Python tools depend on BioPhyton, and should compatible with both python 2 and 3.
Perl tools depend on the module menafmod.pm which is included, if you place bion_tools into your home they should work straight away, otherwise you have to modify the path at the beginning of each script.
base_env.yml file to creat virtual environment where all tools should work, useful also to generate custom kernels for jupyter notebooks.
Short instructions:
if you never used anaconda create a .condarc file in your home and edit to determine the default location of conda environments and pkgs eg.
envs_dirs:
- /data/fmenar/conda/envs
pkgs_dirs:
- /data/fmenar/conda/pkgs
Than run:
conda env create -f base_env.yml
source activate base_env
if you want to add your environment to the kernel list
ipython kernel install --user --name jupyter_nb_base
conda deactivate
assemble.py: cut, complement and/or reverse sequence from a fasta, works on files with a single sequence, if there are multiple sequences will consider only the first
check_length_fasta.py: check the length of every sequence in a fasta file
check_missing_fasta.py: check the proportion of missing data (gaps, N, X, anything that is not actgACTG) for each sequence in a fasta file
purge_fasta.py: extract or delete sequences from a multi fasta file by name
transpose: transpose a file, needs two arguments, infile and separator
convert_ali: convert alignments between different formats (FASTA NEXUS PHYLIP)
freq_count: tally occurrences of lines in a file