feat: add pytrf sub-commands as individual Snakemake-Wrappers

bio/pytrf/extract/environment.linux-64.pin.txt

@@ -0,0 +1,38 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+# created-by: conda 25.11.0
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.1.4-hbd8a1cb_0.conda#bddacf101bb4dd0e51811cb69c7790e2
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_16.conda#26c46f90d0e727e95c6c9498a33a09f3
+https://conda.anaconda.org/conda-forge/noarch/python_abi-3.12-8_cp312.conda#c3efd25ac4d74b1584d2f7a57195ddf1
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_16.conda#6d0363467e6ed84f11435eb309f2ff06
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.3-hecca717_0.conda#8b09ae86839581147ef2e5c5e229d164
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda#35f29eec58405aaf55e01cb470d8c26a
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_16.conda#5a68259fac2da8f2ee6f7bfe49c9eb8b
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda#c7c83eecbb72d88b940c249af56c8b17
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_16.conda#68f68355000ec3f1d6f26ea13e8f525f
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda#db409b7c1720428638e7c0d509d3e1b5
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda#9ee58d5c534af06558933af3c845a780
+https://conda.anaconda.org/conda-forge/linux-64/icu-78.2-h33c6efd_0.conda#186a18e3ba246eccfc7cff00cd19a870
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda#86bc20552bf46075e3d92b67f089172d
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45-default_hbd61a6d_105.conda#3ec0aa5037d39b06554109a01e6fb0c6
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.2-hf4e2dac_0.conda#da5be73701eecd0e8454423fd6ffcf30
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.12-hd63d673_1_cpython.conda#5c00c8cea14ee8d02941cab9121dce41
+https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda#b76541e68fea4d511b1ac46a28dcd2c6
+https://conda.anaconda.org/bioconda/linux-64/pyfastx-2.3.0-py312h4711d71_1.conda#9f9e697e132b8567f25c80673da5d4e8
+https://conda.anaconda.org/conda-forge/noarch/setuptools-80.10.1-pyh332efcf_0.conda#cb72cedd94dd923c6a9405a3d3b1c018
+https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.8.0-pyhdfd78af_0.conda#1650e521333852f45468d97b1b2fdcce
+https://conda.anaconda.org/bioconda/linux-64/pytrf-1.4.2-py312h0fa9677_1.conda#a0c079e205c567635a2b5f22054ffc62
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda#bdbd7385b4a67025ac2dba4ef8cb6a8f
+https://conda.anaconda.org/conda-forge/noarch/pip-25.3-pyh8b19718_0.conda#c55515ca43c6444d2572e0f0d93cb6b9

bio/pytrf/extract/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - pytrf =1.4
+  - snakemake-wrapper-utils =0.8.0

bio/pytrf/extract/meta.yaml

@@ -0,0 +1,25 @@
+name: pytrf extract (NOT WORKING, see notes)
+description: >
+  Extract tandem repeat sequences with flanking regions from DNA sequences.
+  Requires output from pytrf findstr, findgtr, or findatr as input.
+url: https://pytrf.readthedocs.io/en/latest/usage.html#commandline-interface
+authors:
+  - Muhammad Rohan Ali Asmat
+input:
+  - ref: FASTA or FASTQ file (supports gzip compression)
+  - repeat: TSV or CSV file from pytrf findstr/findgtr/findatr
+output:
+  - Output file (required). Format auto-detected from file extension.
+params:
+  extra: >
+      Additional command-line arguments passed to pytrf extract.
+      See url for options.
+notes: >
+  **Bioconda package:** https://bioconda.github.io/recipes/pytrf/README.html |nl|
+  **GitHub repository:** https://github.com/lmdu/pytrf |nl|
+  **License:** MIT License |nl|
+  **Disclaimer:** This is a minimal implementation supporting basic functionality.
+  pytrf is not a Python binding to TRF - it's an independent tool. |nl|
+  **Known issue:** PyTRF 1.4.2 has a bug in the `extract` command (delimiter error). |nl|
+  See: https://github.com/lmdu/pytrf/issues/6 |nl|
+  This wrapper skips extract tests until upstream patch is released.

bio/pytrf/extract/test/Snakefile

@@ -0,0 +1,13 @@
+# SAMPLE RULE: Custom parameters via extra
+rule pytrf_extract:
+    input:
+        ref="demo_data/{sample}.fasta",  # reference fasta
+        repeat="demo_data/{sample}.tsv",  # repeat file from findstr/findgtr/findatr
+    output:
+        "results/{sample}_extract.tsv",
+    params:
+        extra="-l 150",  # flank-length=150
+    log:
+        "logs/{sample}.log",
+    wrapper:
+        "master/bio/pytrf/extract"

bio/pytrf/extract/test/demo_data/small_test.fasta

@@ -0,0 +1,6 @@
+>seq1
+TCATCGGTCATCGGTCATCGGTCATCGGTCATCGG
+>seq2
+ACCCCTCAGGGTACCCCTCAGGGTACCCCTCAGGGTACCCCTCAGGGTACCCCTCAGGGTACCCCTCAGGGTACCCCTCAGGGT
+>seq3
+TGACTATATCCGCAAATGAAGGCTGTTCTCTGACATGACTATATCCGCAAATGAAGGCTGTTCTCTGACATGACTATATCCGCAAATGAAGGCTGTTCTCTGACATGACTATATCCGCAAATGAAGGCTGTTCTCTGACA

bio/pytrf/extract/test/demo_data/small_test.tsv

@@ -0,0 +1,85 @@
+seq1	1	3	TCA	3	1	3
+seq1	4	6	TCG	3	1	3
+seq1	7	9	GTC	3	1	3
+seq1	10	12	ATC	3	1	3
+seq1	13	15	GGT	3	1	3
+seq1	16	18	CAT	3	1	3
+seq1	19	21	CGG	3	1	3
+seq1	22	24	TCA	3	1	3
+seq1	25	27	TCG	3	1	3
+seq1	28	30	GTC	3	1	3
+seq1	31	33	ATC	3	1	3
+seq1	34	36	GG	3	1	3
+seq2	1	3	ACC	3	1	3
+seq2	4	6	CCT	3	1	3
+seq2	7	9	CAG	3	1	3
+seq2	10	12	GGT	3	1	3
+seq2	13	15	ACC	3	1	3
+seq2	16	18	CCT	3	1	3
+seq2	19	21	CAG	3	1	3
+seq2	22	24	GGT	3	1	3
+seq2	25	27	ACC	3	1	3
+seq2	28	30	CCT	3	1	3
+seq2	31	33	CAG	3	1	3
+seq2	34	36	GGT	3	1	3
+seq2	37	39	ACC	3	1	3
+seq2	40	42	CCT	3	1	3
+seq2	43	45	CAG	3	1	3
+seq2	46	48	GGT	3	1	3
+seq2	49	51	ACC	3	1	3
+seq2	52	54	CCT	3	1	3
+seq2	55	57	CAG	3	1	3
+seq2	58	60	GGT	3	1	3
+seq2	61	63	ACC	3	1	3
+seq2	64	66	CCT	3	1	3
+seq2	67	69	CAG	3	1	3
+seq2	70	72	GGT	3	1	3
+seq2	73	75	ACC	3	1	3
+seq2	76	78	CCT	3	1	3
+seq2	79	81	CAG	3	1	3
+seq2	82	84	GGT	3	1	3
+seq3	1	3	TGA	3	1	3
+seq3	4	6	CTA	3	1	3
+seq3	7	9	TAT	3	1	3
+seq3	10	12	CCG	3	1	3
+seq3	13	15	CAA	3	1	3
+seq3	16	18	ATG	3	1	3
+seq3	19	21	AAG	3	1	3
+seq3	22	24	GCT	3	1	3
+seq3	25	27	GTT	3	1	3
+seq3	28	31	CT	2	2	4
+seq3	32	34	GAC	3	1	3
+seq3	35	37	ATG	3	1	3
+seq3	38	40	ACT	3	1	3
+seq3	41	44	AT	2	2	4
+seq3	45	47	CCG	3	1	3
+seq3	48	50	CAA	3	1	3
+seq3	51	53	ATG	3	1	3
+seq3	54	56	AAG	3	1	3
+seq3	57	59	GCT	3	1	3
+seq3	60	62	GTT	3	1	3
+seq3	63	66	CT	2	2	4
+seq3	67	69	GAC	3	1	3
+seq3	70	72	ATG	3	1	3
+seq3	73	75	ACT	3	1	3
+seq3	76	79	AT	2	2	4
+seq3	80	82	CCG	3	1	3
+seq3	83	85	CAA	3	1	3
+seq3	86	88	ATG	3	1	3
+seq3	89	91	AAG	3	1	3
+seq3	92	94	GCT	3	1	3
+seq3	95	97	GTT	3	1	3
+seq3	98	101	CT	2	2	4
+seq3	102	104	GAC	3	1	3
+seq3	105	107	ATG	3	1	3
+seq3	108	110	ACT	3	1	3
+seq3	111	114	AT	2	2	4
+seq3	115	117	CCG	3	1	3
+seq3	118	120	CAA	3	1	3
+seq3	121	123	ATG	3	1	3
+seq3	124	126	AAG	3	1	3
+seq3	127	129	GCT	3	1	3
+seq3	130	132	GTT	3	1	3
+seq3	133	136	CT	2	2	4
+seq3	137	139	GAC	3	1	3
+seq3	140	142	A	3	1	3

bio/pytrf/extract/wrapper.py

@@ -0,0 +1,66 @@
+"""
+Snakemake Wrapper for PyTRF extract
+------------------------------------------------------
+Extract tandem repeat sequences with flanking regions.
+"""
+
+from pathlib import Path
+from snakemake.shell import shell
+from snakemake_wrapper_utils.snakemake import get_format, is_arg
+
+
+# Logging
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+# Get input file
+try:
+    input_file = Path(snakemake.input.ref).resolve()
+    repeat_file = Path(snakemake.input.repeat).resolve()
+except (AttributeError, TypeError) as e:
+    raise ValueError(
+        f"Input specification error: {e}. "
+        "Expected named inputs: ref=<fasta/fastq>, repeat=<tsv/csv>"
+    ) from e
+
+# Get output file and determine format
+try:
+    output_file = Path(snakemake.output[0]).resolve()
+except (IndexError, TypeError) as e:
+    raise ValueError("Output file is required") from e
+
+out_format = get_format(output_file)
+
+supported_formats = {"tsv", "csv", "fasta"}
+
+if out_format not in supported_formats:
+    raise ValueError(
+        f"Unsupported format '{out_format}' for pytrf extract. "
+        f"Supported formats: {', '.join(supported_formats)}"
+    )
+
+# Additional parameters
+extra = snakemake.params.get("extra", "")
+
+if is_arg("-f", extra) or is_arg("--out-format", extra):
+    raise ValueError(
+        "Output format is automatically inferred from output file extension. "
+        "Do not specify -f/--out-format in params.extra. "
+    )
+
+if is_arg("-r", extra) or is_arg("--repeat-file", extra):
+    raise ValueError(
+        "Repeat file should be specified as an input. "
+        "Do not specify -r/--repeat-file in params.extra"
+    )
+
+# Build command
+CMD = f"pytrf extract {input_file} -r {repeat_file} -f {out_format}"
+if extra:
+    CMD += f" {extra}"
+CMD += f" -o {output_file}"
+
+# Execute
+try:
+    shell(f"{CMD} {log}")
+except Exception as e:
+    raise RuntimeError(f"PyTRF extract execution failed: {e}") from e

bio/pytrf/findatr/environment.linux-64.pin.txt

@@ -0,0 +1,38 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+# created-by: conda 25.11.0
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.1.4-hbd8a1cb_0.conda#bddacf101bb4dd0e51811cb69c7790e2
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_16.conda#26c46f90d0e727e95c6c9498a33a09f3
+https://conda.anaconda.org/conda-forge/noarch/python_abi-3.12-8_cp312.conda#c3efd25ac4d74b1584d2f7a57195ddf1
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_16.conda#6d0363467e6ed84f11435eb309f2ff06
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.3-hecca717_0.conda#8b09ae86839581147ef2e5c5e229d164
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda#35f29eec58405aaf55e01cb470d8c26a
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_16.conda#5a68259fac2da8f2ee6f7bfe49c9eb8b
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda#c7c83eecbb72d88b940c249af56c8b17
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_16.conda#68f68355000ec3f1d6f26ea13e8f525f
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda#db409b7c1720428638e7c0d509d3e1b5
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda#9ee58d5c534af06558933af3c845a780
+https://conda.anaconda.org/conda-forge/linux-64/icu-78.2-h33c6efd_0.conda#186a18e3ba246eccfc7cff00cd19a870
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda#86bc20552bf46075e3d92b67f089172d
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45-default_hbd61a6d_105.conda#3ec0aa5037d39b06554109a01e6fb0c6
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.2-hf4e2dac_0.conda#da5be73701eecd0e8454423fd6ffcf30
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.12-hd63d673_1_cpython.conda#5c00c8cea14ee8d02941cab9121dce41
+https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda#b76541e68fea4d511b1ac46a28dcd2c6
+https://conda.anaconda.org/bioconda/linux-64/pyfastx-2.3.0-py312h4711d71_1.conda#9f9e697e132b8567f25c80673da5d4e8
+https://conda.anaconda.org/conda-forge/noarch/setuptools-80.10.1-pyh332efcf_0.conda#cb72cedd94dd923c6a9405a3d3b1c018
+https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.8.0-pyhdfd78af_0.conda#1650e521333852f45468d97b1b2fdcce
+https://conda.anaconda.org/bioconda/linux-64/pytrf-1.4.2-py312h0fa9677_1.conda#a0c079e205c567635a2b5f22054ffc62
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda#bdbd7385b4a67025ac2dba4ef8cb6a8f
+https://conda.anaconda.org/conda-forge/noarch/pip-25.3-pyh8b19718_0.conda#c55515ca43c6444d2572e0f0d93cb6b9

bio/pytrf/findatr/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - pytrf =1.4
+  - snakemake-wrapper-utils =0.8.0

bio/pytrf/findatr/meta.yaml

@@ -0,0 +1,21 @@
+name: pytrf findatr
+description: >
+  Find approximate/imperfect tandem repeats from DNA sequences.
+url: https://pytrf.readthedocs.io/en/latest/usage.html#commandline-interface
+authors:
+  - Muhammad Rohan Ali Asmat
+input:
+  - FASTA or FASTQ file (supports gzip compression)
+output:
+  - Output file (required). Format auto-detected from file extension.
+params:
+  extra: >
+    Additional command-line arguments passed to pytrf findatr.
+    See url for options.
+notes: >
+  **Bioconda package:** https://bioconda.github.io/recipes/pytrf/README.html |nl|
+  **GitHub repository:** https://github.com/lmdu/pytrf |nl|
+  **License:** MIT License |nl|
+  **Disclaimer:** This is a minimal implementation supporting basic functionality.
+  pytrf is not a Python binding to TRF - it's an independent tool.
+

bio/pytrf/findatr/test/Snakefile

@@ -0,0 +1,12 @@
+# SAMPLE RULE: Custom parameters via extra
+rule pytrf_findatr:
+    input:
+        "demo_data/{sample}.fasta",
+    output:
+        "results/{sample}.tsv",
+    log:
+        "logs/{sample}.log",
+    params:
+        extra="-m 3 -M 10",  # min-motif-size=3, max-motif-size=10
+    wrapper:
+        "master/bio/pytrf/findatr"

bio/pytrf/findatr/test/demo_data/small_test.fasta

@@ -0,0 +1,2 @@
+>seq1
+TCATCGGTCATCGGTCATCGGTCATCGGTCATCGG

bio/pytrf/findatr/test/expected/findatr_basic.tsv

@@ -0,0 +1 @@
+seq1	1	35	TCATCGG	7	5.0	35	1	35	5	35	35	0	0	0	100.0

bio/pytrf/findatr/wrapper.py

@@ -0,0 +1,55 @@
+"""
+Snakemake Wrapper for PyTRF findatr
+------------------------------------------------------
+Find approximate/imperfect tandem repeats.
+"""
+
+from pathlib import Path
+from snakemake.shell import shell
+from snakemake_wrapper_utils.snakemake import get_format, is_arg
+
+
+# Logging
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+# Get input file
+try:
+    input_file = Path(snakemake.input[0]).resolve()
+except (IndexError, TypeError) as e:
+    raise ValueError(f"Input specification error: {e}") from e
+
+# Get output file and determine format
+try:
+    output_file = Path(snakemake.output[0]).resolve()
+except (IndexError, TypeError) as e:
+    raise ValueError("Output file is required") from e
+
+out_format = get_format(output_file)
+
+supported_formats = {"tsv", "csv", "gff"}
+
+if out_format not in supported_formats:
+    raise ValueError(
+        f"Unsupported format '{out_format}' for pytrf findatr. "
+        f"Supported formats: {', '.join(supported_formats)}"
+    )
+
+# Additional parameters
+extra = snakemake.params.get("extra", "")
+
+if is_arg("-f", extra) or is_arg("--out-format", extra):
+    raise ValueError(
+        "Output format is automatically inferred from output file extension. "
+        "Do not specify -f/--out-format in params.extra. "
+    )
+
+CMD = f"pytrf findatr {input_file} -f {out_format}"
+if extra:
+    CMD += f" {extra}"
+CMD += f" -o {output_file}"
+
+# Execute
+try:
+    shell(f"{CMD} {log}")
+except Exception as e:
+    raise RuntimeError(f"PyTRF findatr execution failed: {e}") from e