updates

YaqiangCao · Sep 18, 2023 · bfaf4a2 · bfaf4a2
1 parent d0e52db
commit bfaf4a2
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Showing 3 changed files with 6 additions and 2 deletions.
diff --git a/build/scripts-3.10/tracPre2.py b/build/scripts-3.10/tracPre2.py
@@ -1,7 +1,7 @@
 #!/home/caoy7/anaconda3/envs/astroBoy/bin/python
 #--coding:utf-8--
 """
-tracPre.py
+tracPre2.py
 Pre-processing code for Hi-Trac data, implemented with cLoops2, from fastq to bedpe files and qc report.
 2020-02-27: finished and well tested.
 2020-06-30: add linker filter, new stat, and changing mapping to end-to-end
@@ -357,9 +357,11 @@ def main():
     Batch converting from bam to bedpe.
     """
     #prepare everything
+    global logger
     op = help()
     date = time.strftime(' %Y-%m-%d', time.localtime(time.time()))
     logger = getLogger(fn=op.output + "/" + date.strip() + "_" + os.path.basename(__file__) + ".log")
+
     for t in ["bowtie2", "samtools", "bamToBed"]:
         if not isTool(t):
             logger.error("%s not exits! Please install through conda." % t)

diff --git a/dist/cLoops2-0.0.5-py3.10.egg b/dist/cLoops2-0.0.5-py3.10.egg
diff --git a/scripts/tracPre2.py b/scripts/tracPre2.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #--coding:utf-8--
 """
-tracPre.py
+tracPre2.py
 Pre-processing code for Hi-Trac data, implemented with cLoops2, from fastq to bedpe files and qc report.
 2020-02-27: finished and well tested.
 2020-06-30: add linker filter, new stat, and changing mapping to end-to-end
@@ -357,9 +357,11 @@ def main():
     Batch converting from bam to bedpe.
     """
     #prepare everything
+    global logger
     op = help()
     date = time.strftime(' %Y-%m-%d', time.localtime(time.time()))
     logger = getLogger(fn=op.output + "/" + date.strip() + "_" + os.path.basename(__file__) + ".log")
+
     for t in ["bowtie2", "samtools", "bamToBed"]:
         if not isTool(t):
             logger.error("%s not exits! Please install through conda." % t)