Help us shape the future of Go! Take the 2026 Go Developer Survey

treat

package module
v0.0.2 Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: Jan 6, 2016 License: GPL-3.0 Imports: 16 Imported by: 0

README 

===============================================================================
Trypanosome RNA Editing Alignment Tool
===============================================================================

.. image:: docs/treat-logo-lg.png

------------------------------------------------------------------------
What is TREAT?
------------------------------------------------------------------------

TREAT is a multiple sequence alignment and visualization tool specifically
designed to analyze variation in sequences caused by Uridine insertion/deletion
RNA editing. This phenomenon occurs in trypanosomes, a group of unicellular
parasitic flagellate protozoa such the subspecies of Trypanosoma brucei which
are the causative agents of Human African Trypanosomiasis (HAT or African
Sleeping Sickness). The pre-mRNA sequences in trypanosomes are
posttranscriptionally edited by the insertion/deletion of uridylate residues.
TREAT aligns sequences using three bases and assembles editing sites to detect
the extent of editing of the fourth base, called the edit base. The edit base
is configurable in TREAT and by default uses 'T'. TREAT is written in Go and is
released under the GPLv3 free software license. 

------------------------------------------------------------------------
Installation
------------------------------------------------------------------------

Download the latest binary release for your system `here <https://github.com/ubccr/treat/releases>`_.
Extract the zip file::

  $ unzip treat-0.0.1.zip
  $ cd treat-0.0.1
  $ ./treat --help

------------------------------------------------------------------------
Simple Alignment
------------------------------------------------------------------------

TREAT can perform a global alignment between two arbitrary sequences detecting
the amount of insertion/deletions (indels) of a single base (called the "edit
base"). The default edit base in TREAT is "T". For example::

  $ ./treat align -1 ATCTGTATGT -2 ATTCGATTG -b T
  A-TCTGTA-TGT
  ATTC-G-ATTG-

------------------------------------------------------------------------
Alignment with Templates
------------------------------------------------------------------------

TREAT can perform global alignments using template sequences.  TREAT requires
two user provided template sequences: fully edited and pre-edited. The fully
edited template represents a mature edited mRNA transcript (completely
precisely edited mRNA). The pre-edited template represents the sequence that
will be edited in the mature RNA. TREAT accepts input sequences in FASTA
format. For example::

  # simple-templates.fa
  >Fully Edited
  CTTAATACACTTTTGATTAACAAACTTTAAA
  >Pre-Edited
  CTAATTACACTTTGATAACAAACTAAA

  # simple-sequences.fa
  >example-1
  CTTAATTACACTTTGATTAACAAACTTTAAA

Save the above sequence files and run the alignment using TREAT::

  $ ./treat align -t simple-templates.fa -f simple-sequences.fa
  ================================================================================
  example-1
  ================================================================================
  EditStop: 11
  JuncEnd: 18
  JuncLen: 7
  ================================================================================

  FE: CTTAA-TACACTTTTGATTAACAAACTTTAAA
  PE: C-TAATTACAC-TTTGA-TAACAAAC--TAAA
  CL: CTTAATTACAC-TTTGATTAACAAACTTTAAA

TREAT computes the extent of canonical editing and reports various
editing site characteristics as shown below:

.. image:: docs/treat-alignment.png

------------------------------------------------------------------------
Large Scale Alignment Analysis
------------------------------------------------------------------------

TREAT can optionally store alignments into a database for more complex
analysis, searching, and viewing in a web browser. TREAT has been tested on
RNA-Seq data containing millions of sequences reads. Here's an example using
sequences from ribosomal protein S12 (RPS12) from Trypanosoma brucei
mitochondria. 

TREAT accepts sequencing data in FASTA format. An example FASTA file
(templates.fasta) containing the Fully Edited, Pre-Edited and one alternatively
Edited template sequences is shown below::

  >RPS12-FE Fully Edited
  CTAATACACTTTTGATAACAAACTAAAGTAAAtAtAttttGttttttttGCGtAtGtGAT
  TTTTGtAtGGttGttGtttACGttttGttttAtttGttttAtGttAttAtAtGAGtCCGC
  GAttGCCCAGttCCGGtAACCGACGtGtAttGtAtGCCGtAttttAttTAtAtAAttttG
  tttGGAtGttGCGttGttttttttGttGttttAttGGtttAGttAtGTCAttAtttAttA
  tAGAGGGTGGtGGttttGttGAtttACCCGGtGTAAAGtAttAtACACGTAttGtAAGtt
  AGATTTAGAtATAAGATATGTTTTT
  >RPS12-PE Pre-Edited
  CTAATACACTTTTGATAACAAACTAAAGTAAAAAGGCGAGGATTTTTTGAGTGGGACTGG
  AGAGAAAGAGCCGTTCGAGCCCAGCCGGAACCGACGGAGAGCTTCTTTTGAATAAAAGGG
  AGGCGGGGAGGAGAGTTTCAAAAAGATTTGGGTGGGGGGAACCCTTTGTTTTGGTTAAAG
  AAACATCGTTTAGAAGAGATTTTAGAATAAGATATGTTTTT
  >RPS12-A0 Alternative Editing (Cruz-Reyes 2013) alt_start=27 alt_stop=34
  CTAATACACTTTTGATAACAAACTAAAGTAAAtAtAttttGttttttttGCGtAtGtGAT
  TTTTGtAtGGttGttGtttACGttttGttttAtttGttttAtGttAttAtAtGAGtCCGC
  GAttGCCCAGttCCGGtAACCGACGtGtAttGtAtGCCGtAttttAttTAtAtAAttttG
  tttGGAtGttGCGttGttttttttGttGttttAttGGtttAGttAtGTCAttAtttAttA
  tAGAGGGTGGtGGttttGttGAtttACCtCGttGGttTAtAtAGtAttAtACACGTAttG
  tAAGttAGATTTAGAtATAAGATATGTTTTT

FASTA file with our DNA fragment reads (sample-A.fasta)::

  >1-10
  CTAATACACTTTTGATAACAAACTAAAGATATAATATTTTTGTTTTTTTTGCGTATGTGA
  TTTTTGTATGGTTGTTGTTTACGTTTTGTTTTATTTGTTTTATGTTATTATATGAGTCCG
  CGATTGCCCAGTTCCGGTAACCGACGTGTATTGTATGCCGTATTTTATTTATATAATTTT
  GTTTGGATGTTGCGTTGTTTTTTTTGTTGTTTTATTGGTTTAGTTATGTCATTATTTATT
  ATAGAGGGTGGTGGTTTTGTTGATTTACCCGGTGTAAAGTATTATACACGTATTGTAAGT
  TAGATTTAGATATAAGATATGTTTTT
  >2-9
  CTAATACACTTTTGATAACAAACTAAAGTAAAAAGGCGAGGATTTTTTGAGTGGGATTCGGT
  ATTTGTTTTATGTTATTATATGAGTCCGCGATTGCCCAGCTCTGGTAACCGACGTGTATTGT
  ATGCCGTATTTTATTTATATAATTTTGTTTGGATGTTGCGTTGTTTTTTTTGTTGTTTTATT
  GGTTTAGTTATGTCATTATTTATTATAGAGGGTGGTGGTTTTGTTGATTTACCCGGTGTAAA
  GTATTATACACGTATTGTAAGTTAGATTTAGATATAAGATATGTTTTT
  >3-120
  CTAATACACTTTTGATAACAAACTAAAGTAAAAAGGCGAGGATTTTTTGAGTGGGATTCGGTA
  TTTGTTTTATGTTATTATATGAGTCCGCGATTGCCCAGCTCTGGTAACCGACGTGTATTGTAT
  GCCGTATTTTATTTATATAATTTTGTTTGGATGTTGCGTTGTTTTTTTTGTTGTTTTATTGGT
  TTAGTTATGTCATTATTTATTATAGAGGGTGGTGGTTTTGTTGATTTACCCGGTGTAAAGTAT
  TATACACGTATTGTAAGTTAGATTTAGATATAACATATGTTTTT

Load the sample data using TREAT::

  $ ./treat --db treat.db load -g RPS12 -f sample-1.fa -t templates.fa
  Total reads across all samples: 139
  Normalizing to average read count:: 139.0000
  Computing total read count for file: sample-1.fa
  Total reads for file: 139
  Normalized scaling factor: 1.0000
  Processing fragments for sample name : sample-1
  Loaded 3 fragment sequences for sample sample-1

A new database file has been created called "treat.db". Searching the
data using the TREAT command line tool::

  $ ./treat --db treat.db search -g RPS12 -l 10 --csv
  gene,sample,norm,read_count,alt_editing,has_mutation,edit_stop,junc_end,junc_len,junc_seq
  RPS12,sample-1,10.0000,10,0,0,137,143,6,ATATAATATTTTTG
  RPS12,sample-1,9.0000,9,0,0,95,123,28,TTCGGTATTTGTTTTATGTTATTATATGAGTCCGCGATTGCCCAGCTCTG

Search options are described below::

  $ ./treat help search
  NAME:
     search - Search database

  USAGE:
     command search [command options] [arguments...]

  OPTIONS:
     --gene, -g                       Gene Name
     --sample, -s                     One or more samples
     --edit-stop "-1"                 Edit stop
     --junc-end "-1"                  Junction end
     --junc-len "-1"                  Junction len
     --alt "0"                        Alt editing region
     --offset, -o "0"                 offset
     --limit, -l "0"                  limit
     --has-mutation                   Has mutation
     --all, -a                        Include all sequences
     --has-alt                        Has Alternative Editing
     --csv                            Output in csv format
     --no-header, -x                  Exclude header from output

Start the TREAT server and view the sequences in a web browser::

  $ ./treat --db treat.db server -p 8080
  Computing edit stop site cache for gene RPS12...
  Using template dir: /path/to/treat
  Running on http://127.0.0.1:8080

.. image:: docs/treat-screen-shot.png

------------------------------------------------------------------------
License
------------------------------------------------------------------------

TREAT is released under the GPLv3 license. See the LICENSE file. TREAT logo
designed by Nicole B. Laski.

Documentation

Index

Constants

This section is empty.

Variables

View Source 
var BASE_COMP = map[byte]byte{
	[]byte("A")[0]: []byte("T")[0],
	[]byte("C")[0]: []byte("G")[0],
	[]byte("G")[0]: []byte("C")[0],
	[]byte("T")[0]: []byte("A")[0],
	[]byte("N")[0]: []byte("N")[0],
}

Functions

This section is empty.

Types

type Alignment 

type Alignment struct {
	Key         *AlignmentKey `json:"-"`
	Id          uint64        `json:"-"`
	EditStop    int           `json:"edit_stop"`
	JuncStart   int           `json:"junc_start"`
	JuncEnd     int           `json:"junc_end"`
	JuncLen     int           `json:"junc_len"`
	ReadCount   uint32        `json:"read_count"`
	Norm        float64       `json:"norm_count"`
	HasMutation uint8         `json:"has_mutation"`
	Mismatches  uint8         `json:"mismatches"`
	Indel       uint8         `json:"indel"`
	AltEditing  uint8         `json:"alt_editing"`
	JuncSeq     string        `json:"-"`
}

func NewAlignment 

func NewAlignment(frag *Fragment, tmpl *Template, excludeSnps bool) *Alignment

func (*Alignment) MarshalBinary 

func (a *Alignment) MarshalBinary() ([]byte, error)

func (*Alignment) SimpleAlign 

func (a *Alignment) SimpleAlign(f1, f2 *Fragment) (string, string)

func (*Alignment) UnmarshalBinary 

func (a *Alignment) UnmarshalBinary(buf []byte) error

func (*Alignment) WriteTo 

func (a *Alignment) WriteTo(w io.Writer, frag *Fragment, template *Template, tw int) error

type AlignmentKey 

type AlignmentKey struct {
	Gene   string
	Sample string
}

func (*AlignmentKey) MarshalBinary 

func (k *AlignmentKey) MarshalBinary() ([]byte, error)

func (*AlignmentKey) UnmarshalBinary 

func (k *AlignmentKey) UnmarshalBinary(data []byte) error

type AltRegion 

type AltRegion struct {
	Start int
	End   int
}

type Fragment 

type Fragment struct {
	Name      string
	ReadCount uint32
	Norm      float64
	Bases     string
	EditBase  rune
	EditSite  []uint32
}

func NewFragment 

func NewFragment(name, seq string, orientation OrientationType, base rune) *Fragment

func (*Fragment) DecodeMsgpack added in v0.0.2 

func (f *Fragment) DecodeMsgpack(dec *msgpack.Decoder) error

func (*Fragment) EncodeMsgpack added in v0.0.2 

func (f *Fragment) EncodeMsgpack(enc *msgpack.Encoder) error

func (*Fragment) Len added in v0.0.2 

func (f *Fragment) Len() int

func (*Fragment) MarshalBytes 

func (f *Fragment) MarshalBytes() ([]byte, error)

func (*Fragment) String 

func (f *Fragment) String() string

func (*Fragment) ToFasta 

func (f *Fragment) ToFasta() string

func (*Fragment) UnmarshalBytes 

func (f *Fragment) UnmarshalBytes(data []byte) error

type OrientationType 

type OrientationType int8
const FORWARD OrientationType = 1
const REVERSE OrientationType = -1

type Template 

type Template struct {
	Bases      string
	EditOffset uint32
	EditStop   int
	EditBase   rune
	EditSite   [][]uint32
	BaseIndex  []uint32
	AltRegion  []*AltRegion
}

func NewTemplate 

func NewTemplate(full, pre *Fragment, alt []*Fragment, altRegion []*AltRegion) (*Template, error)

func NewTemplateFromFasta 

func NewTemplateFromFasta(path string, orientation OrientationType, base rune) (*Template, error)

func (*Template) IndexLabel added in v0.0.2 

func (tmpl *Template) IndexLabel(i int) int

func (*Template) Len 

func (tmpl *Template) Len() int

func (*Template) MarshalBytes 

func (tmpl *Template) MarshalBytes() ([]byte, error)

func (*Template) Max 

func (tmpl *Template) Max(i int) uint32

func (*Template) Size 

func (tmpl *Template) Size() int

func (*Template) String 

func (tmpl *Template) String() string

func (*Template) UnmarshalBytes 

func (tmpl *Template) UnmarshalBytes(data []byte) error

Source Files

View all Source files

Directories

Path Synopsis
cmd
treat command

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.