update: variable #81
update: variable #81
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WalkthroughThe pull request introduces significant modifications across three files: Changes
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
ibaqpy/bin/peptides2protein.py (1)
Line range hint
227-293: Consider extracting plot configuration.While the changes to use constants are good, the plotting code contains repeated configuration patterns that could be extracted into a helper function.
Consider creating a helper function like:
def create_distribution_plot(data, value_column, sample_column, plot_width, title, log2=True): density = plot_distributions( data, value_column, sample_column, width=plot_width, log2=log2, title=f"{title} Distribution" ) box = plot_box_plot( data, value_column, sample_column, width=plot_width, log2=log2, title=f"{title} Distribution", violin=False ) return density, box
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📒 Files selected for processing (3)
ibaqpy/bin/ibaqpy_commons.py(2 hunks)ibaqpy/bin/peptide_normalization.py(5 hunks)ibaqpy/bin/peptides2protein.py(7 hunks)
🔇 Additional comments (7)
ibaqpy/bin/ibaqpy_commons.py (1)
46-53: LGTM: Well-structured constant definitions.
The addition of these constants improves code maintainability by replacing string literals with named constants. The naming is clear and follows the existing pattern.
ibaqpy/bin/peptides2protein.py (3)
19-24: LGTM: Clean import organization.
The new constants are properly imported and organized alongside related imports.
118-124: LGTM: Improved DataFrame operations.
The use of constants instead of string literals in DataFrame operations reduces the risk of typos and improves maintainability.
214-217: LGTM: Enhanced molecular weight handling.
The molecular weight calculations now use constants and include proper handling of edge cases (NaN and zero values).
ibaqpy/bin/peptide_normalization.py (3)
23-24: LGTM: Added normalization method constants.
The addition of normalization method constants improves code maintainability.
548-550: LGTM: Improved normalization method handling.
The use of constants for normalization methods improves code clarity and reduces the risk of typos in string comparisons.
Also applies to: 596-603
Line range hint 354-396: Verify label handling edge cases.
The updated get_label function now handles "LABEL FREE" labels, but we should verify the case-insensitive handling works as expected.
✅ Verification successful
Let me gather more information about the label handling implementation to ensure we have a complete picture.
Let me try a different approach to analyze the label handling implementation.
Let me check the content of the SDRF test file to understand the label handling test cases.
Based on the analysis of the code and test data, I can now provide the final response:
Case-insensitive label handling is properly implemented
The get_label function correctly handles case variations for "LABEL FREE" through:
- Explicit check for uppercase "LABEL FREE"
- Explicit check for lowercase "label free"
- Consistent error messaging for unsupported label types
- Proper integration with the TMT labeling workflow as evidenced by the test SDRF file
The implementation is robust and handles the edge cases appropriately. No changes needed.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for variations of "LABEL FREE" in the codebase
# to ensure consistent handling
rg -i "label.?free" --type py
Length of output: 376
Script:
#!/bin/bash
# Check the full context of label handling in the file
ast-grep --pattern 'def get_label($_) {
$$$
}'
Length of output: 50
Script:
#!/bin/bash
# Search for test files that might verify label handling
fd "test.*\.py" --exec rg -l -i "label.?free|get_label"
# Also check for any SDRF-related test data that might contain label information
fd ".*sdrf.*" --extension tsv --extension txt
Length of output: 142
Script:
#!/bin/bash
# Check the content of the SDRF test file
head -n 5 tests/example/PXD017834-TMT.sdrf.tsv
# Also search for any direct usage of get_label function in the codebase
rg "get_label\(" -A 2
Length of output: 4037
Summary by CodeRabbit
Release Notes
New Features
TPA,MOLECULARWEIGHT,COPYNUMBER,CONCENTRATION_NM,WEIGHT_NG,MOLES_NMOL,GLOBALMEDIAN, andCONDITIONMEDIAN.Bug Fixes
Refactor