multiple features including coding genes, prophage, CRISPR, tRNA, rRNA and other ncRNAs. It has a customizable framework to integrate additional tools and databases. Generally, the annotation can be classified into 2 categories: structural annotation and functional annotation. Structural annotation is the identification of the genetic elements on the sequence and functional annotation is to assign functions to those elements.

* Install

  To install the latest release of micronota:
  #+BEGIN_SRC sh
    conda install micronota
  #+END_SRC


  Or you can install through ~pip~:
  #+BEGIN_SRC sh
    pip install micronota
  #+END_SRC

  To install the latest developping version:
  #+BEGIN_SRC
    pip install git+git://github.com/biocore/micronota.git
  #+END_SRC

* Prepare Databases

  To prepare (download and format) the files of TIGRFAM to the right form read by micronota:
  #+BEGIN_SRC
    micronota database prepare tigrfam --cache_dir ~/database
  #+END_SRC

* Config File

  By default, micronota will read =~/.micronota.conf= file to set up the environment or tune the parameters, if this config file exists.

  For example, the default directory to store the database files is =~/micronota_db=, but you can override it to =/home/username/db= by setting this in =~/.micronota.conf=:
  #+BEGIN_EXAMPLE
    [GENERAL]
    db_path = /home/username/db
  #+END_EXAMPLE

  micronota will look for the key =db_path= in the section =GENERAL= to update the database path.

  Besides setting up the environment, you can also specify the tools to run and the order to run. Here is an example:
  #+BEGIN_EXAMPLE
    [GENERAL]
    # overwrite the default setting
    db_path = db

    [FEATURE]
    # run prodigal first
    prodigal = 1
    # don't run infernal
    infernal = 0

    # next to annotate CDS
    [CDS]
    # run diamond tegother with uniref database
    diamond = uniref
    # skip running hmmer
    hmmer = 0
  #+END_EXAMPLE

  The format of the config file is widely used in different OS platforms and described [[https://docs.python.org/3/library/configparser.html#supported-ini-file-structure][here]]. =0= / =1=, =no= / =yes= , =false= / =true=, =on= / =off= can all be used to turn off or on each tool. If the tool need a database file to run with, specify the database instead of the indicator.

* Parameter File
  You can specify the parameter for each individual tools. For example, if you want to run Prodigal with genetic translation table 1, instead of the default translation table, you can create a file param.cfg:
  #+BEGIN_EXAMPLE
    [prodigal]
    # set translation table to 1
    -t = 1
  #+END_EXAMPLE

  Here, Prodigal has an option =-t= to specify translation table, so you set =-t= to =1=. All the options of all the supported tools should be able to be set up this way.

  After creating the config file, then you can run:
  #+BEGIN_SRC sh
    micronota annotate -i input.fa -o output_dir --param param.cfg
  #+END_SRC

* Print Configure Info

  To check the micronota setup, you can run:
  #+BEGIN_SRC
    micronota info
  #+END_SRC

  It will print out the system info, databases available, external tools, and other configuration info.

* Sequence Features to Identify

    | Features                | Supported | Tools                                            |
    |-------------------------+-----------+--------------------------------------------------|
    | coding gene             | yes       | Prodigal                                         |
    | tRNA                    | ongoing   | Aragorn                                          |
    | ncRNA                   | yes       | Infernal                                         |
    | CRISPR                  | ongoing   | MinCED                                           |
    | ribosomal binding sites | ongoing   | RBSFinder                                        |
    | prophage                | ongoing   | PHAST                                            |
    | replication origin      | todo      | Ori-Finder 1 (bacteria) & Ori-Finder 2 (archaea) |
    | microsatellites         | todo      | nhmmer?                                          |
    | signal peptide          | ongoing   | SignalP                                          |
    | transmembrane proteins  | ongoing   | TMHMM                                            |

* Databases Supported

    | Databases | Supported |
    |-----------+-----------|
    | TIGRFAM   | yes       |
    | UniRef    | yes       |
    | Rfam      | ongoing   |

* Getting help

To get help with micronota, you should use the [[https://biostars.org/t/micronota][micronota tag]] on Biostars. The developers regularly monitor the =micronota= tag on Biostars.


* Developing

If you're interested in getting involved in micronota development, see [[https://github.com/biocore/micronota/blob/master/CONTRIBUTING.md][CONTRIBUTING.md]].

See the list of [[https://github.com/biocore/micronota/graphs/contributors][micronota's contributors]].


* Licensing

micronota is available under the new BSD license. See [[https://github.com/biocore/micronota/blob/master/COPYING.txt][COPYING.txt]] for micronota's license, and [[https://github.com/biocore/micronota/tree/master/licenses][the licenses directory]] for the licenses of third-party software and databasese that are (either partially or entirely) distributed with micronota.