bps-fbi-sp-ecoli 0.0.1

TODO

bps_fbi_sp_ecoli

Install

pip install bps_fbi_sp_ecoli

How to use

Determines the serotype and virulence in ecoli through kmer alignment

! FBI_run_bifrostecolipostkma -h

usage: FBI_run_bifrostecolipostkma [-h] [--input INPUT]
                                   [--sample_sheet SAMPLE_SHEET]
                                   [--output OUTPUT] [--db_path DB_PATH]
                                   [--kma_path KMA_PATH]
                                   [--command_file COMMAND_FILE] [--execute]
                                   [--to_stdout] [--overwrite]
                                   [--config_file CONFIG_FILE]

This program takes as input a folder containing fastq.gz files and a
sample_sheet containing SampleID Organism SupplyingLab ecoli1 Ecoli FBI and
allows you to run bifrostecolipostkma.py on all Ecoli samples.

options:
  -h, --help                   show this help message and exit
  --input INPUT                Path to input folder that contains the .fastq.gz
                               files
  --sample_sheet SAMPLE_SHEET  Name of the sample_sheet file
  --output OUTPUT              Path to the output directory
  --db_path DB_PATH            Path to db folder that contains the indexed
                               database files e.g., file.comp.b, file.fsa,
                               file.index.db, file.lenght.b, file.name,
                               file.seq.b
  --kma_path KMA_PATH          Path to kma program
  --command_file COMMAND_FILE  Path to file to write commands to
  --execute                    Run commands in command file (default: False)
  --to_stdout                  If true, will write to stdout instead of file,
                               mutually exclusive with output_file (default:
                               False)
  --overwrite                  If true, will overwrite output_file if it exists
                               (default: False)
  --config_file CONFIG_FILE    Config file to overwrite default settings, arg
                               parse values will override config file values,

#! FBI_run_bifrostecolipostkma --input input/231116_CUSTOM_SSIFBI_ECOLI --sample_sheet sample_sheet.xlsx --output output/231116_CUSTOM_SSIFBI_ECOLI --command_file output/231116_CUSTOM_SSIFBI_ECOLI/run_bifrostecolipostkma.tsv --execute

! FBI_run_qcecolisummary -h

usage: FBI_run_qcecolisummary [-h] [--input INPUT] [--output OUTPUT]
                              [--command_file COMMAND_FILE] [--execute]
                              [--to_stdout] [--overwrite]
                              [--config_file CONFIG_FILE]

This program takes as input a folder containing .tsv files and allows you to run
qcecolisummary.py on all Ecoli samples.

options:
  -h, --help                   show this help message and exit
  --input INPUT                Path to input folder that contains the results of
                               kma matching against the ecoligenes db (the
                               folder)
  --output OUTPUT              Path to the output directory
  --command_file COMMAND_FILE  Path to file to write commands to
  --execute                    Run commands in command file (default: False)
  --to_stdout                  If true, will write to stdout instead of file,
                               mutually exclusive with output_file (default:
                               False)
  --overwrite                  If true, will overwrite output_file if it exists
                               (default: False)
  --config_file CONFIG_FILE    Config file to overwrite default settings, arg
                               parse values will override config file values,

#! FBI_run_bifrostecolipostkma --input input/231116_CUSTOM_SSIFBI_ECOLI --sample_sheet sample_sheet.xlsx --output output/231116_CUSTOM_SSIFBI_ECOLI --command_file output/231116_CUSTOM_SSIFBI_ECOLI/run_bifrostecolipostkma.tsv --execute