feat: amplicon simulation on input fasta

mess/__main__.py

@@ -64,7 +64,7 @@
         ],
     },
     {
-        "name": "Amplicons options",
+        "name": "Amplicon extraction options",
         "options": [
             "--fw",
             "--rv",
@@ -73,17 +73,18 @@
             "--amp-minlen",
             "--amp-maxlen",
             "--cut",
-            "--orient",
+            "--keep-orient",
+            "--amp",
         ],
     },
     {
         "name": "art_illumina options",
         "options": [
             "--custom-err",
-            "--errfree",
             "--paired",
             "--frag-len",
             "--frag-sd",
+            "--errfree",
         ],
     },
     {

mess/util.py

@@ -295,13 +295,18 @@ def sim_options(func):
             show_default=True,
         ),
         click.option(
-            "--orient",
-            help="Orient reverse amplicon strands in the forward orientation",
+            "--keep-orient",
+            help="Keep original sequence orientation (default: reverse complement if forward primer is on reverse strand)",
             type=bool,
-            default=True,
+            default=False,
             is_flag=True,
             show_default=True,
         ),
+        click.option(
+            "--amp",
+            help="Fasta files are amplicons (skips primersearch)",
+            is_flag=True,
+        ),
         click.option(
             "--tech",
             help="Sequencing technology",
@@ -354,7 +359,7 @@ def sim_options(func):
         click.option(
             "--rep-sd",
             help="Standard deviation between replicate coverages (0: no deviation)",
-            type=int,
+            type=float,
             default=0,
             show_default=True,
         ),

mess/workflow/rules/preflight/functions.smk

@@ -130,7 +130,7 @@ def fasta_input(wildcards):
 
 def list_fastas(wildcards):
     df = get_fasta_table(wildcards)
-    if AMPLICONS:
+    if PRIMERSEARCH:
         return expand(
             os.path.join(dir.out.processing, "{fasta}.amplicons.fasta"),
             fasta=list(set(df.index)),
@@ -183,7 +183,7 @@ def get_value(value, wildcards):
 
 
 def get_asm_summary(wildcards):
-    if AMPLICONS or FASTA_DIR or FASTA_PATH:
+    if PRIMERSEARCH or FASTA_DIR or FASTA_PATH:
         return os.path.join(dir.out.processing, "seqkit_stats.tsv")
     else:
         try:

mess/workflow/rules/processing/coverages.smk

@@ -31,7 +31,7 @@ checkpoint calculate_genome_coverages:
         read_len=MEAN_LEN,
         pairing=PAIRED,
         seed=SEED,
-        amplicons=AMPLICONS,
+        amplicons=PRIMERSEARCH,
     resources:
         mem_mb=config.resources.sml.mem,
         mem=str(config.resources.sml.mem) + "MB",

mess/workflow/rules/processing/fastas.smk

@@ -20,7 +20,7 @@ rule rename_fastas:
         """
 
 
-if AMPLICONS:
+if PRIMERSEARCH:
 
     if PRIMERS:
         primers = os.path.abspath(PRIMERS)
@@ -58,8 +58,8 @@ if AMPLICONS:
     amp_args = ""
     if CUT:
         amp_args += "--cut "
-    if ORIENT:
-        amp_args += "--orient "
+    if KEEP_ORIENT:
+        amp_args += "--keep-orient "
 
     rule get_amplicons:
         input:
@@ -77,12 +77,12 @@ if AMPLICONS:
             os.path.join(dir.out.logs, "primersearch", "{fasta}_summary.log"),
         shell:
             """
-            python {params.script} \\
-            --input {input.search} \\
-            --fasta {input.fasta} \\
-            --primers {input.primers} \\
-            --minlen {params.minlen} \\
-            --maxlen {params.maxlen} \\
+            {params.script} \\
+            -i {input.search} \\
+            -f {input.fasta} \\
+            -p {input.primers} \\
+            -m {params.minlen} \\
+            -M {params.maxlen} \\
             {params.args} \\
             --output {output} \\
             --log 2> {log}
@@ -96,7 +96,7 @@ rule get_fasta_stats:
         os.path.join(dir.out.processing, "seqkit_stats.tsv"),
     params:
         os.path.join(dir.out.processing, "*.fasta")
-        if not AMPLICONS
+        if not PRIMERSEARCH
         else os.path.join(dir.out.processing, "*.amplicons.fasta"),
     log:
         os.path.join(dir.out.logs, "seqkit", "stats.log"),
@@ -129,7 +129,7 @@ checkpoint split_contigs:
     params:
         circular=CIRCULAR,
         rotate=ROTATE,
-        amplicons=AMPLICONS,
+        amplicons=PRIMERSEARCH,
         read_len=MEAN_LEN,
     resources:
         mem_mb=config.resources.sml.mem,

mess/workflow/scripts/get_amplicons.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import argparse
 import sys
 from Bio.Emboss import PrimerSearch
@@ -43,13 +45,13 @@ def parse_args():
         "-c",
         "--cut",
         action="store_true",
-        help="Cut primers from amplicons sequences",
+        help="Cut primers from amplicon sequences (default: False)",
     )
     parser.add_argument(
-        "-r",
-        "--orient",
+        "-k",
+        "--keep-orient",
         action="store_true",
-        help="Orient reverse sequences to forward",
+        help="Kepp original sequence orientation (default: reverse complement if forward primer is on reverse strand)",
     )
     parser.add_argument(
         "-m",
@@ -80,7 +82,7 @@ def parse_args():
         action="store_true",
         help="Print summary table to stderr",
     )
-    parser.set_defaults(orient=False, cut=False, log=False)
+    parser.set_defaults(keep_orient=False, cut=False, log=False)
     return parser.parse_args()
 
 
@@ -140,6 +142,11 @@ def parse_primersearch(results, seq2strand, minlen, maxlen):
                 continue
             info = hit.hit_info.split("\n\t")
             mismatches = 0
+            fw_primer = None
+            rv_primer = None
+            start = None
+            end = None
+            forward_on_reverse = None
             for match in info[1:]:
                 mismatches += int(match.split("with ")[1].split(" ")[0])
                 if "forward" in match:
@@ -178,15 +185,19 @@ def parse_primersearch(results, seq2strand, minlen, maxlen):
         return pd.DataFrame.from_records(d)
 
 
-def get_amplicon_record(row, seqid2record, cut, orient):
-    amp_id = f"{row.seq_id}_{row.amplimer}_{row.primer}"
-    amp_seq = seqid2record[row.seq_id].seq[row.start_forward - 1 : -row.end_reverse + 1]
+def get_amplicon_record(row, seqid2record, cut, keep_orient):
+    amp_id = f"{row['seq_id']}_{row['amplimer']}_{row['primer']}"
+    amp_seq = seqid2record[row["seq_id"]].seq[
+        row["start_forward"] - 1 : -row["end_reverse"] + 1
+    ]
 
     if cut:
-        amp_seq = amp_seq[len(row.fw_primer) : len(amp_seq) - len(row.rv_primer)]
+        amp_seq = amp_seq[len(row["fw_primer"]) : len(amp_seq) - len(row["rv_primer"])]
+
+    if row["forward_match_on_reverse"]:
+        if not keep_orient:
+            amp_seq = amp_seq.reverse_complement()
 
-    if orient and row.forward_match_on_reverse:
-        amp_seq = amp_seq.reverse_complement()
     return SeqRecord(amp_seq, id=amp_id, description=amp_id)
 
 
@@ -220,20 +231,20 @@ def main():
         )
     )
     df = parse_primersearch(results, seq2strand, args.minlen, args.maxlen)
-    if df.empty:
+    if df is None or df.empty:
         amplicons = SeqRecord(Seq(""), id="no_amps", description="no_amps")
     else:
-        amplicons = df.apply(
-            lambda row: get_amplicon_record(row, seqid2record, args.cut, args.orient),
-            axis=1,
-        ).tolist()
+        amplicons = [
+            get_amplicon_record(row, seqid2record, args.cut, args.keep_orient)
+            for _, row in df.iterrows()
+        ]
     SeqIO.write(
         amplicons,
         args.output,
         "fasta",
     )
     if args.log:
-        if df.empty:
+        if df is None or df.empty:
             print(
                 "No amplicons found ! \n"
                 "Try less stringent mismatches, minlen or maxlen parameters",

mess/workflow/simulate.smk

@@ -27,16 +27,17 @@ SEQ_TECH = config.args.tech
 PRIMERS = config.args.primers
 FORWARD_PRIMER = config.args.fw
 REVERSE_PRIMER = config.args.rv
-
-AMPLICONS = False
+AMPLICONS = config.args.amp
+PRIMERSEARCH = False
 if PRIMERS or (FORWARD_PRIMER and REVERSE_PRIMER):
+    PRIMERSEARCH = True
     AMPLICONS = True
 
 AMP_MINLEN = config.args.amp_minlen
 AMP_MAXLEN = config.args.amp_maxlen
 MISMATCH = config.args.mismatch
 CUT = config.args.cut
-ORIENT = config.args.orient
+KEEP_ORIENT = config.args.keep_orient
 
 BASES = config.args.bases
 PAIRED = config.args.paired