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rename goutils to obiutils

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Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
This commit is contained in:
Eric Coissac
2023-03-24 10:25:12 +07:00
parent 42aae88520
commit d5e84ec676
33 changed files with 245 additions and 156 deletions
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20
doc/man/test.md Normal file
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@ -0,0 +1,20 @@
% obigrep(1)
% Eric Coissac
% February 2023
# NAME
obigrep -- filters sequence files according to numerous conditions
# SYNOPSIS
**snowplough**␣\[**-h**\]␣\[**--configfile**␣*CONFIGFILE*\]␣\[**--sort**\]␣\[**--vim**\]␣*keyword*␣\[*keyword␣...*\]␣\[**--configfile**␣*CONFIGFILE*\]␣\[**--sort**\]␣\[**--vim**\]␣*keyword*␣\[*keyword␣...*\]␣\[**--configfile**␣*CONFIGFILE*\]␣\[**--sort**\]␣\[**--vim**\]␣*keyword*␣\[*keyword␣...*\]
# DESCRIPTION
**snowplough** is a simple-minded tool which creates indices and body-searches vast quantities of ServiceNow tickets, which is useful to find out how someone before you solved one particular problem.
# GENERAL OPTIONS
**-h**, **--help**
: Display a friendly help message.

37
pkg/goutils/minmax.go
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@ -1,37 +0,0 @@
package goutils
func MinInt(x, y int) int {
if x < y {
return x
}
return y
}
func MaxInt(x, y int) int {
if x < y {
return y
}
return x
}
func MinMaxInt(x, y int) (int,int) {
if x < y {
return x,y
}
return y,x
}
func MinUInt16(x, y uint16) uint16 {
if x < y {
return x
}
return y
}
func MaxUInt16(x, y uint16) uint16 {
if x < y {
return y
}
return x
}

10
pkg/obialign/fastlcs.go
View File

@ -1,7 +1,7 @@
package obialign
// import (
// "git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
// "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
// "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
// )
@ -113,11 +113,11 @@ var _notavail = encodeValues(0, 30000, false)
// // in_matrix := false
// x1 := y - lB + extra
// x2 := extra - y
// xs := goutils.MaxInt(goutils.MaxInt(x1, x2), 0)
// xs := obiutils.MaxInt(obiutils.MaxInt(x1, x2), 0)
// x1 = y + extra
// x2 = lA + extra - y
// xf := goutils.MinInt(goutils.MinInt(x1, x2), even-1) + 1
// xf := obiutils.MinInt(obiutils.MinInt(x1, x2), even-1) + 1
// for x := xs; x < xf; x++ {
@ -174,11 +174,11 @@ var _notavail = encodeValues(0, 30000, false)
// // . 9 10 + 2 - 1
// x1 = y - lB + extra + even
// x2 = extra - y + even - 1
// xs = goutils.MaxInt(goutils.MaxInt(x1, x2), even)
// xs = obiutils.MaxInt(obiutils.MaxInt(x1, x2), even)
// x1 = y + extra + even
// x2 = lA + extra - y + even - 1
// xf = goutils.MinInt(goutils.MinInt(x1, x2), width-1) + 1
// xf = obiutils.MinInt(obiutils.MinInt(x1, x2), width-1) + 1
// for x := xs; x < xf; x++ {

10
pkg/obialign/fastlcsegf.go
View File

@ -1,8 +1,8 @@
package obialign
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
@ -109,11 +109,11 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
// in_matrix := false
x1 := y - lB + extra
x2 := extra - y
xs := goutils.MaxInt(goutils.MaxInt(x1, x2), 0)
xs := obiutils.MaxInt(obiutils.MaxInt(x1, x2), 0)
x1 = y + extra
x2 = lA + extra - y
xf := goutils.MinInt(goutils.MinInt(x1, x2), even-1) + 1
xf := obiutils.MinInt(obiutils.MinInt(x1, x2), even-1) + 1
for x := xs; x < xf; x++ {
@ -201,11 +201,11 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
// . 9 10 + 2 - 1
x1 = y - lB + extra + even
x2 = extra - y + even - 1
xs = goutils.MaxInt(goutils.MaxInt(x1, x2), even)
xs = obiutils.MaxInt(obiutils.MaxInt(x1, x2), even)
x1 = y + extra + even
x2 = lA + extra - y + even - 1
xf = goutils.MinInt(goutils.MinInt(x1, x2), width-1) + 1
xf = obiutils.MinInt(obiutils.MinInt(x1, x2), width-1) + 1
for x := xs; x < xf; x++ {

8
pkg/obiapat/pattern.go
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@ -13,9 +13,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
var _MaxPatLen = int(C.MAX_PAT_LEN)
@ -355,8 +355,8 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
start = best[0] - nerr
end = best[0] + int(pattern.pointer.pointer.patlen) + nerr
start = goutils.MaxInt(start, 0)
end = goutils.MinInt(end, sequence.Len())
start = obiutils.MaxInt(start, 0)
end = obiutils.MinInt(end, sequence.Len())
cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
cseq := (*[1 << 30]byte)(unsafe.Pointer(sequence.pointer.pointer.cseq))
@ -374,7 +374,7 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
nerr = lali - score
start = best[0] + int(pattern.pointer.pointer.patlen) - lali
end = start + lali
end = start + lali
log.Debugln("results", score, lali, start, nerr)
return
}

10
pkg/obiapat/pcr.go
View File

@ -3,8 +3,8 @@ package obiapat
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
type _Options struct {
@ -210,7 +210,7 @@ func _Pcr(seq ApatSequence,
reverse := opt.pointer.reverse
crev := opt.pointer.crev
forwardMatches := forward.FindAllIndex(seq,0,-1)
forwardMatches := forward.FindAllIndex(seq, 0, -1)
if len(forwardMatches) > 0 {
@ -256,7 +256,7 @@ func _Pcr(seq ApatSequence,
(opt.MaxLength() == 0 || length <= opt.MaxLength()) {
amplicon, _ := sequence.Subsequence(fm[1], rm[0], opt.pointer.circular)
annot := amplicon.Annotations()
goutils.MustFillMap(annot, sequence.Annotations())
obiutils.MustFillMap(annot, sequence.Annotations())
annot["forward_primer"] = forward.String()
match, _ := sequence.Subsequence(fm[0], fm[1], opt.pointer.circular)
@ -284,7 +284,7 @@ func _Pcr(seq ApatSequence,
}
}
forwardMatches = reverse.FindAllIndex(seq,0,-1)
forwardMatches = reverse.FindAllIndex(seq, 0, -1)
if forwardMatches != nil {
begin := forwardMatches[0][0]
@ -331,7 +331,7 @@ func _Pcr(seq ApatSequence,
amplicon = amplicon.ReverseComplement(true)
annot := amplicon.Annotations()
goutils.MustFillMap(annot, sequence.Annotations())
obiutils.MustFillMap(annot, sequence.Annotations())
annot["forward_primer"] = forward.String()
match, _ := sequence.Subsequence(rm[0], rm[1], opt.pointer.circular)

4
pkg/obiformats/batch_of_files_reader.go
View File

@ -3,8 +3,8 @@ package obiformats
import (
"log"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
func ReadSequencesBatchFromFiles(filenames []string,
@ -17,7 +17,7 @@ func ReadSequencesBatchFromFiles(filenames []string,
}
batchiter := obiiter.MakeIBioSequence(0)
nextCounter := goutils.AtomicCounter()
nextCounter := obiutils.AtomicCounter()
batchiter.Add(concurrent_readers)

6
pkg/obiformats/csv_writer.go
View File

@ -9,9 +9,9 @@ import (
"sync"
"time"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
@ -52,7 +52,7 @@ func CSVRecord(sequence *obiseq.BioSequence, opt Options) []string {
value = opt.CSVNAValue()
}
svalue, _ := goutils.InterfaceToString(value)
svalue, _ := obiutils.InterfaceToString(value)
record = append(record, svalue)
}
@ -132,7 +132,7 @@ func WriteCSV(iterator obiiter.IBioSequence,
options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
newIter := obiiter.MakeIBioSequence()

4
pkg/obiformats/fastseq_json_header.go
View File

@ -6,8 +6,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"github.com/goccy/go-json"
)
@ -71,7 +71,7 @@ func FormatFastSeqJsonHeader(sequence *obiseq.BioSequence) string {
annotations := sequence.Annotations()
if len(annotations) > 0 {
text, err := goutils.JsonMarshal(sequence.Annotations())
text, err := obiutils.JsonMarshal(sequence.Annotations())
if err != nil {
panic(err)

4
pkg/obiformats/fastseq_obi_header.go
View File

@ -9,8 +9,8 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"github.com/goccy/go-json"
)
@ -305,7 +305,7 @@ func FormatFastSeqOBIHeader(sequence *obiseq.BioSequence) string {
map[string]string,
map[string]interface{},
obiseq.StatsOnValues:
tv, err := goutils.JsonMarshal(t)
tv, err := obiutils.JsonMarshal(t)
if err != nil {
log.Fatalf("Cannot convert %v value", value)
}

4
pkg/obiformats/fastseq_write_fasta.go
View File

@ -11,9 +11,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
func min(x, y int) int {
@ -70,7 +70,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
opt := MakeOptions(options)
iterator = iterator.Rebatch(10000)
file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
newIter := obiiter.MakeIBioSequence()

4
pkg/obiformats/fastseq_write_fastq.go
View File

@ -10,9 +10,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
func FormatFastq(seq *obiseq.BioSequence, quality_shift int, formater FormatHeader) string {
@ -61,7 +61,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
opt := MakeOptions(options)
file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
newIter := obiiter.MakeIBioSequence()

4
pkg/obiiter/batchiterator.go
View File

@ -10,8 +10,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"github.com/tevino/abool/v2"
)
@ -375,7 +375,7 @@ func (iterator IBioSequence) Pool(iterators ...IBioSequence) IBioSequence {
allPaired = allPaired && i.IsPaired()
}
nextCounter := goutils.AtomicCounter()
nextCounter := obiutils.AtomicCounter()
newIter := MakeIBioSequence()
newIter.Add(niterator)

4
pkg/obiiter/sequence_workers.go
View File

@ -2,7 +2,7 @@ package obiiter
// func MakeSetAttributeWorker(rank string) obiiter.SeqWorker {
// if !goutils.Contains(taxonomy.RankList(), rank) {
// if !obiutils.Contains(taxonomy.RankList(), rank) {
// log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
// rank,
// taxonomy.RankList())
@ -14,4 +14,4 @@ package obiiter
// }
// return w
// }
// }

10
pkg/obikmer/counting.go
View File

@ -3,8 +3,8 @@ package obikmer
import (
"math"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
type Table4mer [256]uint16
@ -32,7 +32,7 @@ func Count4Mer(seq *obiseq.BioSequence, buffer *[]byte, counts *Table4mer) *Tabl
func Common4Mer(count1, count2 *Table4mer) int {
sum := 0
for i := 0; i < 256; i++ {
sum += int(goutils.MinUInt16((*count1)[i], (*count2)[i]))
sum += int(obiutils.MinUInt16((*count1)[i], (*count2)[i]))
}
return sum
}
@ -48,7 +48,7 @@ func Sum4Mer(count *Table4mer) int {
func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
s1 := Sum4Mer(count1)
s2 := Sum4Mer(count2)
smin := goutils.MinInt(s1, s2)
smin := obiutils.MinInt(s1, s2)
cw := Common4Mer(count1, count2)
@ -65,11 +65,11 @@ func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
func Error4MerBounds(count1, count2 *Table4mer) (int, int) {
s1 := Sum4Mer(count1)
s2 := Sum4Mer(count2)
smax := goutils.MaxInt(s1, s2)
smax := obiutils.MaxInt(s1, s2)
cw := Common4Mer(count1, count2)
errorMax := smax - cw + 2* int(math.Floor(float64(cw+5)/8.0))
errorMax := smax - cw + 2*int(math.Floor(float64(cw+5)/8.0))
errorMin := int(math.Ceil(float64(errorMax) / 4.0))
return errorMin, errorMax

27
pkg/obingslibrary/match.go
View File

@ -7,9 +7,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
type DemultiplexMatch struct {
@ -104,16 +104,14 @@ func (marker *Marker) Compile(forward, reverse string, maxError int, allowsIndel
return nil
}
func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
aseq, _ := obiapat.MakeApatSequence(sequence, false)
start, end, nerr ,matched := marker.forward.BestMatch(aseq, marker.taglength,-1)
start, end, nerr, matched := marker.forward.BestMatch(aseq, marker.taglength, -1)
if matched {
sseq := sequence.String()
direct := sseq[start:end]
tagstart := goutils.MaxInt(start - marker.taglength,0)
tagstart := obiutils.MaxInt(start-marker.taglength, 0)
ftag := strings.ToLower(sseq[tagstart:start])
m := DemultiplexMatch{
@ -125,15 +123,15 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
Error: nil,
}
start, end, nerr ,matched = marker.creverse.BestMatch(aseq, start,-1)
start, end, nerr, matched = marker.creverse.BestMatch(aseq, start, -1)
if matched {
// extracting primer matches
reverse, _ := sequence.Subsequence(start,end, false)
reverse, _ := sequence.Subsequence(start, end, false)
defer reverse.Recycle()
reverse = reverse.ReverseComplement(true)
endtag := goutils.MinInt(end+marker.taglength,sequence.Len())
endtag := obiutils.MinInt(end+marker.taglength, sequence.Len())
rtag, err := sequence.Subsequence(end, endtag, false)
defer rtag.Recycle()
srtag := ""
@ -165,14 +163,13 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
return &m
}
start, end, nerr ,matched = marker.reverse.BestMatch(aseq, marker.taglength,-1)
start, end, nerr, matched = marker.reverse.BestMatch(aseq, marker.taglength, -1)
if matched {
sseq := sequence.String()
reverse := strings.ToLower(sseq[start:end])
tagstart := goutils.MaxInt(start - marker.taglength,0)
tagstart := obiutils.MaxInt(start-marker.taglength, 0)
rtag := strings.ToLower(sseq[tagstart:start])
m := DemultiplexMatch{
@ -184,16 +181,16 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
Error: nil,
}
start, end, nerr ,matched = marker.cforward.BestMatch(aseq, end,-1)
start, end, nerr, matched = marker.cforward.BestMatch(aseq, end, -1)
if matched {
direct, _ := sequence.Subsequence(start,end, false)
direct, _ := sequence.Subsequence(start, end, false)
defer direct.Recycle()
direct = direct.ReverseComplement(true)
endtag := goutils.MinInt(end+marker.taglength,sequence.Len())
ftag, err := sequence.Subsequence(end,endtag, false)
endtag := obiutils.MinInt(end+marker.taglength, sequence.Len())
ftag, err := sequence.Subsequence(end, endtag, false)
defer ftag.Recycle()
sftag := ""
if err != nil {

26
pkg/obiseq/attributes.go
View File

@ -4,7 +4,7 @@ import (
"fmt"
"strconv"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
@ -17,6 +17,7 @@ func (s *BioSequence) HasAttribute(key string) bool {
return ok
}
// A method that returns the value of the key in the annotation map.
func (s *BioSequence) GetAttribute(key string) (interface{}, bool) {
var val interface{}
@ -43,7 +44,7 @@ func (s *BioSequence) GetIntAttribute(key string) (int, bool) {
v, ok := s.GetAttribute(key)
if ok {
val, err = goutils.InterfaceToInt(v)
val, err = obiutils.InterfaceToInt(v)
ok = err == nil
}
@ -52,15 +53,15 @@ func (s *BioSequence) GetIntAttribute(key string) (int, bool) {
// Deleting the key from the annotation map.
func (s *BioSequence) DeleteAttribute(key string) {
delete(s.Annotations(),key)
delete(s.Annotations(), key)
}
// Renaming the key in the annotation map.
func (s *BioSequence) RenameAttribute(newName, oldName string) {
val,ok := s.GetAttribute(oldName)
val, ok := s.GetAttribute(oldName)
if (ok) {
s.SetAttribute(newName,val)
if ok {
s.SetAttribute(newName, val)
s.DeleteAttribute(oldName)
}
}
@ -73,14 +74,13 @@ func (s *BioSequence) GetNumericAttribute(key string) (float64, bool) {
v, ok := s.GetAttribute(key)
if ok {
val, err = goutils.InterfaceToFloat64(v)
val, err = obiutils.InterfaceToFloat64(v)
ok = err == nil
}
return val, ok
}
// A method that returns the value of the key in the annotation map.
func (s *BioSequence) GetStringAttribute(key string) (string, bool) {
var val string
@ -101,7 +101,7 @@ func (s *BioSequence) GetBoolAttribute(key string) (bool, bool) {
v, ok := s.GetAttribute(key)
if ok {
val, err = goutils.InterfaceToBool(v)
val, err = obiutils.InterfaceToBool(v)
ok = err == nil
}
@ -115,7 +115,7 @@ func (s *BioSequence) GetIntMap(key string) (map[string]int, bool) {
v, ok := s.GetAttribute(key)
if ok {
val, err = goutils.InterfaceToIntMap(v)
val, err = obiutils.InterfaceToIntMap(v)
ok = err == nil
}
@ -139,7 +139,6 @@ func (s *BioSequence) SetCount(count int) {
annot["count"] = count
}
// Returning the taxid of the sequence.
func (s *BioSequence) Taxid() int {
taxid, ok := s.GetIntAttribute("taxid")
@ -157,7 +156,6 @@ func (s *BioSequence) SetTaxid(taxid int) {
annot["taxid"] = taxid
}
func (s *BioSequence) OBITagRefIndex() map[int]string {
var val map[int]string
@ -179,7 +177,7 @@ func (s *BioSequence) OBITagRefIndex() map[int]string {
log.Panicln(err)
}
val[score], err = goutils.InterfaceToString(v)
val[score], err = obiutils.InterfaceToString(v)
if err != nil {
log.Panicln(err)
}

4
pkg/obiseq/class.go
View File

@ -6,7 +6,7 @@ import (
"strconv"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
@ -135,7 +135,7 @@ func DualAnnotationClassifier(key1, key2 string, na string) *BioSequenceClassifi
locke.Lock()
defer locke.Unlock()
jb, _ := goutils.JsonMarshal([2]string{val1, val2})
jb, _ := obiutils.JsonMarshal([2]string{val1, val2})
json := string(jb)
k, ok := encode[json]

13
pkg/obiseq/language.go
View File

@ -5,7 +5,7 @@ import (
"log"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"github.com/PaesslerAG/gval"
)
@ -136,11 +136,11 @@ func minFloatMap(values map[string]float64) float64 {
var OBILang = gval.NewLanguage(
gval.Full(),
gval.Function("len", func(args ...interface{}) (interface{}, error) {
length := goutils.Len(args[0])
length := obiutils.Len(args[0])
return (float64)(length), nil
}),
gval.Function("ismap", func(args ...interface{}) (interface{}, error) {
ismap := goutils.IsAMap(args[0])
ismap := obiutils.IsAMap(args[0])
return ismap, nil
}),
gval.Function("printf", func(args ...interface{}) (interface{}, error) {
@ -152,7 +152,7 @@ var OBILang = gval.NewLanguage(
return text, nil
}),
gval.Function("int", func(args ...interface{}) (interface{}, error) {
val, err := goutils.InterfaceToInt(args[0])
val, err := obiutils.InterfaceToInt(args[0])
if err != nil {
log.Fatalf("%v cannot be converted to an integer value", args[0])
@ -160,7 +160,7 @@ var OBILang = gval.NewLanguage(
return val, nil
}),
gval.Function("numeric", func(args ...interface{}) (interface{}, error) {
val, err := goutils.InterfaceToFloat64(args[0])
val, err := obiutils.InterfaceToFloat64(args[0])
if err != nil {
log.Fatalf("%v cannot be converted to a numeric value", args[0])
@ -168,7 +168,7 @@ var OBILang = gval.NewLanguage(
return val, nil
}),
gval.Function("bool", func(args ...interface{}) (interface{}, error) {
val, err := goutils.InterfaceToBool(args[0])
val, err := obiutils.InterfaceToBool(args[0])
if err != nil {
log.Fatalf("%v cannot be converted to a boolan value", args[0])
@ -189,4 +189,3 @@ var OBILang = gval.NewLanguage(
gval.Function("composition", func(args ...interface{}) (interface{}, error) {
return (args[0].(*BioSequence)).Composition(), nil
}))

4
pkg/obiseq/merge.go
View File

@ -5,7 +5,7 @@ import (
"reflect"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
@ -53,7 +53,7 @@ func (sequence *BioSequence) StatsOn(key string, na string) StatsOnValues {
newstat = false
var err error
for k, v := range istat {
stats[k], err = goutils.InterfaceToInt(v)
stats[k], err = obiutils.InterfaceToInt(v)
if err != nil {
log.Panicf("In sequence %s : %s stat tag not only containing integer values %s",
sequence.Id(), mkey, istat)

4
pkg/obiseq/pool.go
View File

@ -4,7 +4,7 @@ import (
"log"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
var _BioSequenceByteSlicePool = sync.Pool{
@ -72,7 +72,7 @@ func GetAnnotation(values ...Annotation) Annotation {
}
if len(values) > 0 {
goutils.MustFillMap(a, values[0])
obiutils.MustFillMap(a, values[0])
}
return a

4
pkg/obitax/sequence_predicate.go
View File

@ -3,8 +3,8 @@ package obitax
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
func (taxonomy *Taxonomy) IsAValidTaxon(withAutoCorrection ...bool) obiseq.SequencePredicate {
@ -59,7 +59,7 @@ func (taxonomy *Taxonomy) IsSubCladeOf(taxid int) obiseq.SequencePredicate {
func (taxonomy *Taxonomy) HasRequiredRank(rank string) obiseq.SequencePredicate {
if !goutils.Contains(taxonomy.RankList(), rank) {
if !obiutils.Contains(taxonomy.RankList(), rank) {
log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
rank,
taxonomy.RankList())

4
pkg/obitax/sequence_workers.go
View File

@ -1,14 +1,14 @@
package obitax
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiseq.SeqWorker {
if !goutils.Contains(taxonomy.RankList(), rank) {
if !obiutils.Contains(taxonomy.RankList(), rank) {
log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
rank,
taxonomy.RankList())

10
pkg/obitools/obiclean/obiclean.go
View File

@ -4,10 +4,10 @@ import (
"fmt"
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"github.com/schollz/progressbar/v3"
log "github.com/sirupsen/logrus"
)
@ -120,7 +120,7 @@ func HeadCount(sequence *obiseq.BioSequence) int {
value := 0
if ok {
value, err = goutils.InterfaceToInt(value)
value, err = obiutils.InterfaceToInt(value)
if err != nil {
log.Panic("obiclean_headcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
}
@ -136,7 +136,7 @@ func InternalCount(sequence *obiseq.BioSequence) int {
value := 0
if ok {
value, err = goutils.InterfaceToInt(value)
value, err = obiutils.InterfaceToInt(value)
if err != nil {
log.Panic("obiclean_internalcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
}
@ -152,7 +152,7 @@ func SingletonCount(sequence *obiseq.BioSequence) int {
value := 0
if ok {
value, err = goutils.InterfaceToInt(value)
value, err = obiutils.InterfaceToInt(value)
if err != nil {
log.Panic("obiclean_samplecount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
}
@ -271,7 +271,7 @@ func Weight(sequence *obiseq.BioSequence) map[string]int {
case map[string]interface{}:
weight = make(map[string]int)
for k, v := range iobistatus {
weight[k], err = goutils.InterfaceToInt(v)
weight[k], err = obiutils.InterfaceToInt(v)
if err != nil {
log.Panicf("Weight value %v cannnot be casted to an integer value\n", v)
}

14
pkg/obitools/obicsv/options.go
View File

@ -1,8 +1,8 @@
package obicsv
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"github.com/DavidGamba/go-getoptions"
)
@ -103,18 +103,18 @@ func CLIToBeKeptAttributes() []string {
_keepOnly = append(_keepOnly, _softAttributes["obipairing"]...)
}
if i := goutils.LookFor(_keepOnly, "count"); i >= 0 {
_keepOnly = goutils.RemoveIndex(_keepOnly, i)
if i := obiutils.LookFor(_keepOnly, "count"); i >= 0 {
_keepOnly = obiutils.RemoveIndex(_keepOnly, i)
_outputCount = true
}
if i := goutils.LookFor(_keepOnly, "taxid"); i >= 0 {
_keepOnly = goutils.RemoveIndex(_keepOnly, i)
if i := obiutils.LookFor(_keepOnly, "taxid"); i >= 0 {
_keepOnly = obiutils.RemoveIndex(_keepOnly, i)
_outputTaxon = true
}
if i := goutils.LookFor(_keepOnly, "scientific_name"); i >= 0 {
_keepOnly = goutils.RemoveIndex(_keepOnly, i)
if i := obiutils.LookFor(_keepOnly, "scientific_name"); i >= 0 {
_keepOnly = obiutils.RemoveIndex(_keepOnly, i)
_outputTaxon = true
}

4
pkg/obitools/obigrep/options.go
View File

@ -5,11 +5,11 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"github.com/DavidGamba/go-getoptions"
)
@ -345,7 +345,7 @@ func CLIIdPatternPredicate() obiseq.SequencePredicate {
func CLIIdListPredicate() obiseq.SequencePredicate {
if _IdList != "" {
ids, err := goutils.ReadLines(_IdList)
ids, err := obiutils.ReadLines(_IdList)
if err != nil {
log.Fatalf("cannot read the id file %s : %v", _IdList, err)

6
pkg/obitools/obirefidx/obirefidx.go
View File

@ -5,7 +5,6 @@ import (
"log"
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
@ -13,6 +12,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"github.com/schollz/progressbar/v3"
)
@ -38,7 +38,7 @@ func IndexSequence(seqidx int,
// log.Println("Redone : ",r,"/",t,"(",w,")")
o := goutils.IntOrder(score)
o := obiutils.IntOrder(score)
current_taxid, err := taxo.Taxon(references[o[0]].Taxid())
current_score := score[o[0]]
@ -121,7 +121,7 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
indexed := obiiter.MakeIBioSequence()
go func() {
for i := 0; i < len(references); i += 10 {
limits <- [2]int{i, goutils.MinInt(i+10, len(references))}
limits <- [2]int{i, obiutils.MinInt(i+10, len(references))}
}
close(limits)
}()

8
pkg/obitools/obitag/obitag.go
View File

@ -6,7 +6,6 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
@ -15,6 +14,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obirefidx"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
func FindClosests(sequence *obiseq.BioSequence,
@ -31,7 +31,7 @@ func FindClosests(sequence *obiseq.BioSequence,
cw[i] = obikmer.Common4Mer(seqwords, ref)
}
o := goutils.ReverseIntOrder(cw)
o := obiutils.ReverseIntOrder(cw)
// mcw := 100000
// for _, i := range o {
@ -57,11 +57,11 @@ func FindClosests(sequence *obiseq.BioSequence,
for i, j := range o {
ref := references[j]
lmin, lmax := goutils.MinMaxInt(sequence.Len(), ref.Len())
lmin, lmax := obiutils.MinMaxInt(sequence.Len(), ref.Len())
atMost := lmax - lmin + int(math.Ceil(float64(lmin-3-cw[j])/4.0)) - 2
if i == 0 {
maxe = goutils.MaxInt(sequence.Len(), ref.Len())
maxe = obiutils.MaxInt(sequence.Len(), ref.Len())
}
// log.Println(sequence.Id(),cw[j], maxe)

4
pkg/goutils/goutils.go → pkg/obiutils/goutils.go
View File

@ -1,4 +1,4 @@
package goutils
package obiutils
import (
"bufio"
@ -13,7 +13,6 @@ import (
"github.com/barkimedes/go-deepcopy"
)
// InterfaceToInt converts a interface{} to an integer value if possible.
// If not a "NotAnInteger" error is returned via the err
// return value and val is set to 0.
@ -197,7 +196,6 @@ func InterfaceToFloat64Map(i interface{}) (val map[string]float64, err error) {
return
}
// NotABoolean defines a new type of Error : "NotABoolean"
type NotABoolean struct {
message string

2
pkg/goutils/gzipfile.go → pkg/obiutils/gzipfile.go
View File

@ -1,4 +1,4 @@
package goutils
package obiutils
import (
"bufio"

83
pkg/obiutils/minmax.go Normal file
View File

@ -0,0 +1,83 @@
package obiutils
import "golang.org/x/exp/constraints"
func MinInt(x, y int) int {
if x < y {
return x
}
return y
}
func MaxInt(x, y int) int {
if x < y {
return y
}
return x
}
func MinMaxInt(x, y int) (int, int) {
if x < y {
return x, y
}
return y, x
}
func MinUInt16(x, y uint16) uint16 {
if x < y {
return x
}
return y
}
func MaxUInt16(x, y uint16) uint16 {
if x < y {
return y
}
return x
}
func MinSlice[T constraints.Ordered](vec []T) T {
if len(vec) == 0 {
panic("empty slice")
}
min := vec[0]
for _, v := range vec {
if v < min {
min = v
}
}
return min
}
func MaxSlice[T constraints.Ordered](vec []T) T {
if len(vec) == 0 {
panic("empty slice")
}
max := vec[0]
for _, v := range vec {
if v > max {
max = v
}
}
return max
}
func RangeSlice[T constraints.Ordered](vec []T) (min, max T) {
if len(vec) == 0 {
panic("empty slice")
}
min = vec[0]
max = vec[0]
for _, v := range vec {
if v > max {
max = v
}
if v < min {
min = v
}
}
return
}

40
pkg/goutils/ranks.go → pkg/obiutils/ranks.go
View File

@ -1,6 +1,8 @@
package goutils
package obiutils
import "sort"
import (
"sort"
)
// intRanker is a helper type for the rank function.
type intRanker struct {
@ -29,7 +31,7 @@ func IntOrder(data []int) []int {
}
sort.Sort(rk)
return r
}
@ -49,6 +51,36 @@ func ReverseIntOrder(data []int) []int {
}
sort.Sort(sort.Reverse(rk))
return r
}
type Ranker[T sort.Interface] struct {
x T // Data to be ranked.
r []int // A list of indexes into f that reflects rank order after sorting.
}
// ranker satisfies the sort.Interface without mutating the reference slice, f.
func (r Ranker[_]) Len() int { return len(r.r) }
func (r Ranker[T]) Less(i, j int) bool { return r.x.Less(r.r[i], r.r[j]) }
func (r Ranker[_]) Swap(i, j int) { r.r[i], r.r[j] = r.r[j], r.r[i] }
func Order[T sort.Interface](data T) []int {
ldata := data.Len()
if ldata == 0 {
return nil
}
r := make([]int, ldata)
rk := Ranker[T]{
x: data,
r: r,
}
for i := 0; i < ldata; i++ {
rk.r[i] = i
}
sort.Sort(rk)
return r
}

5
pkg/goutils/slices.go → pkg/obiutils/slices.go
View File

@ -1,5 +1,4 @@
package goutils
package obiutils
func Contains[T comparable](arr []T, x T) bool {
for _, v := range arr {
@ -20,5 +19,5 @@ func LookFor[T comparable](arr []T, x T) int {
}
func RemoveIndex[T comparable](s []T, index int) []T {
return append(s[:index], s[index+1:]...)
return append(s[:index], s[index+1:]...)
}