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WGLab · Jan 26, 2021 · 5a893b8 · 5a893b8
1 parent ef6d066
commit 5a893b8
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Showing 8 changed files with 14 additions and 6 deletions.
diff --git a/build/lib/liqa_src/PreProcess_gtf.pl b/build/lib/liqa_src/PreProcess_gtf.pl
@@ -83,6 +83,9 @@
     }
 }
 
+my $number_genes = scalar keys %knownGene;
+print "$number_genes genes are being processed...\n";
+
 #open(REF, $ref
 open (RRR, ">$output");
 

diff --git a/build/lib/liqa_src/quantify.py b/build/lib/liqa_src/quantify.py
@@ -141,7 +141,7 @@ def auto_dict():
                 tmpisolength[iii] = tmpisolength[iii]/2566
             #print(gene+"\t"+str(tmpisolength[iii]))
     else:
-        genelength = 1
+        genelength = 100
         tmpisolength = tmpisoinf[0].split(",")
         for iii in range(len(tmpisolength)-1):
             tmpisolength[iii] = 0
@@ -525,11 +525,13 @@ def auto_dict():
 
     print(gene+"\t"+str(iterCount)+" iterations\tDone!")
 
-    rpg_lengthcorrected = readCount/genelength*100
+    #rpg_lengthcorrected = readCount/genelength*100
     for i in range(len(Alpha)):
         #isoformRelativeAbundances[i] = (Alpha[i]/isoformLength[isoformNames[i]]+tmpisolength[i]*weightF) /(sumTheta)
         isoformRelativeAbundances[i] = (Alpha[i] + tmpisolength[i]*weightF) /(sumTheta)
         #print(gene+"\t"+str(geneCount)+"\t"+str(iterCount)+"\t"+isoformNames[i]+"\t"+str(isoformRelativeAbundances[i])+"\t"+str(tmpTime))
+
+        rpg_lengthcorrected = readCount/genelength*100*isoformRelativeAbundances[i]
 
         #OUT.write(gene+"\t"+isoformNames[i]+"\t"+str(readCount)+"\t"+str(isoformRelativeAbundances[i])+"\t"+str(rpg_lengthcorrected)+"\n") ## write results into specified file
         OUT.write(gene+"\t"+isoformNames[i]+"\t"+str(isoformRelativeAbundances[i])+"\t"+str(rpg_lengthcorrected)+"\n")

diff --git a/build/scripts-3.7/PreProcess_gtf.pl b/build/scripts-3.7/PreProcess_gtf.pl
@@ -83,6 +83,9 @@
     }
 }
 
+my $number_genes = scalar keys %knownGene;
+print "$number_genes genes are being processed...\n";
+
 #open(REF, $ref
 open (RRR, ">$output");
 

diff --git a/dist/liqa-1.1.15-py3-none-any.whl b/dist/liqa-1.1.15-py3-none-any.whl
diff --git a/dist/liqa-1.1.15.tar.gz b/dist/liqa-1.1.15.tar.gz
diff --git a/liqa.egg-info/PKG-INFO b/liqa.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liqa
-Version: 1.1.13
+Version: 1.1.15
 Summary: A statistical tool to quantify isoform-specific expression using long-read RNA-seq
 Home-page: https://github.com/WGLab/LIQA
 Author: Yu Hu

diff --git a/liqa_src/quantify.py b/liqa_src/quantify.py
@@ -108,7 +108,7 @@ def auto_dict():
 startTime = time.time()
 
 #OUT.write("GeneName\tIsoformName\tNumberOfReads\tRelativeAbundance\n") ## Header of Results
-OUT.write("GeneName\tIsoformName\tRelativeAbundance\tReadPerGene_corrected\n")
+OUT.write("GeneName\tIsoformName\tReadPerGene_corrected\tRelativeAbundance\n")
 
 for gene in geneStructureInformation:
 
@@ -534,7 +534,7 @@ def auto_dict():
         rpg_lengthcorrected = readCount/genelength*100*isoformRelativeAbundances[i]
 
         #OUT.write(gene+"\t"+isoformNames[i]+"\t"+str(readCount)+"\t"+str(isoformRelativeAbundances[i])+"\t"+str(rpg_lengthcorrected)+"\n") ## write results into specified file
-        OUT.write(gene+"\t"+isoformNames[i]+"\t"+str(isoformRelativeAbundances[i])+"\t"+str(rpg_lengthcorrected)+"\n")
+        OUT.write(gene+"\t"+isoformNames[i]+"\t"+str(rpg_lengthcorrected)+"\t"+str(isoformRelativeAbundances[i])+"\n")
 
 OUT.close()
 

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="liqa",
-    version="1.1.13",
+    version="1.1.15",
     author="Yu Hu",
     author_email="[email protected]",
     description="A statistical tool to quantify isoform-specific expression using long-read RNA-seq",