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fixes to gff3-merge - use id instead of name in replace process
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mpoelchau committed Mar 1, 2024
1 parent 7f2a81a commit b46da89
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Showing 2 changed files with 5 additions and 5 deletions.
8 changes: 4 additions & 4 deletions gff3tool/lib/auto_assignment/gen_spreadsheet.pl
Original file line number Diff line number Diff line change
Expand Up @@ -18,9 +18,9 @@
$_ =~ s/\R//g;
my @t = split("\t", $_);
if (defined $hit{$t[2]}){
$hit{$t[2]} .= ",$t[5]";
$hit{$t[2]} .= ",$t[3]";
}else{
$hit{$t[2]} = $t[5];
$hit{$t[2]} = $t[3];
}
}
close FI;
Expand All @@ -33,9 +33,9 @@
$_ =~ s/\R//g;
my @t = split("\t", $_);
if (defined $hit2{$t[2]}){
$hit2{$t[2]} .= ",$t[5]";
$hit2{$t[2]} .= ",$t[3]";
}else{
$hit2{$t[2]} = $t[5];
$hit2{$t[2]} = $t[3];
}
}
close FI;
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2 changes: 1 addition & 1 deletion gff3tool/lib/gff3_merge/merge.py
Original file line number Diff line number Diff line change
Expand Up @@ -239,7 +239,7 @@ def main(gff_file1, gff_file2, output_gff, report_fh, user_defined1=None, user_d
for tp in gff3M.collect_roots(t):
gid_list.append(tp['attributes']['ID'])
gid = ','.join(gid_list)
if tname not in not_orphan:
if tid not in not_orphan:
tmpid = 'NA'
report_fh.write('{0:s}\t{1:s}\t{2:s}\t{3:s}\t{4:s}\n'.format(ReplaceGroups.mapType2Log[child['attributes']['replace_type']], gid, tid, tname, tmpid))
del child['attributes']['replace_type']
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