Run MicFunPred

Printing help message

MicFunPred provides a single command to run the whole pipeline (MicFunPred_run_pipeline.py)

MicFunPred_run_pipeline.py -h

usage: MicFunPred_run_pipeline.py [-h] [-i PATH] [-r PATH] [-p PERC_IDENT] [-b PATH] [-c GENECOV] [-o PATH] [-t INT] [-v] [--contrib] [--plot]

optional arguments:
  -h, --help            show this help message and exit

Required:
  -i PATH, --otu_table PATH
                        Tab delimited OTU table
  -r PATH, --repset_seq PATH
                        Multi-fasta file of OTU/ASV sequences

Optional:
  -p PERC_IDENT, --perc_ident PERC_IDENT
                        [Optional] Percent identity cut-off to assign genus. (default: 97)
  -b PATH, --blastout PATH
                        Blast output of ASV/OTU sequences with any database in output format 6
  -c GENECOV, --genecov GENECOV
                        [Optional] Percentage of organism in a genus which should have gene to define it as core. Value ranges from 0 to 1 (default: 0.5)
  -o PATH, --output PATH
                        [Optional] Output directory (default: MicFunPred_out)
  -t INT, --threads INT
                        (Optional) number of threads to be used. (default: 1)
  -v, --verbose         Print message of each step to stdout.
  --contrib             Calculate taxon contribution of functions
  --plot                Plot contribution for KEGG pathways

Input data format

MicFunPred requires abundance (tab separated) and sequence (FASTA format) file to run the prediction. You refer to test data under test_data directory. test_counts.tsv and test.fasta

Example

MicFunPred_run_pipeline.py -i test_data/test_counts.tsv -r test_data/test.fasta -o test_data/micfunpred_out --verbose