From ad4b4593f115647bb9ae86d2b79dba52135b3b50 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Tue, 9 Jan 2024 10:11:05 +0100
Subject: [PATCH] add method: strainline

---
 .../method_definitions/strainline.py          | 93 +++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 resources/auxiliary_workflows/benchmark/resources/method_definitions/strainline.py

diff --git a/resources/auxiliary_workflows/benchmark/resources/method_definitions/strainline.py b/resources/auxiliary_workflows/benchmark/resources/method_definitions/strainline.py
new file mode 100644
index 00000000..3392e63a
--- /dev/null
+++ b/resources/auxiliary_workflows/benchmark/resources/method_definitions/strainline.py
@@ -0,0 +1,93 @@
+# GROUP: global
+# CONDA: minimap2 = 2.24
+# CONDA: spoa
+# CONDA: samtools
+# CONDA: dazz_db
+# CONDA: daligner
+# CONDA: metabat2
+# CONDA: biopython = 1.79
+
+import subprocess
+from pathlib import Path
+from Bio import SeqIO
+
+
+def fastq_to_fasta(input_file, output_file):
+    """
+    Converts a Fastq file to a Fasta file.
+
+    Args:
+        input_file (str): Path to the input Fastq file.
+        output_file (str): Path to save the output Fasta file.
+    """
+
+    with open(output_file, "w") as f_out:
+        for record in SeqIO.parse(input_file, "fastq"):
+            SeqIO.write(record, f_out, "fasta")
+
+
+
+def main(fname_bam,
+         fname_reference,
+         fname_result,
+         fname_result_haplos,
+         dname_work,
+         seq_type,
+         threads,):
+
+    if seq_type == "illumina":
+        # strainline doesn't work for illumina
+        # create fake files such that snakemake is happy
+
+        # create empty haplotype files
+        open(fname_result_haplos, "a").close()
+
+        # create empty vcf files
+        f = open(fname_results_snv, "a")
+        f.write("#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO")
+        f.close()
+    else:
+        # run strainline
+
+        if seq_type == "pacbio":
+            seq_platform = "pb"
+        elif seq_type == "nanopore":
+            seq_platform = "ont"
+
+        # fastq to fasta
+        fname_reads_fastq = str(fname_bam.resolve()).split("bam")[0]+"fastq"
+        fname_reads_fasta = str(fname_bam.resolve()).split("bam")[0]+"fasta"
+        fastq_to_fasta(fname_reads_fastq, fname_reads_fasta)
+
+        dname_work.mkdir(parents=True, exist_ok=True)
+
+        # execute tool
+        subprocess.run(
+            [
+                "strainline.sh",
+                "-i",
+                fname_reads_fasta,
+                "-o",
+                str(dname_work),
+                "-p",
+                seq_platform,
+                "-threads",
+                str(threads),
+            ],
+            check=True,
+        )
+
+
+
+
+
+if __name__ == "__main__":
+    main(
+        Path(snakemake.input.fname_bam),
+        Path(snakemake.input.fname_reference),
+        Path(snakemake.output.fname_result),
+        Path(snakemake.output.fname_result_haplos),
+        Path(snakemake.output.dname_work),
+        snakemake.wildcards.seq_tech,
+        snakemake.threads,
+    )