List out of index about showtree HOT 2 CLOSED

Hi @acpguedes ,

the required domain input format is the output format of pfam_scan.pl which you can download here: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/
You don't need calcTree, it's an internal tool from my former colleagues. It wasn't so clear in the readme, I updated that now.

Here is an example of the domain input format, maybe you can somehow convert your file to this format?
InR.pfam.txt

Alternatively I could try to implement an option to accept hmmscan files as well. Could you upload your file so I can see what the format looks like?

Cheers, Lukas

from showtree.

I strongly recommend make your script accept hmmscan output format

python3 showTree-master/showTree.py -t blue.tree -m blue.aln2 -d blue.hmmscan -o example.svg

Above I used FastTree calculed tree, a MSA and a HMMER3 hmmscan output.

I received this error

You manually specified the domain annotation(s):
blue.hmmscan

Traceback (most recent call last):
File "showTree-master/showTree.py", line 607, in
lineseq=args.lineseq,
File "showTree-master/showTree.py", line 522, in main
d.collect_domain_info()
File "showTree-master/showTree.py", line 167, in collect_domain_info
self.parse_domain_annotation(dom_annot_path)
File "showTree-master/showTree.py", line 192, in parse_domain_annotation
int(fields[1]), int(fields[2])
ValueError: invalid literal for int() with base 10: 'MNSISQISGNASATSGVTNEANVLSGEaVETMHAL--SKASEEIEAVVGLIQKI'

The it's sound like you are waiting a different format that you didn't specified in your documentation.
Also, you ask for a calcTree configure file output witch community are not able to use.

Anyway, it works without -c and -d options. and worked well. Thanks

from showtree.