feat: add support for multiple input file subcommands in seqkit wrapper (subcommands "common" and "concat")

[dlaehnemann]

QC

• I confirm that I have followed the documentation for contributing to snakemake-wrappers.

While the contributions guidelines are more extensive, please particularly ensure that:

• test.py was updated to call any added or updated example rules in a Snakefile
• input: and output: file paths in the rules can be chosen arbitrarily
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
• the meta.yaml contains a link to the documentation of the respective tool or command under url:
• conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• New Features

  • Introduced two new processing rules for FASTA files: seqkit_common for extracting common sequences and seqkit_concat for concatenating sequences.
  • Added a new FASTA file (b.fa) containing two nucleotide sequences for analysis.

• Tests

  • Added new test functions to validate the functionality of the new seqkit_common and seqkit_concat rules.

These updates enhance the bioinformatics pipeline's capabilities and improve testing coverage.

[coderabbitai]

Walkthrough

The changes introduce two new rules, seqkit_common and seqkit_concat, to the Snakefile, enhancing the processing of FASTA files. A new FASTA file, b.fa, is added, containing multiple sequences for analysis. Modifications in wrapper.py enable the handling of multiple input files for specific commands. Additionally, two new test functions are added to test.py to validate the new functionality of the seqkit tool.

Changes

Files	Change Summary
bio/seqkit/test/Snakefile	Added new rules seqkit_common and seqkit_concat for processing FASTA files.
bio/seqkit/test/data/b.fa	Introduced a new FASTA file b.fa with two sequences: >seq1 and >seq3.
bio/seqkit/wrapper.py	Modified input handling logic to concatenate multiple input files for the commands "concat" and "common".
test.py	Added new test functions test_seqkit_common and test_seqkit_concat to validate new functionality.

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[dlaehnemann]

@fgvieira From what I could see, these two commands were not yet supported, as multiple fasta input files were not yet handled. I think this is the minimal amount of changes to accommodate them, but if you have any better suggestions, they are always welcome.

[coderabbitai]

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between b4267e6 and 79feb85.

Files selected for processing (4)

• bio/seqkit/test/Snakefile (1 hunks)
• bio/seqkit/test/data/b.fa (1 hunks)
• bio/seqkit/wrapper.py (2 hunks)
• test.py (1 hunks)

Files skipped from review due to trivial changes (1)

• bio/seqkit/test/data/b.fa

Additional context used

Path-based instructions (2)

bio/seqkit/wrapper.py (2)

Pattern **/*.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 the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

---

Pattern **/wrapper.py: Do not complain about use of undefined variable called snakemake.

test.py (1)

Pattern **/*.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 the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

Ruff

bio/seqkit/wrapper.py

12-12: Undefined name snakemake

(F821)

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13-13: Undefined name snakemake

(F821)

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15-15: Undefined name snakemake

(F821)

Additional comments not posted (6)

bio/seqkit/wrapper.py (2)

11-15: Approved: Handling of multiple input files.

The logic for handling multiple input files based on the command (concat or common) is correctly implemented. This change allows the script to adapt to different requirements of the seqkit subcommands.

Tools

Ruff

12-12: Undefined name snakemake

(F821)

---

13-13: Undefined name snakemake

(F821)

---

15-15: Undefined name snakemake

(F821)

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47-47: Ensure correct command construction.

The final command string construction uses the dynamically defined input variable. Ensure that this variable is correctly integrated into the command string, especially in the context of different seqkit subcommands.

Verification successful

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Correct Integration of input Variable in Command String

The input variable is correctly integrated into the command string within bio/seqkit/wrapper.py. It is constructed by joining multiple input files or using a single file, and it is appropriately included in the command string. The command construction is consistent with the expected usage for different seqkit subcommands.

• input is defined as " ".join(snakemake.input) or snakemake.input[0].
• The command string includes " {input}".

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the correct integration of the `input` variable in the command string.

# Test: Search for the command string construction. Expect: Correct usage of the `input` variable.
rg --type python -A 5 $'seqkit {snakemake.params.command}'

Length of output: 183

---

Script:

#!/bin/bash
# Description: Verify the correct integration of the `input` variable in the command string.

# Test: Search for the command string construction in the bio/seqkit/wrapper.py file.
rg --type python -A 5 'seqkit \{snakemake.params.command\}' bio/seqkit/wrapper.py

Length of output: 114

---

Script:

#!/bin/bash
# Description: Verify the correct integration of the `input` variable in the command string.

# Test: Search for the command string construction in the bio/seqkit/wrapper.py file.
rg -A 5 'seqkit \{snakemake.params.command\}' bio/seqkit/wrapper.py

Length of output: 244

---

Script:

#!/bin/bash
# Description: Search for the definition and usage of the `input` variable in the bio/seqkit/wrapper.py file.

# Test: Identify how the `input` variable is defined and used.
rg 'input' bio/seqkit/wrapper.py

Length of output: 268

bio/seqkit/test/Snakefile (2)

158-173: Approved: New rule seqkit_common.

The seqkit_common rule is well-defined with clear inputs, outputs, and parameters. This rule enhances the workflow by allowing the extraction of common sequences between two FASTA files.

---

176-191: Approved: New rule seqkit_concat.

The seqkit_concat rule is correctly implemented to handle the concatenation of sequences from two FASTA files. This addition broadens the capabilities of the bioinformatics pipeline.

test.py (2)

432-444: Test function for seqkit common is correctly implemented.

The function test_seqkit_common is well-structured and follows the conventions used throughout the test suite.

The code changes are approved.

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447-459: Test function for seqkit concat is correctly implemented.

The function test_seqkit_concat is consistent with the other test functions and correctly sets up the test environment and parameters for the seqkit concat functionality.

The code changes are approved.