phageCRannotate | Description Take as input NCBI nucleotide id

phageCRannotate is a Python library. phageCRannotate has no bugs, it has no vulnerabilities and it has low support. However phageCRannotate build file is not available. You can download it from GitHub.

Description Take as input NCBI nucleotide id(s) or FASTA sequences of phages and outputs phage 'genome map' annotations. Setup Edit the paths at the top of python/faOrNCBINucIds_to_phageProtAnnots.py to specify the correct installations. Create a an input file, either 1) suffixed .ids containing a list of NCBI nucleotide ids of phages one per line, or 2) suffixed .fa containing sequences in FASTA format, one phage per sequence. Example test Example test of annotating phage lambda. See test_outputs/ for outputs. 1st step: download sequence and annotate via pVOG HMMs and NR protein sequences (by far the slowest step due to diamond, if using the full NR database: uses ~12G and runs for several hours; note it scales better you might expect though due to the diamond implementation) python3 python/faOrNCBINucIds_to_phageProtAnnots.py --input test_input_lambda_phage.ids --evalue 0.1 --threads 8 --genepred prodigal. 2nd step: collate the annotation information python3 python/phageAnnotsFilter.py test_input_lambda_phage.merged_final.out test_input_lambda_phage.merged_final.phageAnnotsFilter.out > test_input_lambda_phage.merged_final.phageAnnotsFilter.log. 3rd step: plot the genome maps Rscript R/gvizPlotPhages.R col_files_nonfiltered/*. See: test_outputs/ for ouputs from each of these steps.