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Make some correction on genbank/embl parser

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Former-commit-id: fb2ebb351f61d78432bb9648d0a509b6557651a2
This commit is contained in:
Eric Coissac
2024-02-27 07:28:56 +01:00
parent 38c49e9f38
commit c9fe6f6ebf
2 changed files with 25 additions and 33 deletions
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13
pkg/obiformats/genbank_read.go
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@ -24,6 +24,7 @@ const (
inDefinition gbstate = 2
inFeature gbstate = 3
inSequence gbstate = 4
inContig gbstate = 5
)
var _seqlenght_rx = regexp.MustCompile(" +([0-9]+) bp")
@ -127,18 +128,22 @@ func _ParseGenbankFile(source string,
state = inSequence
processed = true
case strings.HasPrefix(line, "CONTIG"):
if state != inFeature && state != inContig {
log.Fatalf("Unexpected state %d while reading ORIGIN: %s", state, line)
}
state = inContig
processed = true
case line == "//":
if state != inSequence {
if state != inSequence && state != inContig {
log.Fatalf("Unexpected state %d while reading end of record %s", state, id)
}
// log.Debugln("Total lines := ", nl)
if id == "" {
log.Warn("Empty id when parsing genbank file")
}
if seqBytes.Len() == 0 {
log.Warn("Empty sequence when parsing genbank file")
}
log.Debugf("End of sequence %s: %dbp ", id, seqBytes.Len())