Sequence Module - Batch Analysis Management¶

Management and execution of ChemStation sequences for automated batch analysis.

Overview¶

The Sequence module provides:

Sequence file operations: Load and save sequence files (.S files)
Table editing: Modify sequence parameters row by row
Excel integration: Import sequence data from spreadsheets
Batch control: Start, pause, and resume sequence execution

File Format: ChemStation .S sequence files Default Directory: ChemStation sequence directory (_SEQPATH$)

Sequence File Operations¶

load_sequence()¶

Load an existing sequence from file.

api.sequence.load_sequence(seq_name, seq_dir="_SEQPATH$")

Parameters:

seq_name (str): Sequence filename (without .S extension)
seq_dir (str): Directory containing sequence files (defaults to ChemStation sequence directory)

Examples:

# Load standard sequence
api.sequence.load_sequence("Protein_Analysis_Batch")

# Load from custom directory
api.sequence.load_sequence("TestSeq", "C:\\Custom\\Sequences\\")

# Load daily QC sequence
api.sequence.load_sequence("Daily_QC_2024")

Notes:

Sequence loading overwrites current sequence in memory
All unsaved changes to current sequence are lost
Sequence parameters become active immediately

save_sequence()¶

Save current sequence to file.

api.sequence.save_sequence(seq_name="_SEQFILE$", seq_dir="_SEQPATH$")

Parameters:

seq_name (str): Filename for saved sequence (defaults to current sequence name)
seq_dir (str): Directory for saving sequence (defaults to ChemStation sequence directory)

Examples:

# Save with new name
api.sequence.save_sequence("Modified_Protein_Sequence")

# Overwrite current sequence
api.sequence.save_sequence()

# Save to custom location
api.sequence.save_sequence("Backup_Sequence", "D:\\Backups\\")

Notes:

Saved sequence includes all table data and parameters
Existing files with same name are overwritten
.S extension added automatically

Sequence Table Editing¶

modify_sequence_row()¶

Modify parameters in specific sequence table row.

api.sequence.modify_sequence_row(row, vial_sample="", method="", sample_name="", sample_info="", data_file_name="")

Parameters:

row (int): Row number in sequence table (1-based indexing)
vial_sample (str): Carousel position for sample vial (1-48)
method (str): CE method name (without .M extension)
sample_name (str): Descriptive sample name for identification
sample_info (str): Additional sample metadata and notes
data_file_name (str): Custom data filename (optional)

Examples:

# Modify sample vial and method
api.sequence.modify_sequence_row(
    row=1,
    vial_sample="15",
    method="CE_Protein_Analysis"
)

# Update sample information only
api.sequence.modify_sequence_row(
    row=3,
    sample_name="Unknown_Sample_001",
    sample_info="Customer sample, urgent analysis"
)

# Complete row modification
api.sequence.modify_sequence_row(
    row=5,
    vial_sample="22",
    method="MEKC_SmallMolecules",
    sample_name="Caffeine_Standard",
    sample_info="1mg/mL in water"
)

Notes:

Only specified parameters are modified (empty parameters remain unchanged)
Sequence must be loaded before modification
Changes made to memory - use save_sequence() to persist
Row numbering starts from 1

Excel Integration¶

prepare_sequence_table()¶

Import and create sequence table from Excel spreadsheet.

api.sequence.prepare_sequence_table(excel_file_path, sequence_name=None, sheet_name=0, vial_column=None, method_column=None, filename_column=None, sample_name_column=None, sample_info_column=None, replicate_column=None)

Parameters:

excel_file_path (str): Full path to Excel file containing sequence data
sequence_name (str): Existing sequence to load before modification (optional)
sheet_name (int): Excel worksheet index to read (0-based, default: first sheet)
vial_column (str): Excel column name containing vial positions
method_column (str): Excel column name containing method names
sample_name_column (str): Excel column name containing sample names
sample_info_column (str): Excel column name containing sample metadata
filename_column (str): Excel column name containing custom filenames
replicate_column (str): Excel column name containing replicate information

Examples:

# Basic import
api.sequence.prepare_sequence_table(
    excel_file_path="sample_list.xlsx",
    vial_column="Vial",
    method_column="Method",
    sample_name_column="Sample"
)

# Full import with all columns
api.sequence.prepare_sequence_table(
    excel_file_path="complex_sequence.xlsx",
    sequence_name="Research_Project_2024",
    sheet_name=0,
    vial_column="Vial_Position",
    method_column="CE_Method",
    sample_name_column="Sample_ID",
    sample_info_column="Description",
    filename_column="Data_Name",
    replicate_column="Rep_Number"
)

# Import from second worksheet
api.sequence.prepare_sequence_table(
    excel_file_path="batch_data.xlsx",
    sheet_name=1,
    vial_column="Position",
    method_column="Analysis_Method",
    sample_name_column="Sample_Name"
)

Requirements:

Excel must be installed on the system
File should not be open during import
Column names must match exactly (case-sensitive)
Referenced methods must exist in method directory

Notes:

Excel application briefly visible during processing
Temporary Excel file created during processing
Sequence automatically saved after import
Method names validated against method directory

Sequence Execution Control¶

start()¶

Start execution of the current sequence.

api.sequence.start()

Examples:

# Start loaded sequence
api.sequence.load_sequence("Daily_Analysis")
api.sequence.start()

Notes:

Sequence must be loaded and validated before starting
Instrument enters sequence mode with limited manual control
Progress monitored via system status methods

pause()¶

Pause the currently running sequence.

api.sequence.pause()

Examples:

# Pause during execution
api.sequence.pause()

Notes:

Current analysis completes before pausing
Sequence stops before starting next sample
Manual operations possible while paused

resume()¶

Resume a paused sequence from where it stopped.

api.sequence.resume()

Examples:

# Resume after pause
api.sequence.resume()

Notes:

Resumes from next unprocessed sample
All sequence parameters remain unchanged
Instrument returns to automated sequence mode

Practical Examples¶

Manual Sequence Creation¶

# Load existing sequence or create new
api.sequence.load_sequence("Daily_QC")

# Add samples
api.sequence.modify_sequence_row(
    row=1,
    vial_sample="1",
    method="CE_QC",
    sample_name="QC_Standard",
    sample_info="Daily system suitability"
)

api.sequence.modify_sequence_row(
    row=2,
    vial_sample="10",
    method="CE_Analysis",
    sample_name="Sample_001",
    sample_info="Customer sample"
)

# Save and run
api.sequence.save_sequence("Daily_QC_Modified")
api.sequence.start()

Excel-Based Sequence¶

# Import from Excel
api.sequence.prepare_sequence_table(
    excel_file_path="protein_samples.xlsx",
    vial_column="Vial",
    method_column="Method",
    sample_name_column="Sample_ID",
    sample_info_column="Notes"
)

# Start batch analysis
api.sequence.start()

# Monitor and control
while api.system.method_on():
    print("Sequence running...")
    time.sleep(60)