rename assembly 1

workflow/rules/assemble.smk

@@ -473,22 +473,22 @@ rule rename_contigs:
     input:
         "{sample}/assembly/{sample}_raw_contigs.fasta",
     output:
-        "{sample}/assembly/{sample}_prefilter_contigs.fasta",
-    conda:
-        "%s/required_packages.yaml" % CONDAENV
+        fasta="{sample}/assembly/{sample}_prefilter_contigs.fasta",
+        mapping_table = "{sample}/assembly/old2new_contig_names.tsv"
     threads: config.get("simplejob_threads", 1)
     resources:
         mem=config["simplejob_mem"],
-        time=config["runtime"]["simplejob"],
+        time=config["runtime"]["default"],
     log:
         "{sample}/logs/assembly/post_process/rename_and_filter_size.log",
     params:
         minlength=config["minimum_contig_length"],
-    shell:
-        "rename.sh "
-        " in={input} out={output} ow=t "
-        " prefix={wildcards.sample} "
-        " minscaf={params.minlength} &> {log} "
+    conda:
+        "../envs/fasta.yaml"
+    script:
+        "../scripts/rename_assembly.py"
+
+
 
 
 if config["filter_contigs"]:
@@ -581,7 +581,7 @@ else:  # no filter
 
     rule do_not_filter_contigs:
         input:
-            rules.rename_contigs.output,
+            "{sample}/assembly/{sample}_prefilter_contigs.fasta",
         output:
             "{sample}/assembly/{sample}_final_contigs.fasta",
         threads: 1

workflow/scripts/parse_semibin.py

@@ -57,4 +57,4 @@ def handle_exception(exc_type, exc_value, exc_traceback):
     )
 
     with open(snakemake.output[0], "w") as outf:
-        outf.write("{sample}_0\t{sample}_SemiBin_1\n".format(**snakemake.wildcards))
+        outf.write("{sample}_1\t{sample}_SemiBin_1\n".format(**snakemake.wildcards))

workflow/scripts/parse_vamb.py

@@ -144,4 +144,4 @@ def handle_exception(exc_type, exc_value, exc_traceback):
     for sample in samples_without_bins:
         sample_output_path = cluster_output_path.format(sample=sample)
         with open(sample_output_path, "w") as fout:
-            fout.write(f"{sample}_0\t{sample}_vamb_1\n")
+            fout.write(f"{sample}_1\t{sample}_vamb_1\n")

workflow/scripts/rename_assembly.py

@@ -0,0 +1,55 @@
+#! /usr/bin/env python
+
+
+import sys, os
+import logging, traceback
+
+logging.basicConfig(
+    filename=snakemake.log[0],
+    level=logging.INFO,
+    format="%(asctime)s %(message)s",
+    datefmt="%Y-%m-%d %H:%M:%S",
+)
+
+
+def handle_exception(exc_type, exc_value, exc_traceback):
+    if issubclass(exc_type, KeyboardInterrupt):
+        sys.__excepthook__(exc_type, exc_value, exc_traceback)
+        return
+
+    logging.error(
+        "".join(
+            [
+                "Uncaught exception: ",
+                *traceback.format_exception(exc_type, exc_value, exc_traceback),
+            ]
+        )
+    )
+
+
+# Install exception handler
+sys.excepthook = handle_exception
+
+
+from Bio import SeqIO
+
+# Open the snakemake.output FASTA file and mapping table file for writing
+with open(snakemake.output.fasta, "w") as output_handle, open(
+    snakemake.output.mapping_table, "w"
+) as mapping_table_handle:
+    i = 1
+
+    for record in SeqIO.parse(snakemake.input[0], "fasta"):
+        if len(record) < snakemake.params.minlength:
+            break
+
+        old_name = record.id
+        new_name = f"{snakemake.wildcards.sample}_{i}"
+        record.id = new_name
+        record.description = ""
+
+        SeqIO.write(record, output_handle, "fasta")
+
+        mapping_table_handle.write(f"{new_name}\t{old_name}\n")
+
+        i += 1