From ea0e4d27c77deee335da1f6ac48af73bf26ad1f1 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Fri, 15 Mar 2024 17:06:32 +0000
Subject: [PATCH] Add new meta_min_reads CLI param

---
 ribotricer/cli.py         | 8 ++++++++
 ribotricer/const.py       | 2 ++
 ribotricer/detect_orfs.py | 5 ++++-
 3 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/ribotricer/cli.py b/ribotricer/cli.py
index cc0fc26..2700bf2 100644
--- a/ribotricer/cli.py
+++ b/ribotricer/cli.py
@@ -197,6 +197,13 @@ def prepare_orfs_cmd(
     help=("Whether output all ORFs including those " "non-translating ones"),
     is_flag=True,
 )
+@click.option(
+    "--meta-min-reads",
+    type=int,
+    default=META_MIN_READS,
+    show_default=True,
+    help="Minimum number of reads for a read length to be considered",
+)
 def detect_orfs_cmd(
     bam,
     ribotricer_index,
@@ -210,6 +217,7 @@ def detect_orfs_cmd(
     min_valid_codons_ratio,
     min_read_density,
     report_all,
+    meta_min_reads,
 ):
     if not os.path.isfile(bam):
         sys.exit("Error: BAM file not found")
diff --git a/ribotricer/const.py b/ribotricer/const.py
index 6b3a1f7..5a49f72 100644
--- a/ribotricer/const.py
+++ b/ribotricer/const.py
@@ -29,3 +29,5 @@
 # Minimum read density over ORF
 # defined as the number of reads per unit length of the ORF
 MINIMUM_DENSITY_OVER_ORF = 0.0
+# Minimum number of reads for a read length to be considered
+META_MIN_READS=100000
diff --git a/ribotricer/detect_orfs.py b/ribotricer/detect_orfs.py
index 3af7b0b..d5dd940 100644
--- a/ribotricer/detect_orfs.py
+++ b/ribotricer/detect_orfs.py
@@ -344,6 +344,7 @@ def detect_orfs(
     min_valid_codons_ratio,
     min_density_over_orf,
     report_all,
+    meta_min_reads=100000,
 ):
     """
     Parameters
@@ -371,6 +372,8 @@ def detect_orfs(
     report_all: bool
                 Whether to output all ORFs' scores regardless of translation
                 status
+    meta_min_reads: int
+                    minimum number of reads for a read length to be considered. Passed to metagene_coverage().
     """
     now = datetime.datetime.now()
     print(now.strftime("%b %d %H:%M:%S ..... started ribotricer detect-orfs"))
@@ -416,7 +419,7 @@ def detect_orfs(
             "started calculating metagene profiles. This may take a long time...",
         )
     )
-    metagenes = metagene_coverage(annotated, alignments, read_length_counts, prefix)
+    metagenes = metagene_coverage(annotated, alignments, read_length_counts, prefix, meta_min_reads = meta_min_reads)
 
     # plot metagene profiles
     now = datetime.datetime.now()