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Project Description
pbcommand High Level Overview
=============================

co-owners:

[mpkocher](https://github.com/mpkocher)

[natechols](https://github.com/natechols)

PacBio Officially Supported Library. Note the APIs are still in flux and not yet 1.0.0.

[Full Docs](http://pbcommand.readthedocs.org/en/latest/)

[![Circle CI](https://circleci.com/gh/PacificBiosciences/pbcommand.svg?style=svg)](https://circleci.com/gh/PacificBiosciences/pbcommand)

PacBio library for common utils, models, and tools to interface with pbsmrtpipe workflow engine.

To integrate with the pbsmrtpipe workflow engine you must to be able to generate a **Tool Contract** and to be able to run from a **Resolved Tool Contract**.

A **Tool Contract** contains the metadata of the exe, such as the file types of inputs, outputs and options.

Example [Tool Contract Json](https://github.com/PacificBiosciences/pbcommand/blob/master/tests/data/dev_example_dev_txt_app_tool_contract.json) (and [Avro Schema](https://github.com/PacificBiosciences/pbcommand/blob/master/pbcommand/schemas/tool_contract.avsc))

Example [Resolved Tool Contract Json](https://github.com/PacificBiosciences/pbcommand/blob/master/tests/data/resolved_tool_contract_dev_app.json) (and [Avro Schema](https://github.com/PacificBiosciences/pbcommand/blob/master/pbcommand/schemas/resolved_tool_contract.avsc))

There are two principle use cases, first wrapping/calling python functions that have been defined in external python packages, or scripts. Second, creating a CLI tool that supports emitting tool contracts, running resolved tool contracts and complete argparse style CLI.

Example from **pbcommand.cli.examples**

```python

import sys
import logging

from pbcommand.models import FileTypes
from pbcommand.cli import registry_builder, registry_runner

log = logging.getLogger(__name__)

registry = registry_builder("pbcommand", "python -m pbcommand.cli.examples.dev_quick_hello_world ")


def _example_main(input_files, output_files, **kwargs):
# Simple Function that should imported from your library code
# write mock output files for testing purposes, otherwise the End-to-End test will fail
xs = output_files if isinstance(output_files, (list, tuple)) else [output_files]
for x in xs:
with open(x, 'w') as writer:
writer.write("Mock data\n")
return 0


@registry("dev_qhello_world", "0.2.1", FileTypes.FASTA, FileTypes.FASTA, nproc=1, options=dict(alpha=1234))
def run_rtc(rtc):
return _example_main(rtc.task.input_files[0], rtc.task.output_files[0], nproc=rtc.task.nproc)


@registry("dev_fastq2fasta", "0.1.0", FileTypes.FASTQ, FileTypes.FASTA)
def run_rtc(rtc):
return _example_main(rtc.task.input_files[0], rtc.task.output_files[0])


if __name__ == '__main__':
sys.exit(registry_runner(registry, sys.argv[1:]))

```

A driver is the commandline interface that the workflow engine will call.

The driver will be called with "${exe} /path/to/resolved_tool_contract.json"

The tool contracts can be emitted to a directory and used in [pbsmrtpipe](https://github.com/PacificBiosciences/pbsmrtpipe)

```bash
$> python -m pbcommand.cli.examples.dev_quick_hello_world -o /path/to/my-tool-contracts
```


Creating a Full Commandline Tool with TC/RTC and argparse support
-----------------------------------------------------------------

Three Steps
- define Parser
- add running from argparse and running from Resolved ToolContract funcs to call your main
- add call to driver

Import or define your main function.

```python
def run_my_main(fasta_in, fasta_out, min_length):
# do stuff. Main should return an int exit code
return 0
```

Define a function that will add inputs, outputs and options to your parser.

```python
from pbcommand.models import FileTypes


def add_args_and_options(p):
# FileType, label, name, description
p.add_input_file_type(FileTypes.FASTA, "fasta_in", "Fasta File", "PacBio Spec'ed fasta file")
# File Type, label, name, description, default file name
p.add_output_file_type(FileTypes.FASTA, "fasta_out", "Filtered Fasta file", "Filtered Fasta file", "filter.fasta")
# Option id, label, default value, name, description
# for the argparse, the read-length will be translated to --read-length and (accessible via args.read_length)
p.add_int("pbcommand.task_options.dev_read_length", "read-length", 25, "Length filter", "Min Sequence Length filter")
return p
```

Define Parser

```python
from pbcommand.models import TaskTypes, SymbolTypes, get_pbparser


def get_contract_parser():
tool_id = "example_namespace.tasks.my_id"
version = "0.1.0" # or reuse __version__
display_name = "My Example Tool"
# Number of processors to use, can also be SymbolTypes.MAX_NPROC
nproc = 1
# Log file, tmp dir, tmp file. See ResourceTypes in models, ResourceTypes.TMP_DIR
resource_types = ()
# Commandline exe to call "{exe}" /path/to/resolved-tool-contract.json
driver_exe = "python -m pbcommand.cli.example.dev_app --resolved-tool-contract "
desc = "Dev app for Testing that supports emitting tool contracts"
is_distributed = False
# set to True if you want your task to be submitted to the cluster manager (e.g., SGE) if
# one is provided to the workflow engine.
p = get_pbparser(tool_id, version, display_name, desc, driver_exe, is_distributed=is_distributed, nproc=nproc, resource_types=resource_types)
add_args_and_options(p)
return p
```


Define a Wrapping layer to call your main from both the tool contract and raw argparse IO layer

```python
def _args_runner(args):
# this is the args from parser.parse_args()
# the properties of args are defined as "labels" in the add_args_and_options func.
return run_my_main(args.fasta_in, args.fasta_out, args.read_length)


def _resolved_tool_contract_runner(resolved_tool_contract):
"""
:type resolved_tool_contract: pbcommand.models.ResolvedToolContract"""
rtc = resolved_tool_contract
# all options are referenced by globally namespaced id. This allows tools to use other tools options
# e.g., pbalign to use blasr defined options.
return run_my_main(rtc.task.input_files[0], rtc.task.outputs[0], rtc.task.options["pbcommand.task_options.dev_read_length"])
```




Add running layer

```python
import sys
import logging
from pbcommand.utils import setup_log
from pbcommand.cli import pbparser_runner

log = logging.getLogger(__name__)


def main(argv=sys.argv):
# New interface that supports running resolved tool contracts
log.info("Starting {f} version {v} pbcommand example dev app".format(f=__file__, v="0.1.0"))
return pbparser_runner(argv[1:],
get_contract_parser(),
_args_runner, # argparse runner func
_resolved_tool_contract_runner, # tool contract runner func
log, # log instance
setup_log # setup log func
)
if __name__ == '__main__':
sys.exit(main())
```

Now you can run your tool via the argparse standard interface as well as emitting a **Tool Contract** to stdout from the commandline interface.

```sh
> python -m 'pbcommand.cli.examples.dev_app' --emit-tool-contract
```

And you can run the tool from a **Resolved Tool Contract**

```sh
> python -m pbcommand.cli.example.dev_app --resolved-tool-contract /path/to/resolved_contract.json
```

See the dev apps in ["pbcommand.cli.examples"](https://github.com/PacificBiosciences/pbcommand/blob/master/pbcommand/cli/examples/dev_app.py) for a complete application (They require pbcore to be installed).

In addition to TC/RTC support, there's a complete argparse support for the task options. An example of **help** is shown below.

```sh
(pbcommand_test)pbcommand $> python -m 'pbcommand.cli.examples.dev_app' --help
usage: dev_app.py [-h] [-v] [--versions] [--emit-tool-contract]
[--resolved-tool-contract RESOLVED_TOOL_CONTRACT]
[--log-level LOG_LEVEL] [--debug]
[--read-length READ_LENGTH]
fasta_in fasta_out

Dev app for Testing that supports emitting tool contracts

positional arguments:
fasta_in PacBio Spec'ed fasta file
fasta_out Filtered Fasta file

optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
--versions Show versions of individual components (default: None)
--emit-tool-contract Emit Tool Contract to stdout (default: False)
--resolved-tool-contract RESOLVED_TOOL_CONTRACT
Run Tool directly from a PacBio Resolved tool contract
(default: None)
--log-level LOG_LEVEL
Set log level (default: 10)
--debug Debug to stdout (default: False)
--read-length READ_LENGTH
Min Sequence Length filter (default: 25)
```
Release History

Release History

0.3.29

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pbcommand-0.3.29.tar.gz (80.8 kB) Copy SHA256 Checksum SHA256 Source Jun 14, 2016

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