diff --git a/build/lib/liqa_src/liqa.py b/build/lib/liqa_src/liqa.py index c8fb1f9..a8e1e88 100644 --- a/build/lib/liqa_src/liqa.py +++ b/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 -bamlist -out " + 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] diff --git a/dist/liqa-1.1.3-py3-none-any.whl b/dist/liqa-1.1.3-py3-none-any.whl new file mode 100644 index 0000000..5f57a49 Binary files /dev/null and b/dist/liqa-1.1.3-py3-none-any.whl differ diff --git a/dist/liqa-1.1.3.tar.gz b/dist/liqa-1.1.3.tar.gz new file mode 100644 index 0000000..88c2d96 Binary files /dev/null and b/dist/liqa-1.1.3.tar.gz differ diff --git a/example/.pg_xattr b/example/.pg_xattr new file mode 100755 index 0000000..777a33b --- /dev/null +++ b/example/.pg_xattr @@ -0,0 +1,3 @@ + +example.pgbam:883420:user.PetaGene.internals.decompressed=SF:10100046;M:2229132 +example.pgbam:883420:DONE diff --git a/example/example.bam b/example/example.bam deleted file mode 100644 index 092ada0..0000000 Binary files a/example/example.bam and /dev/null differ diff --git a/example/example.bam b/example/example.bam new file mode 120000 index 0000000..84587df --- /dev/null +++ b/example/example.bam @@ -0,0 +1 @@ +example.pgbam.#.bam \ No newline at end of file diff --git a/example/example.bam.bai b/example/example.bam.bai deleted file mode 100644 index 8f58bfd..0000000 Binary files a/example/example.bam.bai and /dev/null differ diff --git a/example/example.bam.bai b/example/example.bam.bai new file mode 120000 index 0000000..e7dcb41 --- /dev/null +++ b/example/example.bam.bai @@ -0,0 +1 @@ +/mnt/isilon/wang_lab/huyu/bin/liqa/LIQA/example/example.pgbai.#.bai \ No newline at end of file diff --git a/example/example.pgbai b/example/example.pgbai new file mode 100644 index 0000000..62055ac Binary files /dev/null and b/example/example.pgbai differ diff --git a/example/example.pgbam b/example/example.pgbam new file mode 100644 index 0000000..c383f1a Binary files /dev/null and b/example/example.pgbam differ diff --git a/liqa.egg-info/PKG-INFO b/liqa.egg-info/PKG-INFO index eee6d8f..ad55151 100644 --- a/liqa.egg-info/PKG-INFO +++ b/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: huyu999999@gmail.com 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) - - diff --git a/liqa.egg-info/entry_points.txt b/liqa.egg-info/entry_points.txt index e7c677c..56d7991 100644 --- a/liqa.egg-info/entry_points.txt +++ b/liqa.egg-info/entry_points.txt @@ -1,3 +1,2 @@ [console_scripts] liqa = liqa_src.liqa:main - diff --git a/setup.py b/setup.py index a9d0979..a2aef6c 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setuptools.setup( name="liqa", - version="1.1.22", + version="1.1.3", author="Yu Hu", author_email="huyu999999@gmail.com", description="A statistical tool to quantify isoform-specific expression using long-read RNA-seq",