The bioBakery help forum

Graphlan tree file

I have installed graphlan and run the command lines as illustrated in this link

I got the files from here:

  • Tree file: guide.txt
  • Annotation file: guide_rings.txt
    I have downloaded those files on my PC and I have run this command line in cmd:
    graphlan_annotate.py --annot guide_rings.txt guide.txt new_file.xml
    and I got this error: No tree file found: guide.txt
    I really need help and thank you.

Hi Amina,

Thanks for using GraPhlAn. I was unable to reproduce the error you described above. However, the following commands did work for me:

# get the tree file
wget https://raw.githubusercontent.com/biobakery/graphlan/master/examples/guide/guide.txt
# get the annotation file
wget https://raw.githubusercontent.com/biobakery/graphlan/master/examples/guide/annot_3.txt
# annotate the tree
graphlan_annotate.py --annot annot_3.txt guide.txt annotated_tree.xml
# generate the tree
graphlan.py annotated_tree.xml tree.png --dpi 300

Can you try running those commands? Let me know if this works for you.

Regards,
Aaron.