From 28b74d67a61099a66990a1edb266cc02caeed582 Mon Sep 17 00:00:00 2001
From: seina001 <seinarsson@ufl.edu>
Date: Wed, 20 Mar 2024 15:34:22 -0400
Subject: [PATCH] Import logger from main into submodules

---
 itsxpress/Dedup.py           | 2 --
 itsxpress/ITSposition.py     | 1 +
 itsxpress/SeqSample.py       | 1 +
 itsxpress/SeqSamplePaired.py | 1 +
 4 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/itsxpress/Dedup.py b/itsxpress/Dedup.py
index e7fa5d8..7f4c60b 100644
--- a/itsxpress/Dedup.py
+++ b/itsxpress/Dedup.py
@@ -99,8 +99,6 @@ def _map_func(ziprecord):
             start, stop, tlen = itspos.get_position(repseq)
             r2start = tlen - stop
             r2end = tlen - start #calculate end of R2
-            #Log start, stop, and tlen, r2start, r2end with names and sequence ids
-            logging.info("Start: {} Stop: {} Tlen: {} R2start: {} R2end: {} for sequence ID: {}".format(start, stop, tlen, r2start, r2end, record1.id))
             try:
                 if stop > tlen:
                     record1_return = record1[start:]
diff --git a/itsxpress/ITSposition.py b/itsxpress/ITSposition.py
index 47b4a32..caf7589 100644
--- a/itsxpress/ITSposition.py
+++ b/itsxpress/ITSposition.py
@@ -1,4 +1,5 @@
 import logging
+logger = logging.getLogger(__name__)
 
 class ItsPosition:
     """Class for ITS positional information derived from hmmserach domtable files.
diff --git a/itsxpress/SeqSample.py b/itsxpress/SeqSample.py
index 05812fd..47cb747 100644
--- a/itsxpress/SeqSample.py
+++ b/itsxpress/SeqSample.py
@@ -1,5 +1,6 @@
 import os
 import logging
+logger = logging.getLogger(__name__)
 import tempfile
 import subprocess
 
diff --git a/itsxpress/SeqSamplePaired.py b/itsxpress/SeqSamplePaired.py
index 4b674da..e77b5ad 100644
--- a/itsxpress/SeqSamplePaired.py
+++ b/itsxpress/SeqSamplePaired.py
@@ -4,6 +4,7 @@
 
 import subprocess
 import logging
+logger = logging.getLogger(__name__)
 import os
 import pyzstd as zstd