mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-05-01 04:20:40 +00:00
Merge pull request #115 from metabarcoding/push-lkzqoskvyqtr
[4.4.2] Enhanced taxonomy handling, input robustness & PCR tag validation
This commit is contained in:
coissac
@@ -37,6 +37,11 @@ func main() {
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optionParser(os.Args)
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if !obipairing.CLIHasPairedFiles() {
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log.Error("You must provide both a forward file (-F) and a reverse file (-R)")
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os.Exit(1)
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}
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obidefault.SetStrictReadWorker(2)
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obidefault.SetStrictWriteWorker(2)
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pairs, err := obipairing.CLIPairedSequence()
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@@ -1,6 +1,7 @@
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package main
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import (
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"fmt"
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"os"
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log "github.com/sirupsen/logrus"
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@@ -8,6 +9,7 @@ import (
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obimultiplex"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipairing"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitagpcr"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
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@@ -39,6 +41,17 @@ func main() {
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obitagpcr.OptionSet)
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optionParser(os.Args)
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if obimultiplex.CLIAskConfigTemplate() {
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fmt.Print(obimultiplex.CLIConfigTemplate())
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os.Exit(0)
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}
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if !obipairing.CLIHasPairedFiles() {
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log.Error("You must provide both a forward file (-F) and a reverse file (-R)")
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os.Exit(1)
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}
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pairs, err := obipairing.CLIPairedSequence()
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if err != nil {
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@@ -0,0 +1,24 @@
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>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
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gcctgaaactcaaaggacttggcggtgctttacatccct
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>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
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ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
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agcttaaaactcaaaggacttggcggtgctttataccctt
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>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
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ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
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agcttaaaactcaaaggacttggcggtgctttataccctt
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>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
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ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
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gcttaaaactcaaaggacttggcggtgctttatatccct
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>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
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ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
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gattaaacctcaaaggacttggcagtgctttatacccct
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>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
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ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
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agcttaaaactcaaaggacttggcggtgctttataccctt
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>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
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ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
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agcttaaaactcaaaggacttggcggtgctttataccctt
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>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
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ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
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gcttaaaactcaaaggacttggcggtgctttatatccct
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@@ -0,0 +1,48 @@
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taxid,parent,taxonomic_rank,scientific_name
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taxon:1 [root]@no rank,taxon:1 [root]@no rank,no rank,root
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taxon:131567 [cellular organisms]@cellular root,taxon:1 [root]@no rank,cellular root,cellular organisms
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taxon:2759 [Eukaryota]@domain,taxon:131567 [cellular organisms]@cellular root,domain,Eukaryota
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taxon:33154 [Opisthokonta]@clade,taxon:2759 [Eukaryota]@domain,clade,Opisthokonta
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taxon:33208 [Metazoa]@kingdom,taxon:33154 [Opisthokonta]@clade,kingdom,Metazoa
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taxon:6072 [Eumetazoa]@clade,taxon:33208 [Metazoa]@kingdom,clade,Eumetazoa
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taxon:33213 [Bilateria]@clade,taxon:6072 [Eumetazoa]@clade,clade,Bilateria
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taxon:33511 [Deuterostomia]@clade,taxon:33213 [Bilateria]@clade,clade,Deuterostomia
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taxon:7711 [Chordata]@phylum,taxon:33511 [Deuterostomia]@clade,phylum,Chordata
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taxon:89593 [Craniata]@subphylum,taxon:7711 [Chordata]@phylum,subphylum,Craniata
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taxon:7742 [Vertebrata]@clade,taxon:89593 [Craniata]@subphylum,clade,Vertebrata
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taxon:7776 [Gnathostomata]@clade,taxon:7742 [Vertebrata]@clade,clade,Gnathostomata
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taxon:117570 [Teleostomi]@clade,taxon:7776 [Gnathostomata]@clade,clade,Teleostomi
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taxon:117571 [Euteleostomi]@clade,taxon:117570 [Teleostomi]@clade,clade,Euteleostomi
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taxon:8287 [Sarcopterygii]@superclass,taxon:117571 [Euteleostomi]@clade,superclass,Sarcopterygii
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taxon:1338369 [Dipnotetrapodomorpha]@clade,taxon:8287 [Sarcopterygii]@superclass,clade,Dipnotetrapodomorpha
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taxon:32523 [Tetrapoda]@clade,taxon:1338369 [Dipnotetrapodomorpha]@clade,clade,Tetrapoda
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taxon:32524 [Amniota]@clade,taxon:32523 [Tetrapoda]@clade,clade,Amniota
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taxon:40674 [Mammalia]@class,taxon:32524 [Amniota]@clade,class,Mammalia
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taxon:32525 [Theria]@clade,taxon:40674 [Mammalia]@class,clade,Theria
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taxon:9347 [Eutheria]@clade,taxon:32525 [Theria]@clade,clade,Eutheria
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taxon:1437010 [Boreoeutheria]@clade,taxon:9347 [Eutheria]@clade,clade,Boreoeutheria
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taxon:314146 [Euarchontoglires]@superorder,taxon:1437010 [Boreoeutheria]@clade,superorder,Euarchontoglires
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taxon:314145 [Laurasiatheria]@superorder,taxon:1437010 [Boreoeutheria]@clade,superorder,Laurasiatheria
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taxon:33554 [Carnivora]@order,taxon:314145 [Laurasiatheria]@superorder,order,Carnivora
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taxon:91561 [Artiodactyla]@order,taxon:314145 [Laurasiatheria]@superorder,order,Artiodactyla
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taxon:314147 [Glires]@clade,taxon:314146 [Euarchontoglires]@superorder,clade,Glires
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taxon:9845 [Ruminantia]@suborder,taxon:91561 [Artiodactyla]@order,suborder,Ruminantia
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taxon:35500 [Pecora]@infraorder,taxon:9845 [Ruminantia]@suborder,infraorder,Pecora
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taxon:9989 [Rodentia]@order,taxon:314147 [Glires]@clade,order,Rodentia
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taxon:379584 [Caniformia]@suborder,taxon:33554 [Carnivora]@order,suborder,Caniformia
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taxon:9608 [Canidae]@family,taxon:379584 [Caniformia]@suborder,family,Canidae
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taxon:9850 [Cervidae]@family,taxon:35500 [Pecora]@infraorder,family,Cervidae
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taxon:9881 [Odocoileinae]@subfamily,taxon:9850 [Cervidae]@family,subfamily,Odocoileinae
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taxon:33553 [Sciuromorpha]@suborder,taxon:9989 [Rodentia]@order,suborder,Sciuromorpha
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taxon:55153 [Sciuridae]@family,taxon:33553 [Sciuromorpha]@suborder,family,Sciuridae
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taxon:34878 [Cervinae]@subfamily,taxon:9850 [Cervidae]@family,subfamily,Cervinae
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taxon:9611 [Canis]@genus,taxon:9608 [Canidae]@family,genus,Canis
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taxon:9857 [Capreolus]@genus,taxon:9881 [Odocoileinae]@subfamily,genus,Capreolus
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taxon:9612 [Canis lupus]@species,taxon:9611 [Canis]@genus,species,Canis lupus
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taxon:337726 [Xerinae]@subfamily,taxon:55153 [Sciuridae]@family,subfamily,Xerinae
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taxon:9859 [Cervus]@genus,taxon:34878 [Cervinae]@subfamily,genus,Cervus
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taxon:337730 [Marmotini]@tribe,taxon:337726 [Xerinae]@subfamily,tribe,Marmotini
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taxon:9992 [Marmota]@genus,taxon:337730 [Marmotini]@tribe,genus,Marmota
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taxon:9860 [Cervus elaphus]@species,taxon:9859 [Cervus]@genus,species,Cervus elaphus
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taxon:9615 [Canis lupus familiaris]@subspecies,taxon:9612 [Canis lupus]@species,subspecies,Canis lupus familiaris
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taxon:9858 [Capreolus capreolus]@species,taxon:9857 [Capreolus]@genus,species,Capreolus capreolus
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|
@@ -44,7 +44,7 @@ cleanup() {
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rm -rf "$TMPDIR" # Suppress the temporary directory
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if [ $failed -gt 0 ]; then
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log "$TEST_NAME tests failed"
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log "$TEST_NAME tests failed"
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log
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log
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exit 1
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@@ -60,10 +60,10 @@ log() {
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echo -e "[$TEST_NAME @ $(date)] $*" 1>&2
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}
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log "Testing $TEST_NAME..."
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log "Test directory is $TEST_DIR"
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log "obitools directory is $OBITOOLS_DIR"
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log "Temporary directory is $TMPDIR"
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log "Testing $TEST_NAME..."
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log "Test directory is $TEST_DIR"
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log "obitools directory is $OBITOOLS_DIR"
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log "Temporary directory is $TMPDIR"
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log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
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######################################################################
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@@ -94,12 +94,12 @@ log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
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((ntest++))
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if $CMD -h > "${TMPDIR}/help.txt" 2>&1
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if $CMD -h > "${TMPDIR}/help.txt" 2>&1
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then
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log "$MCMD: printing help OK"
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log "$MCMD: printing help OK"
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((success++))
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else
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log "$MCMD: printing help failed"
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log "$MCMD: printing help failed"
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((failed++))
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fi
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@@ -108,15 +108,15 @@ fi
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if obiconvert -Z "${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
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> "${TMPDIR}/xxx.fasta.gz" && \
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zdiff "${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
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"${TMPDIR}/xxx.fasta.gz"
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"${TMPDIR}/xxx.fasta.gz"
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then
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log "$MCMD: converting large fasta file to fasta OK"
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log "$MCMD: converting large fasta file to fasta OK"
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((success++))
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else
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log "$MCMD: converting large fasta file to fasta failed"
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log "$MCMD: converting large fasta file to fasta failed"
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((failed++))
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fi
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((ntest++))
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if obiconvert -Z --fastq-output \
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"${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
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@@ -125,15 +125,139 @@ if obiconvert -Z --fastq-output \
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"${TMPDIR}/xxx.fastq.gz" \
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> "${TMPDIR}/yyy.fasta.gz" && \
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zdiff "${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
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"${TMPDIR}/yyy.fasta.gz"
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"${TMPDIR}/yyy.fasta.gz"
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then
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log "$MCMD: converting large file between fasta and fastq OK"
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log "$MCMD: converting large file between fasta and fastq OK"
|
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((success++))
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else
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log "$MCMD: converting large file between fasta and fastq failed"
|
||||
log "$MCMD: converting large file between fasta and fastq failed"
|
||||
((failed++))
|
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fi
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|
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|
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# ------------------------------------------------------------------
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# --raw-taxid tests (no taxonomy loaded)
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# ------------------------------------------------------------------
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|
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# Running test
|
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((ntest++))
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if obiconvert --raw-taxid "${TEST_DIR}/out_ecotag.fasta" \
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> "${TMPDIR}/raw_taxid.fasta" 2>/dev/null
|
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then
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log "$MCMD --raw-taxid: running OK"
|
||||
((success++))
|
||||
else
|
||||
log "$MCMD --raw-taxid: running failed"
|
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((failed++))
|
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fi
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|
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# Taxids must be bare numbers — no full-format "taxon:ID [Name]@rank" strings
|
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((ntest++))
|
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if grep '"taxid"' "${TMPDIR}/raw_taxid.fasta" | grep -qv '"taxid":"[0-9][0-9]*"'
|
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then
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log "$MCMD --raw-taxid: taxid format check failed (full-format taxid found)"
|
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((failed++))
|
||||
else
|
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log "$MCMD --raw-taxid: taxid format OK (all taxids are bare numbers)"
|
||||
((success++))
|
||||
fi
|
||||
|
||||
# --raw-taxid is idempotent: piping through a second obiconvert --raw-taxid must
|
||||
# produce bit-for-bit identical output.
|
||||
((ntest++))
|
||||
if obiconvert --raw-taxid "${TMPDIR}/raw_taxid.fasta" \
|
||||
> "${TMPDIR}/raw_taxid2.fasta" 2>/dev/null
|
||||
then
|
||||
log "$MCMD --raw-taxid piped: running OK"
|
||||
((success++))
|
||||
else
|
||||
log "$MCMD --raw-taxid piped: running failed"
|
||||
((failed++))
|
||||
fi
|
||||
|
||||
((ntest++))
|
||||
if diff "${TMPDIR}/raw_taxid.fasta" \
|
||||
"${TMPDIR}/raw_taxid2.fasta" > /dev/null
|
||||
then
|
||||
log "$MCMD --raw-taxid piped: idempotency OK"
|
||||
((success++))
|
||||
else
|
||||
log "$MCMD --raw-taxid piped: idempotency failed (outputs differ)"
|
||||
((failed++))
|
||||
fi
|
||||
|
||||
|
||||
# ------------------------------------------------------------------
|
||||
# --taxonomy tests (full-format taxid, no --raw-taxid)
|
||||
# ------------------------------------------------------------------
|
||||
|
||||
# Running test
|
||||
((ntest++))
|
||||
if obiconvert --taxonomy "${TEST_DIR}/taxonomy.csv" \
|
||||
"${TEST_DIR}/out_ecotag.fasta" \
|
||||
> "${TMPDIR}/taxo.fasta" 2>/dev/null
|
||||
then
|
||||
log "$MCMD --taxonomy: running OK"
|
||||
((success++))
|
||||
else
|
||||
log "$MCMD --taxonomy: running failed"
|
||||
((failed++))
|
||||
fi
|
||||
|
||||
# Taxids must be in full "taxon:ID [Name]@rank" format
|
||||
((ntest++))
|
||||
if grep '"taxid"' "${TMPDIR}/taxo.fasta" | grep -q '"taxid":"taxon:[0-9]'
|
||||
then
|
||||
log "$MCMD --taxonomy: taxid format OK (full-format taxids present)"
|
||||
((success++))
|
||||
else
|
||||
log "$MCMD --taxonomy: taxid format check failed (no full-format taxid found)"
|
||||
((failed++))
|
||||
fi
|
||||
|
||||
|
||||
# ------------------------------------------------------------------
|
||||
# --raw-taxid --taxonomy tests
|
||||
# ------------------------------------------------------------------
|
||||
|
||||
# Running test
|
||||
((ntest++))
|
||||
if obiconvert --raw-taxid --taxonomy "${TEST_DIR}/taxonomy.csv" \
|
||||
"${TEST_DIR}/out_ecotag.fasta" \
|
||||
> "${TMPDIR}/raw_taxid_taxo.fasta" 2>/dev/null
|
||||
then
|
||||
log "$MCMD --raw-taxid --taxonomy: running OK"
|
||||
((success++))
|
||||
else
|
||||
log "$MCMD --raw-taxid --taxonomy: running failed"
|
||||
((failed++))
|
||||
fi
|
||||
|
||||
# Taxids must be bare numbers even when taxonomy is loaded
|
||||
((ntest++))
|
||||
if grep '"taxid"' "${TMPDIR}/raw_taxid_taxo.fasta" | grep -qv '"taxid":"[0-9][0-9]*"'
|
||||
then
|
||||
log "$MCMD --raw-taxid --taxonomy: taxid format check failed (full-format taxid found)"
|
||||
((failed++))
|
||||
else
|
||||
log "$MCMD --raw-taxid --taxonomy: taxid format OK (all taxids are bare numbers)"
|
||||
((success++))
|
||||
fi
|
||||
|
||||
# --raw-taxid with or without taxonomy must yield identical taxid values
|
||||
((ntest++))
|
||||
if diff <(grep '"taxid"' "${TMPDIR}/raw_taxid.fasta" | grep -o '"taxid":"[^"]*"' | sort) \
|
||||
<(grep '"taxid"' "${TMPDIR}/raw_taxid_taxo.fasta" | grep -o '"taxid":"[^"]*"' | sort) \
|
||||
> /dev/null
|
||||
then
|
||||
log "$MCMD --raw-taxid vs --raw-taxid --taxonomy: taxid values match OK"
|
||||
((success++))
|
||||
else
|
||||
log "$MCMD --raw-taxid vs --raw-taxid --taxonomy: taxid values differ (unexpected)"
|
||||
((failed++))
|
||||
fi
|
||||
|
||||
|
||||
#########################################
|
||||
#
|
||||
# At the end of the tests
|
||||
|
||||
@@ -0,0 +1,24 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
@@ -631,9 +631,9 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
|
||||
return nil, fmt.Errorf("row %d has %d columns, expected %d", len(data), len(fields), len(header))
|
||||
}
|
||||
|
||||
forward_primer := fields[forward_primerColIndex]
|
||||
reverse_primer := fields[reverse_primerColIndex]
|
||||
tags := _parseMainNGSFilterTags(fields[sample_tagColIndex])
|
||||
forward_primer := strings.TrimSpace(fields[forward_primerColIndex])
|
||||
reverse_primer := strings.TrimSpace(fields[reverse_primerColIndex])
|
||||
tags := _parseMainNGSFilterTags(strings.TrimSpace(fields[sample_tagColIndex]))
|
||||
|
||||
marker, _ := ngsfilter.GetMarker(forward_primer, reverse_primer)
|
||||
pcr, ok := marker.GetPCR(tags.Forward, tags.Reverse)
|
||||
@@ -644,8 +644,8 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
|
||||
i, tags.Forward, tags.Reverse, forward_primer, reverse_primer)
|
||||
}
|
||||
|
||||
pcr.Experiment = fields[experimentColIndex]
|
||||
pcr.Sample = fields[sampleColIndex]
|
||||
pcr.Experiment = strings.TrimSpace(fields[experimentColIndex])
|
||||
pcr.Sample = strings.TrimSpace(fields[sampleColIndex])
|
||||
|
||||
if extraColumns != nil {
|
||||
pcr.Annotations = make(obiseq.Annotation)
|
||||
|
||||
@@ -3,7 +3,7 @@ package obioptions
|
||||
// Version is automatically updated by the Makefile from version.txt
|
||||
// The patch number (third digit) is incremented on each push to the repository
|
||||
|
||||
var _Version = "Release 4.4.41"
|
||||
var _Version = "Release 4.4.42"
|
||||
|
||||
// Version returns the version of the obitools package.
|
||||
//
|
||||
|
||||
@@ -70,6 +70,12 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
|
||||
}
|
||||
}
|
||||
|
||||
} else if obidefault.UseRawTaxids() {
|
||||
// Without a loaded taxonomy, extract the bare ID from full-format strings
|
||||
// like "code:12345 [Name]@rank" so that --raw-taxid is honoured everywhere.
|
||||
if _, rawID, _, _, parseErr := obitax.ParseTaxonString(taxid); parseErr == nil {
|
||||
taxid = rawID
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@@ -177,7 +183,7 @@ func (sequence *BioSequence) SetPath(taxonomy *obitax.Taxonomy) []string {
|
||||
lpath := path.Len() - 1
|
||||
|
||||
for i := lpath; i >= 0; i-- {
|
||||
spath[lpath-i] = path.Get(i).String(taxonomy.Code())
|
||||
spath[lpath-i] = path.Get(i).FullString(taxonomy.Code())
|
||||
}
|
||||
|
||||
sequence.SetAttribute("taxonomic_path", spath)
|
||||
|
||||
+19
-13
@@ -29,6 +29,24 @@ type TaxNode struct {
|
||||
alternatenames *map[*string]*string
|
||||
}
|
||||
|
||||
// FullString returns the full string representation of the TaxNode in the form
|
||||
// "taxonomyCode:id [scientificName]@rank", regardless of the UseRawTaxids setting.
|
||||
// This is used internally when a parseable format is required (e.g. taxonomic_path).
|
||||
func (node *TaxNode) FullString(taxonomyCode string) string {
|
||||
if node.HasScientificName() {
|
||||
return fmt.Sprintf("%s:%v [%s]@%s",
|
||||
taxonomyCode,
|
||||
*node.id,
|
||||
node.ScientificName(),
|
||||
node.Rank(),
|
||||
)
|
||||
}
|
||||
|
||||
return fmt.Sprintf("%s:%v",
|
||||
taxonomyCode,
|
||||
*node.id)
|
||||
}
|
||||
|
||||
// String returns a string representation of the TaxNode, including the taxonomy code,
|
||||
// the node ID, and the scientific name. The output format is "taxonomyCode:id [scientificName]".
|
||||
//
|
||||
@@ -42,19 +60,7 @@ func (node *TaxNode) String(taxonomyCode string) string {
|
||||
return *node.id
|
||||
}
|
||||
|
||||
if node.HasScientificName() {
|
||||
return fmt.Sprintf("%s:%v [%s]@%s",
|
||||
taxonomyCode,
|
||||
*node.id,
|
||||
node.ScientificName(),
|
||||
node.Rank(),
|
||||
)
|
||||
}
|
||||
|
||||
return fmt.Sprintf("%s:%v",
|
||||
taxonomyCode,
|
||||
*node.id)
|
||||
|
||||
return node.FullString(taxonomyCode)
|
||||
}
|
||||
|
||||
// Id returns the unique identifier of the TaxNode.
|
||||
|
||||
@@ -21,12 +21,10 @@ func PairingOptionSet(options *getoptions.GetOpt) {
|
||||
options.StringVar(&_ForwardFile, "forward-reads", "",
|
||||
options.Alias("F"),
|
||||
options.ArgName("FILENAME_F"),
|
||||
options.Required("You must provide at a forward file"),
|
||||
options.Description("The file names containing the forward reads"))
|
||||
options.StringVar(&_ReverseFile, "reverse-reads", "",
|
||||
options.Alias("R"),
|
||||
options.ArgName("FILENAME_R"),
|
||||
options.Required("You must provide a reverse file"),
|
||||
options.Description("The file names containing the reverse reads"))
|
||||
options.IntVar(&_Delta, "delta", _Delta,
|
||||
options.Alias("D"),
|
||||
@@ -72,6 +70,10 @@ func CLIPairedSequence() (obiiter.IBioSequence, error) {
|
||||
return paired, nil
|
||||
}
|
||||
|
||||
func CLIHasPairedFiles() bool {
|
||||
return _ForwardFile != "" && _ReverseFile != ""
|
||||
}
|
||||
|
||||
func CLIDelta() int {
|
||||
return _Delta
|
||||
}
|
||||
|
||||
@@ -114,10 +114,10 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
|
||||
aanot["obimultiplex_direction"] = direction
|
||||
|
||||
aanot["obimultiplex_forward_match"] = forward_match
|
||||
aanot["obimultiplex_forward_mismatches"] = forward_mismatches
|
||||
aanot["obimultiplex_forward_error"] = forward_mismatches
|
||||
|
||||
aanot["obimultiplex_reverse_match"] = reverse_match
|
||||
aanot["obimultiplex_reverse_mismatches"] = reverse_mismatches
|
||||
aanot["obimultiplex_reverse_error"] = reverse_mismatches
|
||||
|
||||
aanot["sample"] = sample
|
||||
aanot["experiment"] = experiment
|
||||
@@ -125,10 +125,10 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
|
||||
banot["obimultiplex_direction"] = direction
|
||||
|
||||
banot["obimultiplex_forward_match"] = forward_match
|
||||
banot["obimultiplex_forward_mismatches"] = forward_mismatches
|
||||
banot["obimultiplex_forward_error"] = forward_mismatches
|
||||
|
||||
banot["obimultiplex_reverse_match"] = reverse_match
|
||||
banot["obimultiplex_reverse_mismatches"] = reverse_mismatches
|
||||
banot["obimultiplex_reverse_error"] = reverse_mismatches
|
||||
|
||||
banot["sample"] = sample
|
||||
banot["experiment"] = experiment
|
||||
|
||||
+1
-1
@@ -1 +1 @@
|
||||
4.4.41
|
||||
4.4.42
|
||||
|
||||
Reference in New Issue
Block a user