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Adds some new columns to the ratio file.

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Former-commit-id: 1b2d6116622b754670e86b683077aceac2db4ce7
This commit is contained in:
Eric Coissac
2023-02-25 15:56:23 +01:00
parent 6f28d2ab68
commit b9bf88d4df
1 changed files with 20 additions and 6 deletions
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26
pkg/obitools/obiclean/graph.go
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@ -26,6 +26,10 @@ type Ratio struct {
CTo int CTo int
Pos int Pos int
Length int Length int
A int
C int
G int
T int
} }
type Edge struct { type Edge struct {
@ -94,16 +98,16 @@ func EmpiricalDistCsv(filename string, data [][]Ratio) {
progressbar.OptionSetWidth(15), progressbar.OptionSetWidth(15),
progressbar.OptionShowIts(), progressbar.OptionShowIts(),
progressbar.OptionSetPredictTime(true), progressbar.OptionSetPredictTime(true),
progressbar.OptionSetDescription("[Save CSV stat ratio file"), progressbar.OptionSetDescription("[Save CSV stat ratio file]"),
) )
bar := progressbar.NewOptions(len(data), pbopt...) bar := progressbar.NewOptions(len(data), pbopt...)
fmt.Fprintln(file, "Sample,Father_id,Father_status,From,To,Weight_from,Weight_to,Count_from,Count_to,Position,length") fmt.Fprintln(file, "Sample,Father_id,Father_status,From,To,Weight_from,Weight_to,Count_from,Count_to,Position,length,A,C,G,T")
for code, dist := range data { for code, dist := range data {
a1, a2 := intToNucPair(code) a1, a2 := intToNucPair(code)
for _, ratio := range dist { for _, ratio := range dist {
fmt.Fprintf(file, "%s,%s,%s,%c,%c,%d,%d,%d,%d,%d,%d\n", fmt.Fprintf(file, "%s,%s,%s,%c,%c,%d,%d,%d,%d,%d,%d,%d,%d,%d,%d\n",
ratio.Sample, ratio.Sample,
ratio.SeqID, ratio.SeqID,
ratio.status, ratio.status,
@ -113,7 +117,12 @@ func EmpiricalDistCsv(filename string, data [][]Ratio) {
ratio.CFrom, ratio.CFrom,
ratio.CTo, ratio.CTo,
ratio.Pos, ratio.Pos,
ratio.Length) ratio.Length,
ratio.A,
ratio.C,
ratio.G,
ratio.T,
)
} }
bar.Add(1) bar.Add(1)
} }
@ -137,7 +146,7 @@ func Gml(seqs *[]*seqPCR, sample string, statThreshold int) string {
h {{ Sqrt $data.Count }} h {{ Sqrt $data.Count }}
w {{ Sqrt $data.Count }} w {{ Sqrt $data.Count }}
] ]
weight {{$data.Count}}
] ]
{{ end }} {{ end }}
{{ end }} {{ end }}
@ -467,13 +476,18 @@ func EstimateRatio(samples map[string]*[]*seqPCR, minStatRatio int) [][]Ratio {
for _, edge := range seq.Edges { for _, edge := range seq.Edges {
father := (*seqs)[edge.Father] father := (*seqs)[edge.Father]
if father.Weight >= minStatRatio && edge.Dist == 1 { if father.Weight >= minStatRatio && edge.Dist == 1 {
s := father.Sequence.Sequence()
ratio[edge.NucPair] = append(ratio[edge.NucPair], ratio[edge.NucPair] = append(ratio[edge.NucPair],
Ratio{name, Ratio{name,
father.Sequence.Id(), Status(father.Sequence)[name], father.Sequence.Id(), Status(father.Sequence)[name],
father.Weight, seq.Weight, father.Weight, seq.Weight,
father.Count, seq.Count, father.Count, seq.Count,
edge.Pos, edge.Pos,
father.Sequence.Len()}) father.Sequence.Len(),
bytes.Count(s, []byte("a")),
bytes.Count(s, []byte("c")),
bytes.Count(s, []byte("g")),
bytes.Count(s, []byte("t"))})
} }
} }