sra

Documentation

Index

• type AccessionRecord
  • func (ar AccessionRecord) String() string
• type Itemer
• type SRASetter
• type SraAnalysis
  • func (sa SraAnalysis) GetAccession() string
  • func (sa SraAnalysis) IMPType() string
  • func (sa SraAnalysis) String() string
  • func (sa SraAnalysis) XMLString() string
• type SraAnalysisSet
  • func (sa SraAnalysisSet) GetAccessions() []string
  • func (sa SraAnalysisSet) GetItems() []Itemer
  • func (sa SraAnalysisSet) String() string
  • func (sa SraAnalysisSet) XMLString() string
• type SraExp
  • func (se SraExp) GetAccession() string
  • func (se SraExp) IMPType() string
  • func (se SraExp) String() string
  • func (se SraExp) XMLString() string
• type SraExpSet
  • func (se SraExpSet) GetAccessions() []string
  • func (se SraExpSet) GetItems() []Itemer
  • func (se SraExpSet) String() string
  • func (se SraExpSet) XMLString() string
• type SraItem
  • func NewSraItemsFromXML(filename string, contents []byte) []*SraItem
  • func (si *SraItem) AddAttrFromAccessionRecords(db *map[string]*AccessionRecord)
  • func (si *SraItem) AddAttrFromUploadRecords(db *map[string][]string)
  • func (si *SraItem) IMPEntityType() string
  • func (si *SraItem) Record(outPtr *os.File)
  • func (si *SraItem) UnmarshalJSON(data []byte) error
• type SraRun
  • func (sr SraRun) GetAccession() string
  • func (sr SraRun) IMPType() string
  • func (sr SraRun) String() string
  • func (sr SraRun) XMLString() string
• type SraRunSet
  • func (sr SraRunSet) GetAccessions() []string
  • func (sr SraRunSet) GetItems() []Itemer
  • func (sr SraRunSet) String() string
  • func (sr SraRunSet) XMLString() string
• type SraSample
  • func (ss SraSample) GetAccession() string
  • func (ss SraSample) IMPType() string
  • func (ss SraSample) String() string
  • func (ss SraSample) XMLString() string
• type SraSampleSet
  • func (ss SraSampleSet) GetAccessions() []string
  • func (ss SraSampleSet) GetItems() []Itemer
  • func (ss SraSampleSet) String() string
  • func (ss SraSampleSet) XMLString() string
• type SraStudy
  • func (ss SraStudy) GetAccession() string
  • func (ss SraStudy) IMPType() string
  • func (ss SraStudy) String() string
  • func (ss SraStudy) XMLString() string
• type SraStudySet
  • func (ss SraStudySet) GetAccessions() []string
  • func (ss SraStudySet) GetItems() []Itemer
  • func (ss SraStudySet) String() string
  • func (ss SraStudySet) XMLString() string
• type SraSubmission
  • func (ss SraSubmission) GetAccession() string
  • func (ss SraSubmission) GetAccessions() []string
  • func (ss SraSubmission) GetItems() []Itemer
  • func (ss SraSubmission) IMPType() string
  • func (ss SraSubmission) String() string
  • func (ss SraSubmission) XMLString() string

Types

type AccessionRecord

type AccessionRecord struct {
	Status       string
	Updated      time.Time
	Published    time.Time
	Received     time.Time
	Type         string
	Visibility   string
	Experiment   string
	Sample       string
	Study        string
	MD5          string
	BioSample    string
	BioProject   string
	Alias        string
	Issues       string
	SubmissionId string
}

func (AccessionRecord) String

func (ar AccessionRecord) String() string

type Itemer

type Itemer interface {
	String() string
	XMLString() string
	GetAccession() string
	IMPType() string
}

type SRASetter

type SRASetter interface {
	GetItems() []Itemer
	GetAccessions() []string
}

type SraAnalysis

type SraAnalysis struct {
	XMLName xml.Name `xml:"ANALYSIS"`
	sraanalysis.TAnalysisType
}

func (SraAnalysis) GetAccession

func (sa SraAnalysis) GetAccession() string

func (SraAnalysis) IMPType

func (sa SraAnalysis) IMPType() string

MGI specific

func (SraAnalysis) String

func (sa SraAnalysis) String() string

func (SraAnalysis) XMLString

func (sa SraAnalysis) XMLString() string

type SraAnalysisSet

type SraAnalysisSet struct {
	XMLName xml.Name `xml:"ANALYSIS_SET"`
	sraanalysis.TAnalysisSetType
}

func (SraAnalysisSet) GetAccessions

func (sa SraAnalysisSet) GetAccessions() []string

func (SraAnalysisSet) GetItems

func (sa SraAnalysisSet) GetItems() []Itemer

func (SraAnalysisSet) String

func (sa SraAnalysisSet) String() string

func (SraAnalysisSet) XMLString

func (sa SraAnalysisSet) XMLString() string

type SraExp

type SraExp struct {
	XMLName xml.Name `xml:"EXPERIMENT"`
	sraexp.TExperimentType
}

func (SraExp) GetAccession

func (se SraExp) GetAccession() string

func (SraExp) IMPType

func (se SraExp) IMPType() string

MGI specific

func (SraExp) String

func (se SraExp) String() string

func (SraExp) XMLString

func (se SraExp) XMLString() string

type SraExpSet

type SraExpSet struct {
	XMLName xml.Name `xml:"EXPERIMENT_SET"`
	sraexp.TExperimentSetType
}

func (SraExpSet) GetAccessions

func (se SraExpSet) GetAccessions() []string

func (SraExpSet) GetItems

func (se SraExpSet) GetItems() []Itemer

func (SraExpSet) String

func (se SraExpSet) String() string

func (SraExpSet) XMLString

func (se SraExpSet) XMLString() string

type SraItem

type SraItem struct {
	Id           string
	SubmissionId string
	XMLFileName  string
	Type         string
	Status       string
	Updated      time.Time
	Published    time.Time
	Received     time.Time
	Visibility   string
	Experiment   string
	Sample       string
	Study        string
	MD5          string
	BioSample    string
	BioProject   string
	Alias        string
	SubmitFiles  []string
	Issues       string
	XML          Itemer
}

func NewSraItemsFromXML

func NewSraItemsFromXML(filename string, contents []byte) []*SraItem

func (*SraItem) AddAttrFromAccessionRecords

func (si *SraItem) AddAttrFromAccessionRecords(
	db *map[string]*AccessionRecord,
)

func (*SraItem) AddAttrFromUploadRecords

func (si *SraItem) AddAttrFromUploadRecords(
	db *map[string][]string,
)

func (*SraItem) IMPEntityType

func (si *SraItem) IMPEntityType() string

MGI specific

func (*SraItem) Record

func (si *SraItem) Record(outPtr *os.File)

func (*SraItem) UnmarshalJSON

func (si *SraItem) UnmarshalJSON(data []byte) error

type SraRun

type SraRun struct {
	XMLName xml.Name `xml:"RUN"`
	srarun.TRunType
}

func (SraRun) GetAccession

func (sr SraRun) GetAccession() string

func (SraRun) IMPType

func (sr SraRun) IMPType() string

MGI Specific

func (SraRun) String

func (sr SraRun) String() string

func (SraRun) XMLString

func (sr SraRun) XMLString() string

type SraRunSet

type SraRunSet struct {
	XMLName xml.Name `xml:"RUN_SET"`
	srarun.TxsdRunSet
}

func (SraRunSet) GetAccessions

func (sr SraRunSet) GetAccessions() []string

func (SraRunSet) GetItems

func (sr SraRunSet) GetItems() []Itemer

func (SraRunSet) String

func (sr SraRunSet) String() string

func (SraRunSet) XMLString

func (sr SraRunSet) XMLString() string

type SraSample

type SraSample struct {
	XMLName xml.Name `xml:"SAMPLE"`
	srasample.TSampleType
}

func (SraSample) GetAccession

func (ss SraSample) GetAccession() string

func (SraSample) IMPType

func (ss SraSample) IMPType() string

MGI specific

func (SraSample) String

func (ss SraSample) String() string

func (SraSample) XMLString

func (ss SraSample) XMLString() string

type SraSampleSet

type SraSampleSet struct {
	XMLName xml.Name `xml:"SAMPLE_SET"`
	srasample.TSampleSetType
}

func (SraSampleSet) GetAccessions

func (ss SraSampleSet) GetAccessions() []string

func (SraSampleSet) GetItems

func (ss SraSampleSet) GetItems() []Itemer

func (SraSampleSet) String

func (ss SraSampleSet) String() string

func (SraSampleSet) XMLString

func (ss SraSampleSet) XMLString() string

type SraStudy

type SraStudy struct {
	XMLName xml.Name `xml:"STUDY"`
	srastudy.TStudyType
}

func (SraStudy) GetAccession

func (ss SraStudy) GetAccession() string

func (SraStudy) IMPType

func (ss SraStudy) IMPType() string

MGI specific

func (SraStudy) String

func (ss SraStudy) String() string

func (SraStudy) XMLString

func (ss SraStudy) XMLString() string

type SraStudySet

type SraStudySet struct {
	XMLName xml.Name `xml:"STUDY_SET"`
	srastudy.TStudySetType
}

func (SraStudySet) GetAccessions

func (ss SraStudySet) GetAccessions() []string

func (SraStudySet) GetItems

func (ss SraStudySet) GetItems() []Itemer

func (SraStudySet) String

func (ss SraStudySet) String() string

func (SraStudySet) XMLString

func (ss SraStudySet) XMLString() string

type SraSubmission

type SraSubmission struct {
	XMLName xml.Name `xml:"SUBMISSION"`
	srasubmission.TSubmissionType
}

func (SraSubmission) GetAccession

func (ss SraSubmission) GetAccession() string

func (SraSubmission) GetAccessions

func (ss SraSubmission) GetAccessions() []string

func (SraSubmission) GetItems

func (ss SraSubmission) GetItems() []Itemer

func (SraSubmission) IMPType

func (ss SraSubmission) IMPType() string

func (SraSubmission) String

func (ss SraSubmission) String() string

func (SraSubmission) XMLString

func (ss SraSubmission) XMLString() string