______ _______ __ _ _____ _____ __ __ _____ _______
| ____ |______ | \ | | | |_____] \_/ |_____] |______
|_____| |______ | \_| |_____| | | | |______
B i o i n f o r m a t i c s pipelines require creating directories, checking intermediate files, checking if those intermediate files have anything in them, checking return/error codes, gzipping, deleting temporary files, converting sam to bam, etc. genopype is a Python package I've developed for creating these bash pipelines quickly, in Python (v2.7+ & 3.5+), and easily.
__author__ = "Josh L. Espinoza"
__cite__ = "TBD"
__contact__ = "jespinoz@jcvi.org, jol.espinoz@gmail.com"
__developmental__ = True
__license__ = "BSD-3"
__version__ = "2023.5.15"
pip install genopype
conda install -c jolespin genopype
# import genopype as gp
from genopype import *
# Set up a directory dictionary
directories = dict()
directories["output"] = create_directory("pipeline_testing")
directories["checkpoints"] = create_directory(os.path.join(directories["output"], "checkpoints"))
directories["logs"] = create_directory(os.path.join(directories["output"], "logs"))
# Create a commands.sh file to write to as you build the pipeline
with open(os.path.join(directories["output"], "commands.sh"), "w") as f_cmds:
ep = ExecutablePipeline(name="Sith", description="The rule of two", f_cmds=f_cmds, checkpoint_directory=directories["checkpoints"], log_directory=directories["logs"], bypass_io_validation_if_checkpoints_exist=True)
# Step 1
output_filepaths = [os.path.join(directories["output"], "holocron.txt")]
message = "Two there should be; no more, no less. One to embody the power, the other to crave it.\n"
ep.add_step(id="Darth Bane",
cmd="echo '{}' > {}".format(message, output_filepaths[0]),
output_filepaths=output_filepaths,
description = "Begin the rule of two",
errors_ok=False,
validate_outputs=True,
)
# Step 2
input_filepaths = [os.path.join(directories["output"], "holocron.txt")]
output_filepaths = [os.path.join(directories["output"], "*.txt")]
ep.add_step(id="Darth Plagueis",
cmd="(cat {} && echo 'jedi') > {} ".format(input_filepaths[0], os.path.join(directories["output"], "wisdom.txt")),
input_filepaths=input_filepaths,
output_filepaths=output_filepaths,
description = "Read the holocron",
errors_ok=False,
validate_inputs=True,
validate_outputs=True,
)
# Step 3
input_filepaths = [os.path.join(directories["output"], "holocron.txt"), os.path.join(directories["output"], "wisdom.txt")]
output_directory = create_directory(os.path.join(directories["output"], "temple"))
output_filepaths = [os.path.join(output_directory, "data-crystal.txt"), output_directory]
cmds = [
"(",
"mkdir -p {}".format(output_directory),
"&&",
"cat {} {} > {}".format(input_filepaths[0], input_filepaths[1], output_filepaths[0]),
")",
]
ep.add_step(id="Darth Sidious",
cmd=cmds,
input_filepaths=input_filepaths,
output_filepaths=output_filepaths,
description = "Move the data",
)
ep.compile()
ep.execute(restart_from_checkpoint=3)
# Directory structure
print("\n", format_header("Directory structure:","_"), "\n", get_directory_tree(directories["output"], ascii=True), sep="", file=sys.stdout)
===========================
. .. ... Compiling ... .. .
===========================
Step: 1, Darth Bane | log_prefix = 1__Darth-Bane | Begin the rule of two
Step: 2, Darth Plagueis | log_prefix = 2__Darth-Plagueis | Read the holocron
Step: 3, Darth Sidious | log_prefix = 3__Darth-Sidious | Move the data
_________________________________________
. .. ... Sith || The rule of two ... .. .
_________________________________________
Restarting pipeline from checkpoint: 3
Executing pipeline: 0%| | 0/3 [00:00<?, ?it/s]==============
. Darth Bane .
==============
Input: []
Output: ['pipeline_testing/holocron.txt']
Command:
echo 'Two there should be; no more, no less. One to embody the power, the other to crave it.
' > pipeline_testing/holocron.txt
Running. .. ... .....
Log files:
pipeline_testing/logs/1__Darth-Bane.*
Validating the following output files:
[=] File exists (88 bytes): pipeline_testing/holocron.txt
Duration: 00:00:00
==================
. Darth Plagueis .
==================
Input: ['pipeline_testing/holocron.txt']
Output: ['pipeline_testing/*.txt']
Command:
(cat pipeline_testing/holocron.txt && echo 'jedi') > pipeline_testing/wisdom.txt
Validating the following input files:
[=] File exists (88 bytes): pipeline_testing/holocron.txt
Running. .. ... .....
Log files:
pipeline_testing/logs/2__Darth-Plagueis.*
Validating the following output files:
[=] File exists (88 bytes): pipeline_testing/holocron.txt
[=] File exists (93 bytes): pipeline_testing/wisdom.txt
Duration: 00:00:00
=================
. Darth Sidious .
=================
Input: ['pipeline_testing/holocron.txt', 'pipeline_testing/wisdom.txt']
Output: ['pipeline_testing/temple/data-crystal.txt', 'pipeline_testing/temple']
Command:
( mkdir -p pipeline_testing/temple && cat pipeline_testing/holocron.txt pipeline_testing/wisdom.txt > pipeline_testing/temple/data-crystal.txt )
Validating the following input files:
[=] File exists (88 bytes): pipeline_testing/holocron.txt
[=] File exists (93 bytes): pipeline_testing/wisdom.txt
Running. .. ... .....
Log files:
pipeline_testing/logs/3__Darth-Sidious.*
Validating the following output files:
[=] File exists (181 bytes): pipeline_testing/temple/data-crystal.txt
[=] Directory exists (181 bytes): pipeline_testing/temple
Duration: 00:00:00
Executing pipeline: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 44.07it/s]
........................
Total duration: 00:00:00
........................
____________________
Directory structure:
____________________
pipeline_testing/
|__ checkpoints/
| |__ 1__Darth-Bane
| |__ 2__Darth-Plagueis
| |__ 3__Darth-Sidious
|__ commands.sh
|__ holocron.txt
|__ logs/
| |__ 1__Darth-Bane.e
| |__ 1__Darth-Bane.o
| |__ 1__Darth-Bane.returncode
| |__ 2__Darth-Plagueis.e
| |__ 2__Darth-Plagueis.o
| |__ 2__Darth-Plagueis.returncode
| |__ 3__Darth-Sidious.e
| |__ 3__Darth-Sidious.o
| |__ 3__Darth-Sidious.returncode
|__ temple/
| |__ data-crystal.txt
|__ wisdom.txt