feat: enable gzip output for bedtools intersect #3642
Conversation
📝 WalkthroughWalkthroughThe changes add conditional logic across multiple bedtools wrapper scripts to detect if the output filename ends with ".gz" and, if so, append a gzip compression pipe to the command execution. Additionally, a new Snakefile rule for generating gzipped intersect outputs has been introduced along with corresponding test updates to cover the new functionality and enhance flag usage. Changes
Sequence Diagram(s)sequenceDiagram
participant S as Snakemake
participant W as Wrapper Script
participant Sh as Shell
S->>W: Execute command for bedtools tool
Note over W: Check if output filename ends with ".gz"
alt Output requires compression
W->>W: Set compress variable to "| gzip"
else
W->>W: Set compress variable to empty string
end
W->>Sh: Run shell command (with optional gzip)
Sh-->>W: Return result
W-->>S: Output generated file
sequenceDiagram
participant SF as Snakefile Rule (bedtools_merge_zip)
participant W as Intersect Wrapper
participant Sh as Shell
SF->>W: Call intersect wrapper
Note over W: Include compression logic based on output extension
W->>Sh: Execute command with optional "| gzip"
Sh-->>W: Return execution result
W-->>SF: Produce gzipped output file
Suggested reviewers
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Actionable comments posted: 0
🧹 Nitpick comments (3)
bio/bedtools/bamtobed/wrapper.py (1)
12-15: LGTM! Compression logic is correctly implemented.The conditional check for
.gzextension and the corresponding compression command setup is accurate.Optional: Consider using a more concise ternary operator:
-if snakemake.output[0].endswith(".gz"): - compress = "| gzip" -else: - compress = "" +compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""🧰 Tools
🪛 Ruff (0.8.2)
12-15: Use ternary operator
compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""instead ofif-else-blockReplace
if-else-block withcompress = "| gzip" if snakemake.output[0].endswith(".gz") else ""(SIM108)
12-12: Undefined name
snakemake(F821)
bio/bedtools/complement/wrapper.py (1)
10-13: LGTM! Compression logic is correctly implemented.The conditional check for
.gzextension and the corresponding compression command setup is accurate.Optional: Consider using a more concise ternary operator:
-if snakemake.output[0].endswith(".gz"): - compress = "| gzip" -else: - compress = "" +compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""🧰 Tools
🪛 Ruff (0.8.2)
10-13: Use ternary operator
compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""instead ofif-else-blockReplace
if-else-block withcompress = "| gzip" if snakemake.output[0].endswith(".gz") else ""(SIM108)
10-10: Undefined name
snakemake(F821)
bio/bedtools/intersect/wrapper.py (1)
12-16: LGTM! Well-documented compression logic.The compression feature is well-documented and correctly implemented.
Optional: Consider using a more concise ternary operator:
-if snakemake.output[0].endswith(".gz"): - compress = "| gzip" -else: - compress = "" +compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""🧰 Tools
🪛 Ruff (0.8.2)
13-16: Use ternary operator
compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""instead ofif-else-blockReplace
if-else-block withcompress = "| gzip" if snakemake.output[0].endswith(".gz") else ""(SIM108)
13-13: Undefined name
snakemake(F821)
📜 Review details
Configuration used: CodeRabbit UI
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📒 Files selected for processing (8)
bio/bedtools/bamtobed/wrapper.py(1 hunks)bio/bedtools/complement/wrapper.py(1 hunks)bio/bedtools/coveragebed/wrapper.py(2 hunks)bio/bedtools/genomecov/wrapper.py(1 hunks)bio/bedtools/intersect/test/Snakefile(1 hunks)bio/bedtools/intersect/wrapper.py(1 hunks)bio/bedtools/merge/wrapper.py(2 hunks)test_wrappers.py(2 hunks)
🧰 Additional context used
📓 Path-based instructions (2)
`**/*.py`: Do not try to improve formatting. Do not suggest ...
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
bio/bedtools/coveragebed/wrapper.pybio/bedtools/merge/wrapper.pybio/bedtools/intersect/wrapper.pybio/bedtools/complement/wrapper.pybio/bedtools/bamtobed/wrapper.pybio/bedtools/genomecov/wrapper.pytest_wrappers.py
`**/wrapper.py`: Do not complain about use of undefined vari...
**/wrapper.py: Do not complain about use of undefined variable calledsnakemake.
bio/bedtools/coveragebed/wrapper.pybio/bedtools/merge/wrapper.pybio/bedtools/intersect/wrapper.pybio/bedtools/complement/wrapper.pybio/bedtools/bamtobed/wrapper.pybio/bedtools/genomecov/wrapper.py
🪛 Ruff (0.8.2)
bio/bedtools/coveragebed/wrapper.py
20-23: Use ternary operator compress = "| gzip" if output_file.endswith(".gz") else "" instead of if-else-block
Replace if-else-block with compress = "| gzip" if output_file.endswith(".gz") else ""
(SIM108)
bio/bedtools/merge/wrapper.py
13-16: Use ternary operator compress = "| gzip" if snakemake.output[0].endswith(".gz") else "" instead of if-else-block
Replace if-else-block with compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""
(SIM108)
13-13: Undefined name snakemake
(F821)
bio/bedtools/intersect/wrapper.py
13-16: Use ternary operator compress = "| gzip" if snakemake.output[0].endswith(".gz") else "" instead of if-else-block
Replace if-else-block with compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""
(SIM108)
13-13: Undefined name snakemake
(F821)
bio/bedtools/complement/wrapper.py
10-13: Use ternary operator compress = "| gzip" if snakemake.output[0].endswith(".gz") else "" instead of if-else-block
Replace if-else-block with compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""
(SIM108)
10-10: Undefined name snakemake
(F821)
16-16: Undefined name snakemake
(F821)
bio/bedtools/bamtobed/wrapper.py
12-15: Use ternary operator compress = "| gzip" if snakemake.output[0].endswith(".gz") else "" instead of if-else-block
Replace if-else-block with compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""
(SIM108)
12-12: Undefined name snakemake
(F821)
bio/bedtools/genomecov/wrapper.py
22-25: Use ternary operator compress = "| gzip" if snakemake.output[0].endswith(".gz") else "" instead of if-else-block
Replace if-else-block with compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""
(SIM108)
22-22: Undefined name snakemake
(F821)
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: Summary
🔇 Additional comments (13)
bio/bedtools/bamtobed/wrapper.py (1)
23-23: LGTM! Shell command is correctly modified.The compression command is properly placed in the shell command before the output redirection.
bio/bedtools/complement/wrapper.py (1)
23-23: LGTM! Shell command is correctly modified.The compression command is properly placed in the shell command before the output redirection.
bio/bedtools/intersect/wrapper.py (1)
23-23: LGTM! Shell command is correctly modified.The compression command is properly placed in the shell command before the output redirection.
bio/bedtools/intersect/test/Snakefile (1)
16-28: Consider using a unique log file for the gzipped output rule.The new rule is well-structured and correctly implements gzipped output. However, both rules are using the same log file path which could lead to log overwrites if both rules are executed in the same workflow.
Consider using a unique log file path for the gzipped output rule:
log: - "logs/intersect/A_B.log" + "logs/intersect/A_B.gz.log"✅ Verification successful
Unique log file needed for gzipped output rule
The current implementation in rule bedtools_merge_zip is using the log file "logs/intersect/A_B.log", which is shared with another rule. This introduces the possibility of log overwrites when both rules run in the same workflow. Changing the log file to a unique name (e.g., "logs/intersect/A_B.gz.log") for the gzipped output rule—as suggested—is appropriate.
- In bio/bedtools/intersect/test/Snakefile (lines 16–28), change the log file path to "logs/intersect/A_B.gz.log".
bio/bedtools/coveragebed/wrapper.py (2)
20-26: LGTM! Compression detection logic is correctly implemented.The implementation correctly detects if the output file should be compressed based on the
.gzextension.🧰 Tools
🪛 Ruff (0.8.2)
20-23: Use ternary operator
compress = "| gzip" if output_file.endswith(".gz") else ""instead ofif-else-blockReplace
if-else-block withcompress = "| gzip" if output_file.endswith(".gz") else ""(SIM108)
35-35: LGTM! Compression pipe is correctly placed.The compression pipe is correctly placed before the output redirection, ensuring proper handling of gzipped output.
bio/bedtools/genomecov/wrapper.py (2)
22-26: LGTM! Compression detection logic is correctly implemented.The implementation correctly detects if the output file should be compressed based on the
.gzextension.🧰 Tools
🪛 Ruff (0.8.2)
22-25: Use ternary operator
compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""instead ofif-else-blockReplace
if-else-block withcompress = "| gzip" if snakemake.output[0].endswith(".gz") else ""(SIM108)
22-22: Undefined name
snakemake(F821)
32-32: LGTM! Compression pipe is correctly placed.The compression pipe is correctly placed before the output redirection, ensuring proper handling of gzipped output.
bio/bedtools/merge/wrapper.py (3)
13-18: LGTM! Compression detection logic is correctly implemented.The implementation correctly detects if the output file should be compressed based on the
.gzextension.🧰 Tools
🪛 Ruff (0.8.2)
13-16: Use ternary operator
compress = "| gzip" if snakemake.output[0].endswith(".gz") else ""instead ofif-else-blockReplace
if-else-block withcompress = "| gzip" if snakemake.output[0].endswith(".gz") else ""(SIM108)
13-13: Undefined name
snakemake(F821)
30-32: LGTM! Compression pipe is correctly placed for multiple input files.The compression pipe is correctly placed before the output redirection when handling multiple input files.
40-41: LGTM! Compression pipe is correctly placed for single input file.The compression pipe is correctly placed before the output redirection when handling a single input file.
test_wrappers.py (2)
1957-1957: LGTM! Appropriate flag addition.The addition of the
-Fflag ensures consistent behavior with force overwrite.
1984-1989: LGTM! Good test coverage for gzip output functionality.The new test function properly verifies the gzip output capability for bedtools intersect.
Let's verify that the test covers all key aspects of the gzip functionality:
✅ Verification successful
🏁 Script executed:
#!/bin/bash # Description: Check if the test covers all necessary aspects of gzip output # Check if the corresponding wrapper handles gzip detection and compression ast-grep --pattern $'if output.endswith(".gz"): $$$ "| gzip" $$$'Length of output: 72
I'll run an additional script to inspect the new test function in "test_wrappers.py" and check for any gzip handling logic in the "bio/bedtools/intersect" wrapper. This should help us verify that the test indeed exercises the gzip-related functionality.
🏁 Script executed:
#!/bin/bash echo "Examining the new test function in test_wrappers.py (lines 1980-1995):" sed -n '1980,1995p' test_wrappers.py echo "" echo "Searching for gzip-related logic in the bedtools intersect wrapper (bio/bedtools/intersect):" rg "\.gz" bio/bedtools/intersect -nLength of output: 986
LGTM: The new test function properly exercises the gzip-specific functionality.
• The new test calls the wrapper with an output filename ending in ".bed.gz", and the wrapper confirms gzip handling by checking for ".gz" in the output.
• The additional "-F" flag in other tests remains consistent with expected behavior.
Enable gzip output for bedtools intersect. Other bedtools to follow.
QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefileinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points tometa.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
New Features
Tests