14261706617

Committed 04 Apr 2025 08:54AM UTC coverage: 89.721% (-0.8%) from 90.508%

Build # 14261706617

Build Type

push

github

Committed by

veghp

Commit Message

Fix cli interface

Run Details

0 of 3 new or added lines in 1 file covered. (0.0%)

2994 of 3337 relevant lines covered (89.72%)

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/dnachisel/cli.py

#!/usr/bin/env python

"""
DNA Chisel Command Line Interface

Usage:
  dnachisel <source> <target> [--circular] [--mute] [--with_sequence_edits]

Where ``source`` is a fasta or Genbank file, and target can be one of:
- A folder name or a zip name (extension .zip). In this case a complete report
  along with the sequence will be generated.
- A Genbank file. In this case, only the optimized sequence file is created.
  The with_sequence_edits option specifies that edits are also annotated in the
  Genbank file. Note that the filename must end with '.gb'.

Note: this CLI will be developed on a per-request basis, so don't hesitate to
ask for more handles and options on Github
(https://github.com/Edinburgh-Genome-Foundry/DnaChisel/issues)

Example to output the result to a genbank:

>>> dnachisel annotated_record.gb optimized_record.gb

Example to output the result to a folder:

>>> dnachisel annotated_record.gb optimization_report/

Example to output the result to a zip archive:

>>> dnachisel annotated_record.gb optimization_report.zip
"""


def main():
    import os
    from docopt import docopt
    from dnachisel import DnaOptimizationProblem, CircularDnaOptimizationProblem

    params = docopt(__doc__)
    source, target = params["<source>"], params["<target>"]

    # VERBOSE PRINT
    def verbose_print(*args):
        if not params["--mute"]:
            print(*args)

    # PARSE THE CIRCULARITY

    if params["--circular"]:
        problem_class = CircularDnaOptimizationProblem
    else:
        problem_class = DnaOptimizationProblem
    problem = problem_class.from_record(
        source, logger=None if params["--mute"] else "bar"
    )
    problem.max_random_iters = 10000
    verbose_print(
        "\n\nBefore optimization:\n\n",
        problem.constraints_text_summary(),
        problem.objectives_text_summary(),
    )

    if target.lower().endswith(".gb"):  # save genbank
        if params["--with_sequence_edits"]:
            annotate_edits = True
        else:
            annotate_edits = False
        verbose_print("Resolving Constraints...")
        problem.resolve_constraints()
        verbose_print("Optimizing...")
        problem.optimize()
        problem.to_record(filepath=target, with_sequence_edits=annotate_edits)

    else:  # save into zip or folder
        project_name = os.path.basename(source)
        problem.optimize_with_report(
            target, project_name=project_name, file_path=source
        )

    verbose_print(
        "\n\nAfter optimization:\n\n",
        problem.constraints_text_summary(),
        problem.objectives_text_summary(),
        "\n\n",
        "Result written to %s" % target,
    )


if __name__ == "__main__":
    main()

1	#!/usr/bin/env python
2
3	"""
4	DNA Chisel Command Line Interface
5
6	Usage:
7	dnachisel <source> <target> [--circular] [--mute] [--with_sequence_edits]
8
9	Where ``source`` is a fasta or Genbank file, and target can be one of:
10	- A folder name or a zip name (extension .zip). In this case a complete report
11	along with the sequence will be generated.
12	- A Genbank file. In this case, only the optimized sequence file is created.
13	The with_sequence_edits option specifies that edits are also annotated in the
14	Genbank file. Note that the filename must end with '.gb'.
15
16	Note: this CLI will be developed on a per-request basis, so don't hesitate to
17	ask for more handles and options on Github
18	(https://github.com/Edinburgh-Genome-Foundry/DnaChisel/issues)
19
20	Example to output the result to a genbank:
21
22	>>> dnachisel annotated_record.gb optimized_record.gb
23
24	Example to output the result to a folder:
25
26	>>> dnachisel annotated_record.gb optimization_report/
27
28	Example to output the result to a zip archive:
29
30	>>> dnachisel annotated_record.gb optimization_report.zip
31	"""
32
33
34	def main():	×
NEW 35	import os	×
NEW 36	from docopt import docopt	×
NEW 37	from dnachisel import DnaOptimizationProblem, CircularDnaOptimizationProblem	×
38
39	params = docopt(__doc__)	×
40	source, target = params["<source>"], params["<target>"]	×
41
42	# VERBOSE PRINT
43	def verbose_print(*args):	×
44	if not params["--mute"]:	×
45	print(*args)	×
46
47	# PARSE THE CIRCULARITY
48
49	if params["--circular"]:	×
50	problem_class = CircularDnaOptimizationProblem	×
51	else:
52	problem_class = DnaOptimizationProblem	×
53	problem = problem_class.from_record(	×
54	source, logger=None if params["--mute"] else "bar"
55	)
56	problem.max_random_iters = 10000	×
57	verbose_print(	×
58	"\n\nBefore optimization:\n\n",
59	problem.constraints_text_summary(),
60	problem.objectives_text_summary(),
61	)
62
63	if target.lower().endswith(".gb"): # save genbank	×
64	if params["--with_sequence_edits"]:	×
65	annotate_edits = True	×
66	else:
67	annotate_edits = False	×
68	verbose_print("Resolving Constraints...")	×
69	problem.resolve_constraints()	×
70	verbose_print("Optimizing...")	×
71	problem.optimize()	×
72	problem.to_record(filepath=target, with_sequence_edits=annotate_edits)	×
73
74	else: # save into zip or folder
75	project_name = os.path.basename(source)	×
76	problem.optimize_with_report(	×
77	target, project_name=project_name, file_path=source
78	)
79
80	verbose_print(	×
81	"\n\nAfter optimization:\n\n",
82	problem.constraints_text_summary(),
83	problem.objectives_text_summary(),
84	"\n\n",
85	"Result written to %s" % target,
86	)
87
88
89	if __name__ == "__main__":	×
90	main()	×

Edinburgh-Genome-Foundry / DnaChisel / 14261706617

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