dat

package
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Published: Apr 2, 2019 License: GPL-3.0 Imports: 16 Imported by: 0

Documentation

Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func Classify

func Classify(s, decoyTag string) (string, *err.Error)

Classify determines what kind of database originated the given sequence

func Run

func Run(m met.Data) (met.Data, *err.Error)

Run is the main entry point for the databse command

Types

type Base

type Base struct {
	UniProtDB string
	CrapDB    string
	TaDeDB    map[string]string
	Records   []Record
}

Base main structure

func New

func New() Base

New constructor

func (*Base) Create

func (d *Base) Create(temp, add, enz, tag string, crap, noD bool) *err.Error

Create processes the given fasta file and add decoy sequences

func (*Base) Deploy

func (d *Base) Deploy(temp string) *err.Error

Deploy crap file to session folder

func (*Base) Fetch

func (d *Base) Fetch(id, temp string, iso, rev bool) *err.Error

Fetch downloads a database file from UniProt

func (*Base) ProcessDB

func (d *Base) ProcessDB(file, decoyTag string) *err.Error

ProcessDB ...

func (*Base) Restore

func (d *Base) Restore() *err.Error

Restore reads philosopher results files and restore the data sctructure

func (*Base) RestoreWithPath

func (d *Base) RestoreWithPath(p string) *err.Error

RestoreWithPath reads philosopher results files and restore the data sctructure

func (*Base) Save

func (d *Base) Save(home, temp, tag string) (string, *err.Error)

Save fasta file to disk

func (*Base) Serialize

func (d *Base) Serialize() *err.Error

Serialize saves to disk a msgpack verison of the database data structure

type Record

type Record struct {
	ID               string
	OriginalHeader   string
	PartHeader       string
	EntryName        string
	ProteinName      string
	Organism         string
	GeneNames        string
	ProteinExistence string
	SequenceVersion  string
	Description      string
	Sequence         string
	Length           int
	IsDecoy          bool
	IsContaminant    bool
}

Record is the root of all database parsers

func ProcessENSEMBL

func ProcessENSEMBL(k, v, decoyTag string) (Record, *err.Error)

ProcessENSEMBL parses ENSEMBL like FASTA records

func ProcessGeneric

func ProcessGeneric(k, v, decoyTag string) (Record, *err.Error)

ProcessGeneric parses generci and uknown database headers

func ProcessNCBI

func ProcessNCBI(k, v, decoyTag string) (Record, *err.Error)

ProcessNCBI parses UniProt like FASTA records

func ProcessUniProtKB

func ProcessUniProtKB(k, v, decoyTag string) (Record, *err.Error)

ProcessUniProtKB parses UniProt like FASTA records

func ProcessUniRef

func ProcessUniRef(k, v, decoyTag string) (Record, *err.Error)

ProcessUniRef parses UniProt like FASTA records

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