Merge pull request #133 from NAL-i5K/fix_replace_id

fixes to gff3-merge - use id instead of name in replace process
NAL-i5K · Mar 27, 2024 · 66cc0c3 · 66cc0c3
2 parents 7f2a81a + b46da89
commit 66cc0c3
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/gff3tool/lib/auto_assignment/gen_spreadsheet.pl b/gff3tool/lib/auto_assignment/gen_spreadsheet.pl
@@ -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;
@@ -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;

diff --git a/gff3tool/lib/gff3_merge/merge.py b/gff3tool/lib/gff3_merge/merge.py
@@ -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']