added deprecated warning for mode

kcleal · Oct 24, 2024 · 7d06045 · 7d06045
1 parent 2691164
commit 7d06045
Showing 1 changed file with 10 additions and 2 deletions.
diff --git a/dysgu/main.py b/dysgu/main.py
@@ -118,6 +118,13 @@ def show_params():
 
 
 def apply_preset(kwargs):
+    if kwargs["mode"] == "pacbio": 
+        logging.warning("Using --mode pacbio is deprecated. Use 'pacbio-sequel2' or 'pacbio-revio' instead. Mode will be set as 'pacbio-revio'")
+        kwargs["mode"] = "pacbio-revio"
+    elif kwargs == ["nanopore"]:
+        logging.warning("Using --mode nanopore is deprecated. Use 'nanopore-r9' or 'nanopore-r10' instead. Mode will be set as 'nanopore-r10'")
+        kwargs["mode"] = "nanopore-r10"
+
     if kwargs["mode"] != "pe":
         kwargs["paired"] = "False"
     p = presets[kwargs["mode"]]
@@ -206,7 +213,7 @@ def cli():
                              f"pacbio-revio: --mq {presets['pacbio-revio']['mq']} --paired False --min-support '{presets['pacbio-revio']['min_support']}' --max-cov {presets['pacbio-revio']['max_cov']} --dist-norm {presets['pacbio-revio']['dist_norm']} --trust-ins-len True --thresholds {presets['pacbio-revio']['thresholds']} --symbolic-sv-size {presets['pacbio-revio']['symbolic_sv_size']} --sd {presets['pacbio-revio']['sd']}."
                              f"nanopore-r9: --mq {presets['nanopore-r9']['mq']} --paired False --min-support '{presets['nanopore-r9']['min_support']}' --max-cov {presets['nanopore-r9']['max_cov']} --dist-norm {presets['nanopore-r9']['dist_norm']} --trust-ins-len False --symbolic-sv-size {presets['nanopore-r9']['symbolic_sv_size']} --sd {presets['nanopore-r9']['sd']} --divergence {presets['nanopore-r9']['divergence']}."
                              f"nanopore-r10: --mq {presets['nanopore-r10']['mq']} --paired False --min-support '{presets['nanopore-r10']['min_support']}' --max-cov {presets['nanopore-r10']['max_cov']} --dist-norm {presets['nanopore-r10']['dist_norm']} --trust-ins-len False --thresholds {presets['nanopore-r10']['thresholds']} --symbolic-sv-size {presets['nanopore-r10']['symbolic_sv_size']} --sd {presets['nanopore-r10']['sd']}",
-              default="pe", type=click.Choice(["pe", "pacbio-sequel2", "pacbio-revio", "nanopore-r9", "nanopore-r10"]), show_default=True)
+              default="pe", type=click.Choice(["pe", "pacbio-sequel2", "pacbio-revio", "nanopore-r9", "nanopore-r10", "pacbio", "nanopore"]), show_default=True)
 @click.option('--pl', help=f"Type of input reads  [default: {defaults['pl']}]",
               type=click.Choice(["pe", "pacbio", "nanopore"]), callback=add_option_set)
 @click.option('--clip-length', help="Minimum soft-clip length, >= threshold are kept. Set to -1 to ignore [default: {deafults['clip_length']}]", type=int, callback=add_option_set)
@@ -267,6 +274,7 @@ def run_pipeline(ctx, **kwargs):
     # Add arguments to context
     t0 = time.time()
     logging.info("[dysgu-run] Version: {}".format(dysgu_version))
+
     make_wd(kwargs)
     apply_preset(kwargs)
     show_params()
@@ -364,7 +372,7 @@ def get_reads(ctx, **kwargs):
                              f"pacbio-revio: --mq {presets['pacbio-revio']['mq']} --paired False --min-support '{presets['pacbio-revio']['min_support']}' --max-cov {presets['pacbio-revio']['max_cov']} --dist-norm {presets['pacbio-revio']['dist_norm']} --trust-ins-len True --thresholds {presets['pacbio-revio']['thresholds']} --symbolic-sv-size {presets['pacbio-revio']['symbolic_sv_size']} --sd {presets['pacbio-revio']['sd']}."
                              f"nanopore-r9: --mq {presets['nanopore-r9']['mq']} --paired False --min-support '{presets['nanopore-r9']['min_support']}' --max-cov {presets['nanopore-r9']['max_cov']} --dist-norm {presets['nanopore-r9']['dist_norm']} --trust-ins-len False --symbolic-sv-size {presets['nanopore-r9']['symbolic_sv_size']} --sd {presets['nanopore-r9']['sd']} --divergence {presets['nanopore-r9']['divergence']}."
                              f"nanopore-r10: --mq {presets['nanopore-r10']['mq']} --paired False --min-support '{presets['nanopore-r10']['min_support']}' --max-cov {presets['nanopore-r10']['max_cov']} --dist-norm {presets['nanopore-r10']['dist_norm']} --trust-ins-len False --thresholds {presets['nanopore-r10']['thresholds']} --symbolic-sv-size {presets['nanopore-r10']['symbolic_sv_size']} --sd {presets['nanopore-r10']['sd']}",
-              default="pe", type=click.Choice(["pe", "pacbio-sequel2", "pacbio-revio", "nanopore-r9", "nanopore-r10"]), show_default=True)
+              default="pe", type=click.Choice(["pe", "pacbio-sequel2", "pacbio-revio", "nanopore-r9", "nanopore-r10", "pacbio", "nanopore"]), show_default=True)
 @click.option('--pl', help=f"Type of input reads  [default: {defaults['pl']}]",
               type=click.Choice(["pe", "pacbio", "nanopore"]), callback=add_option_set)
 @click.option('--clip-length', help="Minimum soft-clip length, >= threshold are kept. Set to -1 to ignore [default: {deafults['clip_length']}]", type=int, callback=add_option_set)