update

build/lib/liqa_src/liqa.py

@@ -10,7 +10,7 @@ def main():
     crtAbsPath = os.getcwd()
 
     task = ""
-    taskList = ["refgene", "quantify", "diff"]
+    taskList = ["refgene", "quantify", "diff", "novel"]
     for i in range(1,len(sys.argv)):
         if sys.argv[i] == "-task" and len(sys.argv)!=i+1:
             task = sys.argv[i+1]
@@ -19,7 +19,8 @@ def main():
         print("\trefgene:   preprocess reference file\n")
         print("\tquantify:   quantify isoform expression\n")
         print("\tdiff:   detect differential splicing gene/isoform\n")
-
+        print("\tnovel:   detect novel isoform\n")
+
     if task == "refgene":
         validArgList = ["-task", "-ref", "-format", "-out"]
         addAbsPath = [0, 1, 0, 3]
@@ -38,6 +39,18 @@ def main():
         else:
             print("Please specify reference file format: gtf/ucsc")
 
+    if task == "novel":
+        validArgList = ["-task", "-ref", "-bamlist", "-out"]
+        addAbsPath = [0, 1, 1, 3]
+        message = "liqa -task novel -ref <reference_file> -bamlist <list of bam file> -out <output_file>"
+        inputs = my.parse_argument(validArgList, addAbsPath, message)
+        refFile = inputs[1]
+        bamList = inputs[2]
+        outFile = inputs[3]
+
+        myCommand = "perl " + fileAbsPath + "/detect.pl -r " + refFile + " -o " + outFile + " -b " + bamList
+        os.system(myCommand)
+
     if task == "quantify":
         validArgList = ["-task", "-refgene", "-bam", "-out", "-max_distance", "-f_weight"]
         addAbsPath = [0, 1, 1, 3, 0, 0]

example/.pg_xattr

@@ -0,0 +1,3 @@
+
+example.pgbam:883420:user.PetaGene.internals.decompressed=SF:10100046;M:2229132
+example.pgbam:883420:DONE

example/example.bam

@@ -0,0 +1 @@
+example.pgbam.#.bam

example/example.bam.bai

@@ -0,0 +1 @@
+/mnt/isilon/wang_lab/huyu/bin/liqa/LIQA/example/example.pgbai.#.bai

liqa.egg-info/PKG-INFO

@@ -1,12 +1,11 @@
 Metadata-Version: 2.1
 Name: liqa
-Version: 1.1.22
+Version: 1.1.3
 Summary: A statistical tool to quantify isoform-specific expression using long-read RNA-seq
 Home-page: https://github.com/WGLab/LIQA
 Author: Yu Hu
 Author-email: [email protected]
 License: MIT
-Platform: UNKNOWN
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
@@ -44,5 +43,3 @@ If you have any questions/issues/bugs, please post them on [GitHub](https://gith
 ## Citation
 
 Yu Hu, Li Fang, Xuelian Chen, Jiang F. Zhong, Mingyao Li, Kai Wang. LIQA: Long-read Isoform Quantification and Analysis. 2020. bioRxiv doi: [https://doi.org/10.1101/2020.09.09.289793](https://www.biorxiv.org/content/10.1101/2020.09.09.289793v1)
-
-

liqa.egg-info/entry_points.txt

@@ -1,3 +1,2 @@
 [console_scripts]
 liqa = liqa_src.liqa:main
-

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="liqa",
-    version="1.1.22",
+    version="1.1.3",
     author="Yu Hu",
     author_email="[email protected]",
     description="A statistical tool to quantify isoform-specific expression using long-read RNA-seq",