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Adds some more error controle on taxonomy reading

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Former-commit-id: 29c9eafd8c32a92d30611094b06e600aff2e09c6
This commit is contained in:
Eric Coissac
2023-12-14 09:17:46 +01:00
parent b9a7961c91
commit 7a31d5b07b
1 changed files with 21 additions and 6 deletions
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27
pkg/obiformats/ncbitaxdump/read.go
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@ -29,13 +29,13 @@ func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
taxid, err := strconv.Atoi(strings.TrimSpace(record[0])) taxid, err := strconv.Atoi(strings.TrimSpace(record[0]))
if err != nil { if err != nil {
log.Panicf("Cannot read taxid at line %d: %v", n, err) log.Panicf("Cannot read taxon taxid at line %d: %v", n, err)
} }
parent, err := strconv.Atoi(strings.TrimSpace(record[1])) parent, err := strconv.Atoi(strings.TrimSpace(record[1]))
if err != nil { if err != nil {
log.Panicf("Cannot read parent taxid at line %d: %v", n, err) log.Panicf("Cannot read taxon parent taxid at line %d: %v", n, err)
} }
rank := strings.TrimSpace(record[2]) rank := strings.TrimSpace(record[2])
@ -56,15 +56,21 @@ func loadNameTable(reader io.Reader, taxonomy *obitax.Taxonomy, onlysn bool) int
file := bufio.NewReader(reader) file := bufio.NewReader(reader)
n := 0 n := 0
l := 0
for line, prefix, err := file.ReadLine(); err == nil; line, prefix, err = file.ReadLine() { for line, prefix, err := file.ReadLine(); err == nil; line, prefix, err = file.ReadLine() {
l++
if prefix { if prefix {
return -1 return -1
} }
record := strings.Split(string(line), "|") record := strings.Split(string(line), "|")
taxid, _ := strconv.Atoi(strings.TrimSpace(record[0])) taxid, err := strconv.Atoi(strings.TrimSpace(record[0]))
if err != nil {
log.Panicf("Cannot read taxon name taxid at line %d: %v", l, err)
}
name := strings.TrimSpace(record[1]) name := strings.TrimSpace(record[1])
classname := strings.TrimSpace(record[3]) classname := strings.TrimSpace(record[3])
@ -87,9 +93,18 @@ func loadMergedTable(reader io.Reader, taxonomy *obitax.Taxonomy) int {
n := 0 n := 0
for record, err := file.Read(); err == nil; record, err = file.Read() { for record, err := file.Read(); err == nil; record, err = file.Read() {
oldtaxid, _ := strconv.Atoi(strings.TrimSpace(record[0]))
newtaxid, _ := strconv.Atoi(strings.TrimSpace(record[1]))
n++ n++
oldtaxid, err := strconv.Atoi(strings.TrimSpace(record[0]))
if err != nil {
log.Panicf("Cannot read alias taxid at line %d: %v", n, err)
}
newtaxid, err := strconv.Atoi(strings.TrimSpace(record[1]))
if err != nil {
log.Panicf("Cannot read alias new taxid at line %d: %v", n, err)
}
taxonomy.AddNewAlias(newtaxid, oldtaxid) taxonomy.AddNewAlias(newtaxid, oldtaxid)
} }