README
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scram2 package files - use in combination with the cmd/scram/scram.go main file.
Documentation
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Index ¶
- func AlignMirnas(seq_map map[string]interface{}, mirna_map map[string]*mirnaSeqDup) map[string]interface{}
- func AlignReads(seq_map map[string]interface{}, ref_slice []*HeaderRef, nt int) map[string]map[string][]int
- func Compare(countsMap1 map[string]interface{}, countsMap2 map[string]interface{}) map[string]interface{}
- func CompareNoSplitCounts(alignmentMap map[string]map[string][]int, seqMap map[string]interface{}) map[string]interface{}
- func CompareSplitCounts(alignmentMap map[string]map[string][]int, seqMap map[string]interface{}) map[string]interface{}
- func CompareToCsv(cdpAlignmentMap map[string]interface{}, nt int, outPrefix string, ...)
- func IndvSeqLoad(seqFiles []string, fileType string, adapter string, minLen int, maxLen int, ...) (map[string]interface{}, []string)
- func MirLoad(mirFile string) map[string]*mirnaSeqDup
- func MirnaCompare(mirnaAlignmentMap1 map[string]interface{}, ...) map[string]interface{}
- func ProfileNoSplit(alignmentMap map[string]map[string][]int, seqMap map[string]interface{}) map[string]interface{}
- func ProfileSplit(alignmentMap map[string]map[string][]int, seqMap map[string]interface{}) map[string]interface{}
- func ProfileToCsv(profileAlignmentsMap map[string]interface{}, refSlice []*HeaderRef, nt int, ...)
- func SeqLoad(seqFiles []string, fileType string, adapter string, minLen int, maxLen int, ...) map[string]interface{}
- type HeaderRef
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
func AlignMirnas ¶
func AlignMirnas(seq_map map[string]interface{}, mirna_map map[string]*mirnaSeqDup) map[string]interface{}
AlignMirnas aligns reads of any length to the miRNAs in the sense orientation only. Only alignments in which len(read)==len(mirna) are retained. A map of mirna_header:mean_se_dup is returned
func AlignReads ¶
func AlignReads(seq_map map[string]interface{}, ref_slice []*HeaderRef, nt int) map[string]map[string][]int
AlignReads aligns reads of length nt to one or more reference sequences, with exact matches in forward or reverse complement accepted. A map of ref_header:[srna_seq:[pos,pos,...],...] is returned.
func Compare ¶
func Compare(countsMap1 map[string]interface{}, countsMap2 map[string]interface{}) map[string]interface{}
Compare combines individual alignments for set sets of sequences (treatments). It returns a map of ref header as key and a slice of set 1 mean/se and set2 mean/se as value.
func CompareNoSplitCounts ¶
func CompareNoSplitCounts(alignmentMap map[string]map[string][]int, seqMap map[string]interface{}) map[string]interface{}
CompareNoSplitCounts takes and alignment map and returns a map with the ref_header as key and the mean_se (mean and standard error) of aligned reads for that ref seq as value. Read counts are NOT split by the number of times a read aligns to all reference sequences.
func CompareSplitCounts ¶
func CompareSplitCounts(alignmentMap map[string]map[string][]int, seqMap map[string]interface{}) map[string]interface{}
CompareSplitCounts takes and alignment map and returns a map with the ref_header as key and the mean_se (mean and standard error) of aligned reads for that ref seq as value. Read counts are split by the number of times a read aligns to all reference sequences.
func CompareToCsv ¶
func CompareToCsv(cdpAlignmentMap map[string]interface{}, nt int, outPrefix string, aFileOrder []string, bFileOrder []string)
CompareToCsv writes the output to a csv file.
func IndvSeqLoad ¶
func IndvSeqLoad(seqFiles []string, fileType string, adapter string, minLen int, maxLen int, minCount float64, noNorm bool) (map[string]interface{}, []string)
IndvSeqLoad loads 1 or more small RNA seq. read files. It returns a map with a read sequence as key and a slice of normalized or raw individual read counts as a value. Little format checking is performed. It is required that the input file is correctly formatted.
func MirLoad ¶
MirLoad loads mature miRNA sequences from a mirna FASTA file (i.e. generated from miRBase) It returns a map of headers : mirna sequences (converted to DNA)
func MirnaCompare ¶
func ProfileNoSplit ¶
func ProfileNoSplit(alignmentMap map[string]map[string][]int, seqMap map[string]interface{}) map[string]interface{}
ProfileNoSplit takes and alignment map and a sequence map as an input. It returns a map of single alignments with a reference header as key and a single alignments struct as value. Each single alignments struct is comprised of single_alignment structs (read seq, position, count, se). The count for each read alignment is NOT split by the number of times a read aligns.
func ProfileSplit ¶
func ProfileSplit(alignmentMap map[string]map[string][]int, seqMap map[string]interface{}) map[string]interface{}
ProfileSplit takes and alignment map and a sequence map as an input. It returns a map of single alignments with a reference header as key and a single alignments struct as value. Each single alignments struct is comprised of single_alignment structs (read seq, position, count, se). The count for each read alignment is split by the number of times a read aligns.
func ProfileToCsv ¶
func ProfileToCsv(profileAlignmentsMap map[string]interface{}, refSlice []*HeaderRef, nt int, outPrefix string, fileOrder []string)
ProfileToCsv writes the den results to a csv file
func SeqLoad ¶
func SeqLoad(seqFiles []string, fileType string, adapter string, minLen int, maxLen int, minCount float64, noNorm bool) map[string]interface{}
SeqLoad loads 1 or more small RNA seq. read files. It returns a map with a read sequence as key and a meanSe struct (normalised or raw read mean and standard error) as a value. Little format checking is performed. It is required that the input file is correctly formatted.
Source Files