From a280f7fc2ab92fdebe51e78d6030bffd94d6e893 Mon Sep 17 00:00:00 2001
From: Tong-Chen <chentong_biology@163.com>
Date: Wed, 27 Sep 2023 09:55:46 +0800
Subject: [PATCH 1/2] add ignore zero anchor parameter for skip no matches in
 batch search

---
 jcvi/compara/catalog.py | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/jcvi/compara/catalog.py b/jcvi/compara/catalog.py
index 80488cc2..eb8e4749 100644
--- a/jcvi/compara/catalog.py
+++ b/jcvi/compara/catalog.py
@@ -666,6 +666,12 @@ def ortholog(args):
     dotplot_group.add_option(
         "--no_dotplot", default=False, action="store_true", help="Do not make dotplot"
     )
+    p.add_option(
+        "--ignore_zero_anchor",
+        default=False,
+        action="store_true",
+        help="Ignore this pair of ortholog identification instead of throwing an error when performing many pairs of cataloging."
+    )
 
     opts, args = p.parse_args(args)
 
@@ -674,6 +680,7 @@ def ortholog(args):
 
     a, b = args
     dbtype = opts.dbtype
+    ignore_zero_anchor = opts.ignore_zero_anchor
     suffix = ".cds" if dbtype == "nucl" else ".pep"
     abed, afasta = a + ".bed", a + suffix
     bbed, bfasta = b + ".bed", b + suffix
@@ -727,7 +734,15 @@ def ortholog(args):
                 dargs += ["--no_strip_names"]
             if opts.liftover_dist:
                 dargs += ["--liftover_dist={}".format(opts.liftover_dist)]
-            scan(dargs)
+            try:
+                scan(dargs)
+            except ValueError as e:
+                if ignore_zero_anchor:
+                    logging.debug(f"{e}")
+                    logging.debug("Ignoring this error and continuing...")
+                    return
+                else:
+                    raise ValueError(e)
         if quota:
             quota_main([lifted_anchors, "--quota={0}".format(quota), "--screen"])
         if need_update(anchors, pdf, warn=True) and not opts.no_dotplot:

From 1e1fbd21b61d92f4e811440daed3d455817ff27b Mon Sep 17 00:00:00 2001
From: Tong-Chen <chentong_biology@163.com>
Date: Sat, 18 Nov 2023 22:18:43 +0800
Subject: [PATCH 2/2] ignore blank line in bed

---
 jcvi/formats/bed.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jcvi/formats/bed.py b/jcvi/formats/bed.py
index df791837..c80ee54c 100755
--- a/jcvi/formats/bed.py
+++ b/jcvi/formats/bed.py
@@ -151,7 +151,7 @@ def __init__(self, filename=None, key=None, sorted=True, juncs=False, include=No
             return
 
         for line in must_open(filename):
-            if line[0] == "#" or (juncs and line.startswith("track name")):
+            if line[0] == "#" or (juncs and line.startswith("track name")) or line.strip()=="":
                 continue
             b = BedLine(line)
             if include and b.accn not in include: