bug(?) for the resulting file*_mitoscaf.fa.gbf.cds.fasta

[linzhi2013]

MitoZ uses this mitoz-tools gbseqextractor command to extract gene sequences from GenBank file, however, currently, this command does not output the sequence from 5' to 3' if the gene is in reversed direction ('-'). The output gene sequences are in the resulting file*_mitoscaf.fa.gbf.cds.fasta

temporary solution:

Firstly, extract such sequences into a separate file:

grep '(-)'  *_mitoscaf.fa.gbf.cds.fasta -A1 >  your_gene_in_reversed_direction.fa

Then use the revseq command:

mamba install -c bioconda emboss

revseq -sequence your_gene_in_reversed_direction.fa -outseq output_rev.fas

[linzhi2013]

fixed in MitoZ 3.4