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Command Line Wrappers

Some of the functionality of NGLess can also be accessed using traditional command-line scripts. These are written in Python and can be installed using Python package management tools:

pip install NGLessPy

All of the wrappers can install NGLess if passed the --auto-install flag.

All of these wrappers also have Common Workflow Language so that they can be used in larger pipelines.

ngless-install.py

This is only supported on Linux

Installs NGLess either for a single user ($HOME/.local/bin/ngless) or globally (/usr/local/bin'). All the other tools in this package can also install NGLess automatically.

usage: ngless-install.py [-h] [-f] [-t TARGET] [-m {user,global}] [--verbose]

optional arguments:
  -h, --help            show this help message and exit
  -f, --force           Install NGLess even if it is already found
  -t TARGET, --target TARGET
                        Output file/path for results
  -m {user,global}, --mode {user,global}
                        Global or user install
  --verbose             Verbose mode

ngless-count.py

This is the equivalent of calling the count function from within NGLess:

usage: ngless-count.py [-h] -i INPUT -o OUTPUT [-f FEATURES]
                       [-m {dist1,all1,1overN,unique_only}] [--auto-install]
                       [--debug]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        SAM/BAM/CRAM file to count reads on
  -o OUTPUT, --output OUTPUT
                        Output file/path for results
  -f FEATURES, --features FEATURES
                        Feature to count
  -m {dist1,all1,1overN,unique_only}, --multiple {dist1,all1,1overN,unique_only}
                        How to handle multiple mappers
  --auto-install        Install NGLess if not found in PATH
  --debug               Prints the payload before submitting to ngless

ngless-map.py

This is the equivalent of calling the map function from within NGLess.

usage: ngless-map.py [-h] -i INPUT [-i2 INPUT_REVERSE] [-s INPUT_SINGLES] -o
                     OUTPUT [--auto-install] [--debug]
                     (-r {sacCer3,susScr11,ce10,dm3,gg4,canFam2,rn4,bosTau4,mm10,hg19} | -f FASTA)

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        FastQ file with reads to map (forward)
  -i2 INPUT_REVERSE, --input-reverse INPUT_REVERSE
                        FastQ file with reads to map (reverse) - if paired end
  -s INPUT_SINGLES, --input-singles INPUT_SINGLES
                        FastQ file with reads to map (singles) - if paired end
                        and unpaired reads exist
  -o OUTPUT, --output OUTPUT
                        Output file/path for results
  --auto-install        Install NGLess if not found in PATH
  --debug               Prints the payload before submitting to ngless
  -r {sacCer3,susScr11,ce10,dm3,gg4,canFam2,rn4,bosTau4,mm10,hg19}, --reference {sacCer3,susScr11,ce10,dm3,gg4,canFam2,rn4,bosTau4,mm10,hg19}
                        Map against a builtin reference
  -f FASTA, --fasta FASTA
                        Map against a given fasta file (will be indexed if
                        index is not available)

ngless-mapstats.py

This is the equivalent of calling the mapstats function from within NGLess. This will take a SAM/BAM file as input and produce some simple statistics.

usage: ngless-mapstats.py [-h] -i INPUT -o OUTPUT [--auto-install] [--debug]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        SAM/BAM/CRAM file filter
  -o OUTPUT, --output OUTPUT
                        Output file/path for results
  --auto-install        Install NGLess if not found in PATH
  --debug               Prints the payload before submitting to ngless

ngless-select.py

This is the equivalent of calling the select function from within NGLess:

usage: ngless-select.py [-h] -i INPUT -o OUTPUT -a {keep_if,drop_if} -c
                        {mapped,unmapped,unique}
                        [{mapped,unmapped,unique} ...] [--auto-install]
                        [--debug]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        SAM/BAM/CRAM file filter
  -o OUTPUT, --output OUTPUT
                        Output file/path for results
  -a {keep_if,drop_if}, --action {keep_if,drop_if}
                        Whether to keep or drop when condition are met
  -c {mapped,unmapped,unique} [{mapped,unmapped,unique} ...], --conditions {mapped,unmapped,unique} [{mapped,unmapped,unique} ...]
                        One or more conditions to filter on
  --auto-install        Install NGLess if not found in PATH
  --debug               Prints the payload before submitting to ngless

ngless-trim.py

This is equivalent of calling the preprocess function trimming the reads (with either substrim or endstrim depending on the arguments passed. Finally, any (trimmed) reads which are not of a minimum length are discard.

usage: ngless-trim.py [-h] -i INPUT -o OUTPUT -m {substrim,endstrim} -q
                      MIN_QUALITY [-d DISCARD] [--auto-install] [--debug]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        FastQ file with reads to trim
  -o OUTPUT, --output OUTPUT
                        Output file/path for results
  -m {substrim,endstrim}, --method {substrim,endstrim}
                        Which trimming method to use
  -q MIN_QUALITY, --min-quality MIN_QUALITY
                        Minimum quality value
  -d DISCARD, --discard DISCARD
                        Discard if shorted than
  --auto-install        Install NGLess if not found in PATH
  --debug               Prints the payload before submitting to ngless

ngless-unique.py

This is the equivalent of calling the count function from within NGLess:

usage: ngless-unique.py [-h] -i INPUT -o OUTPUT [-c MAX_COPIES]
                        [--auto-install] [--debug]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        FastQ file to filter
  -o OUTPUT, --output OUTPUT
                        Output file/path for results
  -c MAX_COPIES, --max-copies MAX_COPIES
                        Max number of duplicate copies to keep
  --auto-install        Install NGLess if not found in PATH
  --debug               Prints the payload before submitting to ngless
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