Hello,
While the script seems to work as advertised otherwise, when given a GFF file with a FASTA at the end of the file, correct_gff_feature_order.pl places the "##FASTA" header in the wrong place in the output file, such that this header is on the second line of the file like so:
1 ##gff-version 3
2 ##FASTA
The problem in the code seems to be here, where you need special handling of the "##FASTA" line:
first write the comments to the output file
for ( @comment_lines ) {
print $ofh "$_\n";
}
Hello,
While the script seems to work as advertised otherwise, when given a GFF file with a FASTA at the end of the file, correct_gff_feature_order.pl places the "##FASTA" header in the wrong place in the output file, such that this header is on the second line of the file like so:
1 ##gff-version 3
2 ##FASTA
The problem in the code seems to be here, where you need special handling of the "##FASTA" line:
first write the comments to the output file
for ( @comment_lines ) {
print $ofh "$_\n";
}