Command-Line Interface

Command-line interface for OligoSeeker

Argument Parser

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create_parser

 create_parser ()

*Create command-line argument parser.

Returns: Configured argument parser*

Command-Line Runner

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validate_args

 validate_args (args:argparse.Namespace)

*Validate command-line arguments.

Args: args: Parsed command-line arguments

Returns: True if arguments are valid, False otherwise*

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args_to_config

 args_to_config (args:argparse.Namespace)

*Convert command-line arguments to pipeline configuration.

Args: args: Parsed command-line arguments

Returns: Pipeline configuration object*

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run_cli

 run_cli (args:Optional[List[str]]=None)

*Run the command-line interface.

Args: args: Command-line arguments (if None, uses sys.argv)

Returns: Exit code (0 for success, non-zero for failure)*

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main

 main ()

Main entry point for command-line execution.

!oligoseeker -m count \
--f1 ../test_files/test_1.fq.gz \
--f2 ../test_files/test_2.fq.gz \
--oligos "GCGGATTACATTNNNAAATAACATCGT,TGTGGTAAGCGGNNNGAAAGCATTTGT,GTCGTAGAAAATNNNTGGGTGATGAGC" \
--output ../test_files/test_outs --prefix test_cm3
/Users/MTinti/miniconda3/envs/work3/lib/python3.10/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.4' currently installed).
  from pandas.core import (
2025-03-17 16:53:47,770 - INFO - Starting OligoCodonPipeline
2025-03-17 16:53:47,770 - INFO - Loading oligo sequences...
2025-03-17 16:53:47,770 - INFO - Loading oligos from provided string
2025-03-17 16:53:47,770 - INFO - Loaded 3 oligo sequences
2025-03-17 16:53:47,770 - INFO - Processing FASTQ files...
2000it [00:00, 57245.66it/s]
2025-03-17 16:53:47,839 - INFO - Formatting results...
2025-03-17 16:53:47,841 - INFO - Saving results to: ../test_files/test_outs/test_cm3_counts.csv
2025-03-17 16:53:47,847 - INFO - Pipeline completed in 0.08 seconds

Results saved to:
  CSV: ../test_files/test_outs/test_cm3_counts.csv

Processed 3 oligos in 0.08 seconds
!oligoseeker -m count \
--f1 ../test_files/test_1.fq.gz \
--f2 ../test_files/test_2.fq.gz \
--oligos-file '../test_files/oligos.txt' \
--output ../test_files/test_outs --prefix test_cm4
/Users/MTinti/miniconda3/envs/work3/lib/python3.10/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.4' currently installed).
  from pandas.core import (
2025-03-11 20:03:03,960 - INFO - Starting OligoCodonPipeline
2025-03-11 20:03:03,961 - INFO - Loading oligo sequences...
2025-03-11 20:03:03,961 - INFO - Loading oligos from file: ../test_files/oligos.txt
2025-03-11 20:03:03,961 - INFO - Loaded 3 oligo sequences
2025-03-11 20:03:03,961 - INFO - Processing FASTQ files...
2000it [00:00, 60738.60it/s]
2025-03-11 20:03:04,009 - INFO - Formatting results...
2025-03-11 20:03:04,011 - INFO - Saving results to: ../test_files/test_outs/test_cm4_counts.csv
2025-03-11 20:03:04,017 - INFO - Pipeline completed in 0.06 seconds

Results saved to:
  CSV: ../test_files/test_outs/test_cm4_counts.csv

Processed 3 oligos in 0.06 seconds
!oligoseeker -m merge \
--output-file 'merge_cl.csv' \
--input-dir ../test_files/test_outs \
--output ../test_files/merged
/Users/MTinti/miniconda3/envs/work3/lib/python3.10/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.4' currently installed).
  from pandas.core import (
Found 4 CSV files to merge
  Loaded ../test_files/test_outs/test2_counts.csv with 4 rows and 3 columns
  Loaded ../test_files/test_outs/test1_counts.csv with 4 rows and 3 columns
  Loaded ../test_files/test_outs/test_cm3_counts.csv with 3 rows and 2 columns
  Loaded ../test_files/test_outs/test_cm4_counts.csv with 4 rows and 3 columns
Merged data saved to ../test_files/merged/merge_cl.csv

Merge completed successfully!
Merged 4 unique codons across all input files
Results contain 3 oligo columns