obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Finalize the correct merging of statistic of occurrences, in I expect every situation

Browse Source
This commit is contained in:
Eric Coissac
2022-06-14 09:54:33 +02:00
parent 6b13729eba
commit f0de4d8f28
1 changed files with 34 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

46
pkg/obiseq/merge.go
View File

@ -10,12 +10,20 @@ import (
type StatsOnValues map[string]int
func StatsOnSlotName(key string) string {
return "merged_" + key
}
/*
Tests if the sequence has already a slot summarizing statistics
of occurrence for a given attribute.
*/
func (sequence *BioSequence) HasStatsOn(key string) bool {
if !sequence.HasAnnotation() {
return false
}
mkey := "merged_" + key
mkey := StatsOnSlotName(key)
annotations := sequence.Annotations()
_, ok := annotations[mkey]
@ -23,7 +31,7 @@ func (sequence *BioSequence) HasStatsOn(key string) bool {
}
func (sequence *BioSequence) StatsOn(key string, na string) StatsOnValues {
mkey := "merged_" + key
mkey := StatsOnSlotName(key)
annotations := sequence.Annotations()
istat, ok := annotations[mkey]
@ -66,6 +74,7 @@ func (sequence *BioSequence) StatsOn(key string, na string) StatsOnValues {
func (sequence *BioSequence) StatsPlusOne(key string, toAdd *BioSequence, na string) bool {
sval := na
annotations := sequence.Annotations()
stats := sequence.StatsOn(key, na)
retval := false
@ -93,8 +102,8 @@ func (sequence *BioSequence) StatsPlusOne(key string, toAdd *BioSequence, na str
if !ok {
old = 0
}
stats[sval] = old + 1
stats[sval] = old + toAdd.Count()
annotations[StatsOnSlotName(key)] = stats
return retval
}
@ -110,6 +119,10 @@ func (stats StatsOnValues) Merge(toMerged StatsOnValues) StatsOnValues {
return stats
}
/*
Merges two sequences
*/
func (sequence *BioSequence) Merge(tomerge *BioSequence, na string, inplace bool, statsOn ...string) *BioSequence {
if !inplace {
sequence = sequence.Copy()
@ -119,7 +132,7 @@ func (sequence *BioSequence) Merge(tomerge *BioSequence, na string, inplace bool
sequence.SetQualities(nil)
}
annotation := sequence.Annotations()
annotations := sequence.Annotations()
count := sequence.Count() + tomerge.Count()
@ -127,7 +140,8 @@ func (sequence *BioSequence) Merge(tomerge *BioSequence, na string, inplace bool
if tomerge.HasStatsOn(key) {
smk := sequence.StatsOn(key, na)
mmk := tomerge.StatsOn(key, na)
smk.Merge(mmk)
annotations[StatsOnSlotName(key)] = smk.Merge(mmk)
} else {
sequence.StatsPlusOne(key, tomerge, na)
}
@ -135,27 +149,35 @@ func (sequence *BioSequence) Merge(tomerge *BioSequence, na string, inplace bool
if tomerge.HasAnnotation() {
ma := tomerge.Annotations()
for k, va := range annotation {
for k, va := range annotations {
if !strings.HasPrefix(k, "merged_") {
vm, ok := ma[k]
if !ok || vm != va {
delete(annotation, k)
delete(annotations, k)
}
}
}
} else {
for k := range annotation {
for k := range annotations {
if !strings.HasPrefix(k, "merged_") {
delete(annotation, k)
delete(annotations, k)
}
}
}
annotation["count"] = count
annotations["count"] = count
return sequence
}
/**
Merges a set of sequence into a single sequence.
The function assumes that every sequence in the batch is
identical in term of sequence. Actually the function only
aggregates the annotations of the different sequences to be merged
Quality information is lost during the merge procedure.
*/
func (sequences BioSequenceSlice) Merge(na string, statsOn []string) *BioSequence {
seq := sequences[0]
//sequences[0] = nil