[fix] fname list name

workflow/scripts/haplotypes.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+import glob
+import subprocess
+
+def unzip(fname):
+    subprocess.run(
+            [
+                "gunzip",
+                str(fname),
+            ],
+        )
+
+
+def main(dname_haplotypes, sample_name, fname_out_haplos):
+
+    for fname in glob.glob(f"{dname_haplotypes}*.reads-support.fas.gz"):
+        unzip(fname)
+
+    all_haplotype_files = [file for file in glob.glob(f"{dname_haplotypes}*.reads-support.fas")]
+
+    # define output file
+    with open(fname_out_haplos, 'w') as out_f:
+        my_seqs = []
+
+        # iterate over all haplotype files
+        for fname_haplotype_region in all_haplotype_files:
+            region = fname_haplotype_region.split(".reads-support.fas")[0].split("w-")[1]
+            for record in SeqIO.parse(fname_haplotype_region, 'fasta'):
+                    new_id = sample_name+'-'+region + '-' +str(record.id)
+                    my_seqs.append(SeqRecord(Seq(record.seq), id = new_id))
+
+        # write all sequences to file
+        SeqIO.write(my_seqs, out_f, "fasta")
+
+
+
+if __name__ == "__main__":
+    main(
+        snakemake.input.dname_haplotypes,
+        snakemake.params.sample,
+        snakemake.output.fname_haplotypes,
+    )