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Dealing with multiple taxids by taking first one (iss#54) #55

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Feb 10, 2021
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Dealing with multiple taxids by taking first one (iss#54) #55

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8 changes: 6 additions & 2 deletions Rfam/Lib/Bio/Rfam/Utils.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -2628,7 +2628,7 @@ sub genbank_fetch_seq_info {
}
$info_HHR->{$accver}{"length"} = $length;

# for taxid and mol_type, we have to fetch from Quailifier_values, and may have more than 1
# for taxid and mol_type, we have to fetch from Qualifier_values, and may have more than 1
# in that case, they will be concatenated together
my $taxid_val = $gbseq->findvalue('./GBSeq_feature-table/GBFeature/GBFeature_quals/GBQualifier/GBQualifier_value[starts-with(text(), "taxon:")]');
my $taxid = undef;
Expand All @@ -2643,7 +2643,11 @@ sub genbank_fetch_seq_info {
$taxid = $cur_taxid;
}
elsif($cur_taxid != $taxid) {
croak "ERROR in $sub_name for $accver, > 1 taxids read: $taxid and $cur_taxid\nFull taxon values read: $orig_taxid_val\n";
; # do nothing, see comment below
# Change Jan 29, 2021: if multiple taxids are returned for a single accession,
# always use the first one and don't complain. Previously we would fail here
# with following croak:
#croak "ERROR in $sub_name for $accver, > 1 taxids read: $taxid and $cur_taxid\nFull taxon values read: $orig_taxid_val\n";
}
$taxid_val =~ s/^taxon\:(\d+)//;
}
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