From 9f963bb71b4c148878794a5c56b4435a8166f0a1 Mon Sep 17 00:00:00 2001
From: Haibao Tang <tanghaibao@gmail.com>
Date: Tue, 30 Apr 2024 20:57:36 -0700
Subject: [PATCH] residuals

---
 jcvi/annotation/reformat.py  |  1 -
 jcvi/assembly/syntenypath.py | 27 +++++++++++++--------------
 jcvi/compara/synteny.py      |  1 -
 3 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/jcvi/annotation/reformat.py b/jcvi/annotation/reformat.py
index 5b661130..26d52af5 100644
--- a/jcvi/annotation/reformat.py
+++ b/jcvi/annotation/reformat.py
@@ -9,7 +9,6 @@
 """
 import os
 import sys
-import logging
 import re
 
 from collections import defaultdict
diff --git a/jcvi/assembly/syntenypath.py b/jcvi/assembly/syntenypath.py
index c0b1e855..7d12d24f 100644
--- a/jcvi/assembly/syntenypath.py
+++ b/jcvi/assembly/syntenypath.py
@@ -5,18 +5,17 @@
 Syntenic path assembly.
 """
 import sys
-import logging
 
 from collections import defaultdict
 from itertools import groupby, combinations
 from more_itertools import pairwise
 
-from jcvi.formats.blast import BlastSlow, Blast
-from jcvi.formats.sizes import Sizes
-from jcvi.formats.base import LineFile, must_open
-from jcvi.utils.range import range_intersect
-from jcvi.algorithms.graph import BiGraph
-from jcvi.apps.base import OptionParser, ActionDispatcher
+from ..algorithms.graph import BiGraph
+from ..apps.base import ActionDispatcher, OptionParser, logger
+from ..formats.base import LineFile, must_open
+from ..formats.blast import Blast, BlastSlow
+from ..formats.sizes import Sizes
+from ..utils.range import range_intersect
 
 
 class OVLLine:
@@ -60,12 +59,12 @@ def __init__(self, filename):
                 alledges[o.a + "-3`"].append(o)
             elif o.tag == "b->a":
                 alledges[o.a + "-5`"].append(o)
-        logging.debug(
+        logger.debug(
             "Imported {} links. Contained tigs: {}".format(len(self), len(contained))
         )
         self.contained = contained
 
-        logging.debug("Pruning edges to keep the mutual best")
+        logger.debug("Pruning edges to keep the mutual best")
         for k, v in alledges.items():
             bo = max(v, key=lambda x: x.score)
             bo.best = True
@@ -360,7 +359,7 @@ def happy(args):
             fw = fw2 if is_uncertain else fw1
             print(e, file=fw)
 
-    logging.debug("Edges written to `{0}`".format(",".join((certain, uncertain))))
+    logger.debug("Edges written to `{0}`".format(",".join((certain, uncertain))))
 
 
 def fromblast(args):
@@ -425,7 +424,7 @@ def graph_to_agp(g, blastfile, subjectfasta, exclude=[], verbose=False):
 
     from jcvi.formats.agp import order_to_agp
 
-    logging.debug(str(g))
+    logger.debug(str(g))
     g.write("graph.txt")
     # g.draw("graph.pdf")
 
@@ -441,7 +440,7 @@ def graph_to_agp(g, blastfile, subjectfasta, exclude=[], verbose=False):
 
     npaths = len(paths)
     ntigs = sum(len(x) for x in paths)
-    logging.debug(
+    logger.debug(
         "Graph decomposed to {0} paths with {1} components.".format(npaths, ntigs)
     )
 
@@ -469,14 +468,14 @@ def graph_to_agp(g, blastfile, subjectfasta, exclude=[], verbose=False):
         object = ctg
         order_to_agp(object, ctgorder, sizes.mapping, fwagp)
         nsingletons += 1
-    logging.debug(
+    logger.debug(
         "scaffolded={} excluded={} singletons={}".format(
             nscaffolded, nexcluded, nsingletons
         )
     )
 
     fwagp.close()
-    logging.debug("AGP file written to `{0}`.".format(agpfile))
+    logger.debug("AGP file written to `{0}`.".format(agpfile))
 
 
 def connect(args):
diff --git a/jcvi/compara/synteny.py b/jcvi/compara/synteny.py
index 7d569f71..31c6a941 100755
--- a/jcvi/compara/synteny.py
+++ b/jcvi/compara/synteny.py
@@ -6,7 +6,6 @@
 
 import os.path as op
 import sys
-import logging
 
 from collections import defaultdict
 from collections.abc import Iterable