Import logger from main into submodules

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:]

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.

itsxpress/SeqSample.py

@@ -1,5 +1,6 @@
 import os
 import logging
+logger = logging.getLogger(__name__)
 import tempfile
 import subprocess
 

itsxpress/SeqSamplePaired.py

@@ -4,6 +4,7 @@
 
 import subprocess
 import logging
+logger = logging.getLogger(__name__)
 import os
 import pyzstd as zstd