Documentation ¶
Index ¶
- Variables
- func AddCmd(cmd *cobra.Command, args []string)
- func Annotate(cmd *cobra.Command, args []string)
- func DeleteCmd(cmd *cobra.Command, args []string)
- func EnzymesAddCmd(cmd *cobra.Command, args []string)
- func EnzymesDeleteCmd(cmd *cobra.Command, args []string)
- func EnzymesReadCmd(cmd *cobra.Command, args []string)
- func Features(flags *Flags, conf *config.Config) [][]*Frag
- func FeaturesAddCmd(cmd *cobra.Command, args []string)
- func FeaturesCmd(cmd *cobra.Command, args []string)
- func FeaturesDeleteCmd(cmd *cobra.Command, args []string)
- func FeaturesReadCmd(cmd *cobra.Command, args []string)
- func FragmentListCmd(cmd *cobra.Command, args []string)
- func FragmentsCmd(cmd *cobra.Command, args []string)
- func ListCmd(cmd *cobra.Command, args []string)
- func NewEnzymeDB() *kv
- func NewFeatureDB() *kv
- func Sequence(flags *Flags, conf *config.Config) [][]*Frag
- func SequenceCmd(cmd *cobra.Command, args []string)
- func SequenceListCmd(cmd *cobra.Command, args []string)
- type Backbone
- type DB
- type Flags
- type Frag
- type Output
- type Primer
- type Solution
Constants ¶
This section is empty.
Variables ¶
var ( // LogLevel is a configurable log level LogLevel = zap.NewAtomicLevelAt(zap.InfoLevel) )
Functions ¶
func Annotate ¶
Annotate is for annotating a plasmid sequence given the features in the feature database. If an output path is provided, the annotated plasmid is writen to that file. Otherwise, the feature matches are written to stdout.
func DeleteCmd ¶ added in v1.0.0
DeleteCmd deletes an existing sequence database from the REPP directory.
func EnzymesAddCmd ¶ added in v1.0.0
EnzymesAddCmd the enzyme's seq in the database (or create if it isn't in the enzyme db).
func EnzymesDeleteCmd ¶ added in v1.0.0
EnzymesDeleteCmd deletes an enzyme from the database
func EnzymesReadCmd ¶ added in v1.0.0
EnzymesReadCmd writes enzymes that are similar in queried name to stdout. if multiple enzyme names include the enzyme name, they are all returned. otherwise a list of enzyme names are returned (those beneath a levenshtein distance cutoff).
func Features ¶
Features assembles a plasmid with all the Features requested with the 'repp Features [feature ...]' command repp assemble Features p10 promoter, mEGFP, T7 terminator
func FeaturesAddCmd ¶ added in v1.0.0
FeaturesAddCmd the feature's seq in the database (or create if it isn't in the feature db)
func FeaturesCmd ¶
FeaturesCmd accepts a cobra commands and assembles a plasmid containing all the features
func FeaturesDeleteCmd ¶ added in v1.0.0
FeaturesDeleteCmd the feature from the database
func FeaturesReadCmd ¶ added in v1.0.0
FeaturesReadCmd returns features that are similar in name to the feature name requested. if multiple feature names include the feature name, they are all returned. otherwise a list of feature names are returned (those beneath a levenshtein distance cutoff)
func FragmentListCmd ¶ added in v1.0.0
FragmentListCmd logs the building fragment with the name passed.
func FragmentsCmd ¶
FragmentsCmd accepts a cobra commands and assembles a list of building fragments in order
func SequenceCmd ¶
SequenceCmd takes a cobra command (with its flags) and runs plasmid.
func SequenceListCmd ¶ added in v1.0.0
SequenceListCmd is for BLAST'ing a sequence against the dbs and finding matches
Types ¶
type Backbone ¶
type Backbone struct { // URL of the backbone fragment's source URL string `json:"url"` // Seq is the sequence of the backbone (unlinearized) Seq string `json:"seq"` // Enzymes is the list of enzymes names used to linearize the backbone Enzymes []string `json:"enzymes"` // cutsites are the indexes where the backbone was cleaved Cutsites []int `json:"recognitionIndex"` // Strands of each cut direction. True if fwd, False if rev direction Strands []bool `json:"strands"` }
Backbone is for information on a linearized backbone in the output payload
type DB ¶ added in v1.0.0
type DB struct { // Name of the db Name string `json:"name"` // Path to the local database in FASTA format. Path string `json:"path"` // Cost per order from this sequence provider. // Eg $65 to order from Addgene. Cost float64 `json:"cost"` }
DB is a single sequence database. It holds the names, sequences, and cost of a single sequence source.
type Flags ¶
type Flags struct {
// contains filtered or unexported fields
}
Flags contains parsed cobra Flags like "in", "out", "dbs", etc that are used by multiple commands.
type Frag ¶
type Frag struct { // ID is a unique identifier for this fragment ID string `json:"id,omitempty"` // type of the fragment in string representation for export Type string `json:"type"` // Cost to make the fragment Cost float64 `json:"cost"` // fragment/plasmid's sequence Seq string `json:"seq,omitempty"` // sequence of a pcr fragment after PCR's addition of bp PCRSeq string `json:"pcrSeq,omitempty"` // primers necessary to create this (if pcr fragment) Primers []Primer `json:"primers,omitempty"` // contains filtered or unexported fields }
Frag is a single building block stretch of DNA for assembly
type Output ¶
type Output struct { // Target's name. In >example_CDS FASTA its "example_CDS" Target string `json:"target"` // Target's sequence TargetSeq string `json:"seq"` // Time, ex: "2018-01-01 20:41:00" Time string `json:"time"` // Execution is the number of seconds it took to execute the command Execution float64 `json:"execution"` // Solutions builds Solutions []Solution `json:"solutions"` // Backbone is the user linearized a backbone fragment Backbone *Backbone `json:"backbone,omitempty"` }
Output is a struct containing design results for the assembly.
type Primer ¶
type Primer struct { // Seq of the primer (in 5' to 3' direction) Seq string `json:"seq"` // Strand of the primer; true if top strand, false if complement Strand bool `json:"strand"` // Penalty score Penalty float64 `json:"penalty"` // PairPenalty score from primer3 PairPenalty float64 `json:"pairPenalty"` // Tm of the primer Tm float64 `json:"tm"` // GC % max GC float64 `json:"gc"` // Range that the primer spans on the fragment Range ranged `json:"-"` }
Primer is a single Primer used to create a PCR fragment
type Solution ¶
type Solution struct { // Count is the number of fragments in this solution Count int `json:"count"` // Cost estimated from the primer and sequence lengths Cost float64 `json:"cost"` // Fragments used to build this solution Fragments []*Frag `json:"fragments"` }
Solution is a single solution to build up the target plasmid.