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Patch a bug on compressed output

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This commit is contained in:
Eric Coissac
2025-02-05 14:18:24 +01:00
parent ceca33998b
commit 773e54965d
8 changed files with 44 additions and 7 deletions
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1
go.mod
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@ -25,6 +25,7 @@ require (
require (
github.com/Clever/csvlint v0.3.0 // indirect
github.com/TuftsBCB/io v0.0.0-20140121014543-22b94e9b23f9 // indirect
github.com/buger/jsonparser v1.1.1 // indirect
github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e // indirect
github.com/davecgh/go-spew v1.1.1 // indirect

2
go.sum
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@ -6,6 +6,8 @@ github.com/PaesslerAG/gval v1.2.2 h1:Y7iBzhgE09IGTt5QgGQ2IdaYYYOU134YGHBThD+wm9E
github.com/PaesslerAG/gval v1.2.2/go.mod h1:XRFLwvmkTEdYziLdaCeCa5ImcGVrfQbeNUbVR+C6xac=
github.com/PaesslerAG/jsonpath v0.1.0 h1:gADYeifvlqK3R3i2cR5B4DGgxLXIPb3TRTH1mGi0jPI=
github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8=
github.com/TuftsBCB/io v0.0.0-20140121014543-22b94e9b23f9 h1:Zc1/GNsUpgZR9qm1EmRSKrnOHA7CCd0bIzGdq0cREN0=
github.com/TuftsBCB/io v0.0.0-20140121014543-22b94e9b23f9/go.mod h1:PZyV4WA3NpqtezSY0h6E6NARAmdDm0qwrydveOyR5Gc=
github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df h1:GSoSVRLoBaFpOOds6QyY1L8AX7uoY+Ln3BHc22W40X0=
github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df/go.mod h1:hiVxq5OP2bUGBRNS3Z/bt/reCLFNbdcST6gISi1fiOM=
github.com/buger/jsonparser v1.1.1 h1:2PnMjfWD7wBILjqQbt530v576A/cAbQvEW9gGIpYMUs=

2
pkg/obioptions/version.go
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@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be
// commited
var _Commit = "b9bee5f"
var _Commit = "ceca339"
var _Version = "Release 4.2.0"
// Version returns the version of the obitools package.

37
pkg/obitax/csvtaxdump_write.go
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@ -1 +1,38 @@
package obitax
import (
"strings"
"github.com/TuftsBCB/io/newick"
)
func (taxonomy *Taxonomy) Newick() string {
if taxonomy == nil {
return ""
}
iterator := taxonomy.AsTaxonSet().Sort().Iterator()
nodes := make(map[*string]*newick.Tree, taxonomy.Len())
trees := make([]*newick.Tree, 0)
for iterator.Next() {
taxon := iterator.Get()
tree := &newick.Tree{Label: taxon.String()}
nodes[taxon.Node.id] = tree
if parent, ok := nodes[taxon.Parent().Node.id]; ok {
parent.Children = append(parent.Children, *tree)
} else {
trees = append(trees, tree)
}
}
rep := strings.Builder{}
for _, tree := range trees {
rep.WriteString(tree.String())
rep.WriteString("\n")
}
return rep.String()
}

1
pkg/obitax/newick_write.go Normal file
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@ -0,0 +1 @@
package obitax

4
pkg/obitools/obiconvert/options.go
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@ -163,10 +163,6 @@ func CLIOutputFormat() string {
}
}
func CLICompressed() bool {
return __compressed__
}
func CLISkipEmpty() bool {
return __skip_empty__
}

2
pkg/obitools/obiconvert/sequence_writer.go
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@ -58,7 +58,7 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obidefault.BatchSize()))
opts = append(opts, obiformats.OptionsCompressed(CLICompressed()))
opts = append(opts, obiformats.OptionsCompressed(obidefault.CompressOutput()))
var err error

2
pkg/obitools/obidistribute/distribute.go
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@ -33,7 +33,7 @@ func CLIDistributeSequence(sequences obiiter.IBioSequence) {
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers),
obiformats.OptionsBatchSize(obidefault.BatchSize()),
obiformats.OptionsAppendFile(CLIAppendSequences()),
obiformats.OptionsCompressed(obiconvert.CLICompressed()))
obiformats.OptionsCompressed(obidefault.CompressOutput()))
var formater obiformats.SequenceBatchWriterToFile