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Code reefactoring

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This commit is contained in:
Eric Coissac
2022-01-14 16:10:19 +01:00
parent 45a1765a03
commit ff40222902
13 changed files with 68 additions and 92 deletions
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62
pkg/obialign/pairedendalign.go
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@ -272,9 +272,9 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
arena PEAlignArena) (int, []int) {
var score, shift int
var startA, startB int
var part_len, over int
var raw_seqA, qual_seqA []byte
var raw_seqB, qual_seqB []byte
var partLen, over int
var rawSeqA, qualSeqA []byte
var rawSeqB, qualSeqB []byte
var extra5, extra3 int
if !_InitializedDnaScore {
@ -286,7 +286,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
&arena.pointer.fastIndex,
&arena.pointer.fastBuffer)
shift, fast_score := obikmer.FastShiftFourMer(index, seqB, nil)
shift, fastScore := obikmer.FastShiftFourMer(index, seqB, nil)
if shift > 0 {
over = seqA.Length() - shift
@ -294,7 +294,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
over = seqB.Length() + shift
}
if fast_score+3 < over {
if fastScore+3 < over {
if shift > 0 {
startA = shift - delta
if startA < 0 {
@ -302,14 +302,14 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
}
extra5 = -startA
startB = 0
raw_seqA = seqA.Sequence()[startA:]
qual_seqA = seqA.Qualities()[startA:]
part_len = len(raw_seqA)
raw_seqB = seqB.Sequence()[0:part_len]
qual_seqB = seqB.Qualities()[0:part_len]
extra3 = seqB.Length() - part_len
rawSeqA = seqA.Sequence()[startA:]
qualSeqA = seqA.Qualities()[startA:]
partLen = len(rawSeqA)
rawSeqB = seqB.Sequence()[0:partLen]
qualSeqB = seqB.Qualities()[0:partLen]
extra3 = seqB.Length() - partLen
score = _FillMatrixPeLeftAlign(
raw_seqA, qual_seqA, raw_seqB, qual_seqB, gap,
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
} else {
@ -319,20 +319,20 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
startB = 0
}
extra5 = startB
raw_seqB = seqB.Sequence()[startB:]
qual_seqB = seqB.Qualities()[startB:]
part_len = len(raw_seqB)
raw_seqA = seqA.Sequence()[:part_len]
qual_seqA = seqA.Qualities()[:part_len]
extra3 = part_len - seqA.Length()
rawSeqB = seqB.Sequence()[startB:]
qualSeqB = seqB.Qualities()[startB:]
partLen = len(rawSeqB)
rawSeqA = seqA.Sequence()[:partLen]
qualSeqA = seqA.Qualities()[:partLen]
extra3 = partLen - seqA.Length()
score = _FillMatrixPeRightAlign(
raw_seqA, qual_seqA, raw_seqB, qual_seqB, gap,
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
}
arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
len(raw_seqA), len(raw_seqB),
len(rawSeqA), len(rawSeqB),
&arena.pointer.path)
} else {
@ -340,27 +340,27 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
startA = shift
startB = 0
extra5 = -startA
qual_seqA = seqA.Qualities()[startA:]
part_len = len(qual_seqA)
qual_seqB = seqB.Qualities()[0:part_len]
extra3 = seqB.Length() - part_len
qualSeqA = seqA.Qualities()[startA:]
partLen = len(qualSeqA)
qualSeqB = seqB.Qualities()[0:partLen]
extra3 = seqB.Length() - partLen
score = 0
} else {
startA = 0
startB = -shift
extra5 = startB
qual_seqB = seqB.Qualities()[startB:]
part_len = len(qual_seqB)
extra3 = part_len - seqA.Length()
qual_seqA = seqA.Qualities()[:part_len]
qualSeqB = seqB.Qualities()[startB:]
partLen = len(qualSeqB)
extra3 = partLen - seqA.Length()
qualSeqA = seqA.Qualities()[:partLen]
}
score = 0
for i, qualA := range qual_seqA {
qualB := qual_seqB[i]
for i, qualA := range qualSeqA {
qualB := qualSeqB[i]
score += _NucScorePartMatchMatch[qualA][qualB]
}
arena.pointer.path = arena.pointer.path[:0]
arena.pointer.path = append(arena.pointer.path, 0, part_len)
arena.pointer.path = append(arena.pointer.path, 0, partLen)
}
arena.pointer.path[0] += extra5

8
pkg/obiapat/pcr.go
View File

@ -195,7 +195,7 @@ func __pcr__(seq ApatSequence, sequence obiseq.BioSequence,
match, _ := sequence.Subsequence(fm[0], fm[1], opt.pointer.circular)
annot["forward_match"] = match.String()
match.Revoke()
match.Destroy()
annot["forward_error"] = erri
@ -203,7 +203,7 @@ func __pcr__(seq ApatSequence, sequence obiseq.BioSequence,
match, _ = sequence.Subsequence(rm[0], rm[1], opt.pointer.circular)
match = match.ReverseComplement(true)
annot["reverse_match"] = match.String()
match.Revoke()
match.Destroy()
annot["reverse_error"] = errj
results = append(results, amplicon)
@ -269,14 +269,14 @@ func __pcr__(seq ApatSequence, sequence obiseq.BioSequence,
match, _ := sequence.Subsequence(rm[0], rm[1], opt.pointer.circular)
match.ReverseComplement(true)
annot["forward_match"] = match.String()
match.Revoke()
match.Destroy()
annot["forward_error"] = errj
annot["reverse_primer"] = reverse.String()
match, _ = sequence.Subsequence(fm[0], fm[1], opt.pointer.circular)
annot["reverse_match"] = match.String()
match.Revoke()
match.Destroy()
annot["reverse_error"] = erri
results = append(results, amplicon)

9
pkg/obiformats/embl_read.go
View File

@ -16,15 +16,6 @@ import (
var __FILE_CHUNK_SIZE__ = 1 << 20
func __slice_grow__(slice []string) []string {
return slice
}
type __embl_chunk__ struct {
entries [][]string
order int
}
type __file_chunk__ struct {
raw io.Reader
order int

3
pkg/obiformats/fastseq_read.go
View File

@ -7,7 +7,6 @@ package obiformats
import "C"
import (
"errors"
"fmt"
"log"
"os"
@ -89,7 +88,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
err = nil
if pointer == nil {
err = errors.New(fmt.Sprintf("Cannot open file %s", filename))
err = fmt.Errorf("cannot open file %s", filename)
return obiseq.NilIBioSequenceBatch, err
}

13
pkg/obiformats/ncbitaxdump/read.go
View File

@ -3,7 +3,6 @@ package ncbitaxdump
import (
"bufio"
"encoding/csv"
"errors"
"fmt"
"io"
"log"
@ -95,8 +94,8 @@ func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
nodefile, err := os.Open(path.Join(directory, "nodes.dmp"))
if err != nil {
return nil, errors.New(fmt.Sprintf("Cannot open nodes file from '%s'",
directory))
return nil, fmt.Errorf("cannot open nodes file from '%s'",
directory)
}
defer nodefile.Close()
@ -112,8 +111,8 @@ func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
namefile, nerr := os.Open(path.Join(directory, "names.dmp"))
if nerr != nil {
return nil, errors.New(fmt.Sprintf("Cannot open names file from '%s'",
directory))
return nil, fmt.Errorf("cannot open names file from '%s'",
directory)
}
defer namefile.Close()
@ -128,8 +127,8 @@ func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
aliasfile, aerr := os.Open(path.Join(directory, "merged.dmp"))
if aerr != nil {
return nil, errors.New(fmt.Sprintf("Cannot open merged file from '%s'",
directory))
return nil, fmt.Errorf("cannot open merged file from '%s'",
directory)
}
defer aliasfile.Close()

4
pkg/obioptions/options.go
View File

@ -8,7 +8,6 @@ import (
)
var __debug__ = false
var __profiling__ = ""
type ArgumentParser func([]string) (*getoptions.GetOpt, []string, error)
@ -16,7 +15,6 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
options := getoptions.New()
options.Bool("help", false, options.Alias("h", "?"))
options.BoolVar(&__debug__, "debug", false)
// options.StringVar(&__profiling__, "profile", "")
for _, o := range optionset {
o(options)
@ -27,7 +25,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
remaining, err := options.Parse(args[1:])
if options.Called("help") {
fmt.Fprintf(os.Stderr, options.Help())
fmt.Fprint(os.Stderr, options.Help())
os.Exit(1)
}
return options, remaining, err

19
pkg/obiseq/join.go
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@ -1,19 +1,12 @@
package obiseq
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
func (sequence BioSequence) Join(seq2 BioSequence, inplace bool) BioSequence {
func (sequence BioSequence) Join(seq2 BioSequence, copy_annot bool) (BioSequence, error) {
new_seq := MakeEmptyBioSequence()
new_seq.SetId(sequence.Id())
new_seq.SetDefinition(sequence.Definition())
new_seq.Write(sequence.Sequence())
new_seq.Write(seq2.Sequence())
if copy_annot {
goutils.CopyMap(new_seq.Annotations(), sequence.Annotations())
if !inplace {
sequence = sequence.Copy()
}
return new_seq, nil
sequence.Write(seq2.Sequence())
return sequence
}

2
pkg/obitax/iterator.go
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@ -39,7 +39,7 @@ func (set *TaxonSlice) Iterator() *ITaxonSet {
return i
}
func (taxonmy *Taxonomy) iterator() *ITaxonSet {
func (taxonmy *Taxonomy) Iterator() *ITaxonSet {
return taxonmy.nodes.Iterator()
}

3
pkg/obitax/path.go
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@ -1,7 +1,6 @@
package obitax
import (
"errors"
"fmt"
)
@ -14,7 +13,7 @@ func (taxon *TaxNode) Path() (*TaxonSlice, error) {
taxon = taxon.pparent
if taxon == nil {
return nil, errors.New(fmt.Sprint("Taxonomy must be reindexed"))
return nil, fmt.Errorf("Taxonomy must be reindexed")
}
path = append(path, taxon)

13
pkg/obitax/taxonomy.go
View File

@ -1,7 +1,6 @@
package obitax
import (
"errors"
"fmt"
"log"
)
@ -42,15 +41,11 @@ func (taxonomy *Taxonomy) Length() int {
return len(*taxonomy.nodes)
}
func (taxonomy *Taxonomy) Iterator() *ITaxonSet {
return taxonomy.nodes.Iterator()
}
func (taxonomy *Taxonomy) AddNewTaxa(taxid, parent int, rank string, replace bool, init bool) (*TaxNode, error) {
if !replace {
_, ok := (*taxonomy.nodes)[taxid]
if ok {
return nil, errors.New(fmt.Sprintf("Trying to add taxoon %d already present in the taxonomy", taxid))
return nil, fmt.Errorf("trying to add taxoon %d already present in the taxonomy", taxid)
}
}
@ -66,7 +61,7 @@ func (taxonomy *Taxonomy) Taxon(taxid int) (*TaxNode, error) {
if !ok {
a, aok := taxonomy.alias[taxid]
if !aok {
return nil, errors.New(fmt.Sprintf("Taxid %d is not part of the taxonomy", taxid))
return nil, fmt.Errorf("Taxid %d is not part of the taxonomy", taxid)
}
log.Printf("Taxid %d is deprecated and must be replaced by %d", taxid, a.taxid)
t = a
@ -109,9 +104,9 @@ func (taxonomy *Taxonomy) ReindexParent() error {
for _, taxon := range *taxonomy.nodes {
taxon.pparent, ok = (*taxonomy.nodes)[taxon.parent]
if !ok {
return errors.New(fmt.Sprintf("Parent %d of taxon %d is not defined in taxonomy",
return fmt.Errorf("Parent %d of taxon %d is not defined in taxonomy",
taxon.taxid,
taxon.parent))
taxon.parent)
}
}

20
pkg/obitools/obiconvert/sequence_reader.go
View File

@ -17,24 +17,24 @@ func __expand_list_of_files__(check_ext bool, filenames ...string) ([]string, er
err = filepath.Walk(fn,
func(path string, info os.FileInfo, err error) error {
var e error
for info.Mode()&os.ModeSymlink == os.ModeSymlink {
path, err = filepath.EvalSymlinks(path)
if err != nil {
return err
path, e = filepath.EvalSymlinks(path)
if e != nil {
return e
}
info, err = os.Stat(path)
if err != nil {
return err
info, e = os.Stat(path)
if e != nil {
return e
}
}
if info.IsDir() {
if path != fn {
subdir, err := __expand_list_of_files__(true, path)
if err != nil {
return err
subdir, e := __expand_list_of_files__(true, path)
if e != nil {
return e
}
list_of_files = append(list_of_files, subdir...)
} else {

2
pkg/obitools/obifind/options.go
View File

@ -86,7 +86,7 @@ func LoadSelectedTaxonomy() (*obitax.Taxonomy, error) {
return __selected_taxonomy__, nil
}
return nil, errors.New("No NCBII taxdump selected using option -t|--taxdump")
return nil, errors.New("no NCBI taxdump selected using option -t|--taxdump")
}
func OptionSet(options *getoptions.GetOpt) {

2
pkg/obitools/obipairing/pairing.go
View File

@ -153,6 +153,8 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
bar.Add(59)
processed += 59
}
A.Destroy()
B.Destroy()
}
bar.Add(batch.Length() - processed)
new_iter.Channel() <- obiseq.MakeBioSequenceBatch(