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Patch the production of the ratio file

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This commit is contained in:
Eric Coissac
2025-02-27 10:19:39 +01:00
parent 791d253edc
commit 0067152c2b
6 changed files with 64 additions and 58 deletions
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2
README.md
View File

@ -37,7 +37,7 @@ curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install
bash -s -- --install-dir test_install --obitools-prefix k
```
In this case, the binaries will be installed in the `test_install` directory and all command names will be prefixed with the letter `k`. Thus `obigrep` will be named `kobigrep`.
In this case, the binaries will be installed in the `test_install` directory and all command names will be prefixed with the letter `k`. Thus, `obigrep` will be named `kobigrep`.
## Continuing the analysis...

24
pkg/obiformats/fastseq_json_header.go
View File

@ -13,7 +13,7 @@ import (
"github.com/buger/jsonparser"
)
func _parse_json_map_string(str []byte, sequence *obiseq.BioSequence) (map[string]string, error) {
func _parse_json_map_string(str []byte) (map[string]string, error) {
values := make(map[string]string)
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -25,7 +25,7 @@ func _parse_json_map_string(str []byte, sequence *obiseq.BioSequence) (map[strin
return values, nil
}
func _parse_json_map_int(str []byte, sequence *obiseq.BioSequence) (map[string]int, error) {
func _parse_json_map_int(str []byte) (map[string]int, error) {
values := make(map[string]int)
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -41,7 +41,7 @@ func _parse_json_map_int(str []byte, sequence *obiseq.BioSequence) (map[string]i
return values, nil
}
func _parse_json_map_float(str []byte, sequence *obiseq.BioSequence) (map[string]float64, error) {
func _parse_json_map_float(str []byte) (map[string]float64, error) {
values := make(map[string]float64)
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -57,7 +57,7 @@ func _parse_json_map_float(str []byte, sequence *obiseq.BioSequence) (map[string
return values, nil
}
func _parse_json_map_bool(str []byte, sequence *obiseq.BioSequence) (map[string]bool, error) {
func _parse_json_map_bool(str []byte) (map[string]bool, error) {
values := make(map[string]bool)
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -73,7 +73,7 @@ func _parse_json_map_bool(str []byte, sequence *obiseq.BioSequence) (map[string]
return values, nil
}
func _parse_json_map_interface(str []byte, sequence *obiseq.BioSequence) (map[string]interface{}, error) {
func _parse_json_map_interface(str []byte) (map[string]interface{}, error) {
values := make(map[string]interface{})
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -100,7 +100,7 @@ func _parse_json_map_interface(str []byte, sequence *obiseq.BioSequence) (map[st
return values, nil
}
func _parse_json_array_string(str []byte, sequence *obiseq.BioSequence) ([]string, error) {
func _parse_json_array_string(str []byte) ([]string, error) {
values := make([]string, 0)
jsonparser.ArrayEach(str,
func(value []byte, dataType jsonparser.ValueType, offset int, err error) {
@ -162,7 +162,7 @@ func _parse_json_array_bool(str []byte, sequence *obiseq.BioSequence) ([]bool, e
return values, nil
}
func _parse_json_array_interface(str []byte, sequence *obiseq.BioSequence) ([]interface{}, error) {
func _parse_json_array_interface(str []byte) ([]interface{}, error) {
values := make([]interface{}, 0)
jsonparser.ArrayEach(str,
func(value []byte, dataType jsonparser.ValueType, offset int, err error) {
@ -261,14 +261,14 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
sequence.SetCount(int(count))
case skey == "obiclean_weight":
weight, err := _parse_json_map_int(value, sequence)
weight, err := _parse_json_map_int(value)
if err != nil {
log.Fatalf("%s: Cannot parse obiclean weight %s", sequence.Id(), string(value))
}
annotations[skey] = weight
case skey == "obiclean_status":
status, err := _parse_json_map_string(value, sequence)
status, err := _parse_json_map_string(value)
if err != nil {
log.Fatalf("%s: Cannot parse obiclean status %s", sequence.Id(), string(value))
}
@ -276,7 +276,7 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
case strings.HasPrefix(skey, "merged_"):
if dataType == jsonparser.Object {
data, err := _parse_json_map_int(value, sequence)
data, err := _parse_json_map_int(value)
if err != nil {
log.Fatalf("%s: Cannot parse merged slot %s: %v", sequence.Id(), skey, err)
} else {
@ -316,9 +316,9 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
annotations[skey], err = strconv.ParseFloat(obiutils.UnsafeString(value), 64)
}
case jsonparser.Array:
annotations[skey], err = _parse_json_array_interface(value, sequence)
annotations[skey], err = _parse_json_array_interface(value)
case jsonparser.Object:
annotations[skey], err = _parse_json_map_interface(value, sequence)
annotations[skey], err = _parse_json_map_interface(value)
case jsonparser.Boolean:
annotations[skey], err = jsonparser.ParseBoolean(value)
case jsonparser.Null:

2
pkg/obioptions/version.go
View File

@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be
// commited
var _Commit = "6245d7f"
var _Commit = "791d253"
var _Version = "Release 4.2.0"
// Version returns the version of the obitools package.

52
pkg/obitools/obiclean/graph.go
View File

@ -20,11 +20,11 @@ import (
type Ratio struct {
Sample string
SeqID string
status string
From int
To int
CFrom int
CTo int
OriginalStatus string
WOriginal int
WMutant int
COriginal int
CMutant int
Pos int
Length int
A int
@ -59,13 +59,15 @@ func makeEdge(father, dist, pos int, from, to byte) Edge {
// ratio
func EmpiricalDistCsv(filename string, data [][]Ratio, compressed bool) {
file, err := os.Create(filename)
defer file.Close()
if err != nil {
fmt.Println(err)
}
destfile, err := obiutils.CompressStream(file, true, true)
if err != nil {
fmt.Println(err)
}
defer destfile.Close()
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
@ -78,19 +80,19 @@ func EmpiricalDistCsv(filename string, data [][]Ratio, compressed bool) {
bar := progressbar.NewOptions(len(data), pbopt...)
fmt.Fprintln(destfile, "Sample,Father_id,Father_status,From,To,Weight_from,Weight_to,Count_from,Count_to,Position,length,A,C,G,T")
fmt.Fprintln(destfile, "Sample,Origin_id,Origin_status,Origin,Mutant,Origin_Weight,Mutant_Weight,Origin_Count,Mutant_Count,Position,Origin_length,A,C,G,T")
for code, dist := range data {
a1, a2 := intToNucPair(code)
for _, ratio := range dist {
fmt.Fprintf(destfile, "%s,%s,%s,%c,%c,%d,%d,%d,%d,%d,%d,%d,%d,%d,%d\n",
ratio.Sample,
ratio.SeqID,
ratio.status,
ratio.OriginalStatus,
a1, a2,
ratio.From,
ratio.To,
ratio.CFrom,
ratio.CTo,
ratio.WOriginal,
ratio.WMutant,
ratio.COriginal,
ratio.CMutant,
ratio.Pos,
ratio.Length,
ratio.A,
@ -453,16 +455,20 @@ func EstimateRatio(samples map[string]*[]*seqPCR, minStatRatio int) [][]Ratio {
if father.Weight >= minStatRatio && edge.Dist == 1 {
s := father.Sequence.Sequence()
ratio[edge.NucPair] = append(ratio[edge.NucPair],
Ratio{name,
father.Sequence.Id(), Status(father.Sequence)[name],
father.Weight, seq.Weight,
father.Count, seq.Count,
edge.Pos,
father.Sequence.Len(),
bytes.Count(s, []byte("a")),
bytes.Count(s, []byte("c")),
bytes.Count(s, []byte("g")),
bytes.Count(s, []byte("t"))})
Ratio{
Sample: name,
SeqID: father.Sequence.Id(),
OriginalStatus: Status(father.Sequence)[name],
WOriginal: father.Weight,
WMutant: seq.Weight,
COriginal: father.Count,
CMutant: seq.Count,
Pos: edge.Pos,
Length: father.Sequence.Len(),
A: bytes.Count(s, []byte("a")),
C: bytes.Count(s, []byte("c")),
G: bytes.Count(s, []byte("g")),
T: bytes.Count(s, []byte("t"))})
}
}

2
pkg/obiutils/set.go
View File

@ -23,7 +23,7 @@ func MakeSet[E comparable](vals ...E) Set[E] {
// It takes a variadic parameter of type E, where E is a comparable type.
// It returns a pointer to a Set of type E.
func NewSet[E comparable](vals ...E) *Set[E] {
s := MakeSet[E](vals...)
s := MakeSet(vals...)
return &s
}

24
pkg/obiutils/set_test.go
View File

@ -50,7 +50,7 @@ func TestNewSet(t *testing.T) {
}
// Test Case 2: Creating a set with multiple values
set2 := NewSet[string]("apple", "banana", "cherry")
set2 := NewSet("apple", "banana", "cherry")
if len(*set2) != 3 {
t.Errorf("Expected size to be 3, but got %d", len(*set2))
}
@ -147,7 +147,7 @@ func TestMembers(t *testing.T) {
}
// Test case 2: Set with multiple elements
set = MakeSet[int](1, 2, 3)
set = MakeSet(1, 2, 3)
expected = []int{1, 2, 3}
actual = set.Members()
sort.Ints(actual)
@ -172,7 +172,7 @@ func TestSetString(t *testing.T) {
}
// Test set with single member
singleMemberSet := NewSet[int](42)
singleMemberSet := NewSet(42)
singleMemberSetString := singleMemberSet.String()
expectedSingleMemberSetString := "[42]"
if singleMemberSetString != expectedSingleMemberSetString {
@ -180,7 +180,7 @@ func TestSetString(t *testing.T) {
}
// Test set with multiple members
multipleMembersSet := NewSet[int](1, 2, 3)
multipleMembersSet := NewSet(1, 2, 3)
multipleMembersSetString := multipleMembersSet.String()
expectedMultipleMembersSetString := "[1 2 3]"
if multipleMembersSetString != expectedMultipleMembersSetString {
@ -213,26 +213,26 @@ func TestUnion(t *testing.T) {
// Test case 2: Union of an empty set and a non-empty set should return the non-empty set
set1 = MakeSet[int]()
set2 = MakeSet[int](1, 2, 3)
expected = MakeSet[int](1, 2, 3)
set2 = MakeSet(1, 2, 3)
expected = MakeSet(1, 2, 3)
result = set1.Union(set2)
if !reflect.DeepEqual(result, expected) {
t.Errorf("Expected %v, but got %v", expected, result)
}
// Test case 3: Union of two non-empty sets with common elements should return a set with unique elements
set1 = MakeSet[int](1, 2, 3)
set2 = MakeSet[int](2, 3, 4)
expected = MakeSet[int](1, 2, 3, 4)
set1 = MakeSet(1, 2, 3)
set2 = MakeSet(2, 3, 4)
expected = MakeSet(1, 2, 3, 4)
result = set1.Union(set2)
if !reflect.DeepEqual(result, expected) {
t.Errorf("Expected %v, but got %v", expected, result)
}
// Test case 4: Union of two non-empty sets with no common elements should return a set with all elements
set1 = MakeSet[int](1, 2, 3)
set2 = MakeSet[int](4, 5, 6)
expected = MakeSet[int](1, 2, 3, 4, 5, 6)
set1 = MakeSet(1, 2, 3)
set2 = MakeSet(4, 5, 6)
expected = MakeSet(1, 2, 3, 4, 5, 6)
result = set1.Union(set2)
if !reflect.DeepEqual(result, expected) {
t.Errorf("Expected %v, but got %v", expected, result)