Protein Fasta format output (.faa)?

[raw937]

How do you output a protein fasta (.faa)?
Also, I keep getting an error for start/stop options?
Do I use prodigal on the orfs this calls?

[deprekate]

The current version on pip (1.5.2) does not have the ability to output faa format. Though the current version on github (1.6.0) does allow for output in all sorts of formats. To install the github version is easy:

git clone https://github.com/deprekate/PHANOTATE.git
python3 -m pip install PHANOTATE

You should not be getting any errors about start/stop codons, but have a feeling it is from when I accidently left in a print command when I was debugging the code to allow for a user to specify the start and stop codons.

[raw937]

I tired this install. As you suggested. It isn't installing the 1.6.0 version.
Let me know?

many thanks,
Rick

[deprekate]

I haven't pushed the 1.6 version to Pypi yet, I was waiting for one of my testers, so you have to manually get the code from github by cloning this repo:

git clone https://github.com/deprekate/PHANOTATE.git
pip3 install PHANOTATE

[raw937]

site-packages is not writeable
Requirement already satisfied: PHANOTATE in /home/docwhite/.local/lib/python3.10/site-packages (1.5.1)
Requirement already satisfied: fastpath>=1.3 in /home/docwhite/.local/lib/python3.10/site-packages (from PHANOTATE) (1.9)

[deprekate]

It might be a permissions issue? You might have to add --user to the pip3 command?
pip3 install PHANOTATE --user

[raw937]

Requirement already satisfied: PHANOTATE in /home/docwhite/.local/lib/python3.10/site-packages (1.5.1)
Requirement already satisfied: fastpath>=1.3 in /home/docwhite/.local/lib/python3.10/site-packages (from PHANOTATE) (1.9)

[deprekate]

maybe add a slash dot to the end to make sure pip is installing the downloaded github repo?

pip3 install PHANOTATE/. --user

[deprekate]

oh, I think I might know, are you by chance on OSX? Macs dont have upper or lowercase filenames so the command

pip install PHANOTATE is really pip install phanotate and so would just the 1.5 from pypi

[raw937]

Linux Ubuntu. Still 1.5.1

[deprekate]

can you check that you have the 1.6 version?

cat PHANOTATE/VERSION

[raw937]

more VERSION
1.6.3

pip3 install PHANOTATE --user
Requirement already satisfied: PHANOTATE in /home/docwhite/miniconda3/lib/python3.7/site-packages/phanotate-1.5.0-py3.7-linux-x86_64.egg (1.5.0)
Requirement already satisfied: fastpath>=1.3 in /home/docwhite/miniconda3/lib/python3.7/site-packages/fastpath-1.9-py3.7-linux-x86_64.egg (from PHANOTATE) (1.9)

[deprekate]

and if you add a slash dot to the pip3 command? I have a feeling pip is not installing the downloaded repo

pip3 install PHANOTATE/. --user

you can also cd into the directory and install:

cd PHANOTATE ; pip3 install .

[raw937]

works!

[raw937]

pip3 install .
works!

[raw937]

How do I get multiple formats? faa, gff, fna, fasta.

[deprekate]

awesome, now hopefully phanotate itself wont have any problems : )

[raw937]

thank you for your help. How do I get multiple formats? faa, gff, fna, fasta.

[deprekate]

just specify each one you want. Though it only does one at a time, so if you want all the formats at once and don't want to rerun phanotate multiple times, just output a genbank file, and then use any available tool to convert it, which only takes a second. I have the genbank package on pypi

so the workflow would be something like:

phanotate.py infile.fasta -f genbank -o outfile.gbk
genbank.py outfile.gbk -f gff -o outfile.gff
genbank.py outfile.gbk -f fna -o outfile.fna
genbank.py outfile.gbk -f faa -o outfile.faa
genbank.py outfile.gbk -f fasta -o outfile.fasta

...well I guess the last one is redundant since outfile.fasta should match infile.fasta

[raw937]

Having issues installing the 1.6.3 version with conda/mamba.

Any thoughts on the new release update to bioconda/conda?

[deprekate]

I haven't pushed the 1.6.x versions to pypi/pip (which is automatically scraped by conda)just yet, since I was really waiting for more testing to be sure there were not any bugs (as there is with 1.6.1).