Merge pull request #62 from ygidtu/dev

Dev 0.1.2

Author: ygidtu

.dockerignore

@@ -3,4 +3,9 @@ example/
 .git/
 Dockerfile
 WebDockerfile
-node_modules/
+node_modules/
+plots/
+dist/
+build/
+*.egg-info/
+ui/

Pipfile

@@ -19,6 +19,7 @@ cairocffi = "*"
 hicmatrix = "*"
 loguru = "*"
 scipy = "*"
+adjusttext = "*"
 
 [dev-packages]
 

Pipfile.lock

@@ -51,26 +51,32 @@ The sashimi.py is written in Python, and user could install it in a variety of w
 __Note:__ if `segment fault` with multiple processing, please try to use docker image, or just run with `-p 1`.
 
 1. install from PiPy
-   
-   ```bash
-   pip install sashimi.py
-   ```
+
+    ```bash
+    pip install sashimi.py
+    ```
+
 2. install from bioconda
-   ```bash
-   conda install -c bioconda sashimi-py
-   
-   # or
+
+    ```bash
+    conda install -c bioconda sashimi-py
    
-   conda create -n sashimi meta.yaml
-   ```
+    # or
+    conda env create -n sashimi -f environment.yaml
+
+    # or
+    conda env create -n sashimi -c conda-forge -c bioconda  -f requirements.txt
+    conda activate sashimi && python setup.py install
+    ```
+
 3. using docker image
+
     ```bash
     docker pull ygidtu/sashimi
     docker run --rm ygidtu/sashimi --help
-    ```
-   or 
 
-    ```bash
+    # or 
+
     git clone from https://github.com/ygidtu/sashimi.py sashimi
     cd sashimi
     docker build -t ygidtu/docker .
@@ -88,9 +94,9 @@ __Note:__ if `segment fault` with multiple processing, please try to use docker
     # pr
     python main.py --help
     ```
-   
+
 5. running from a local webserver
-    
+
    ```bash
     git clone https://github.com/ygidtu/sashimi.py sashimi
     cd sashimi/web

README.md

@@ -1,12 +1,6 @@
-FROM python:3.9-buster
+FROM ygidtu/sashimi
 
 ENV ROOT_DIR=/opt/sashimi
-ENV PYPI=https://pypi.douban.com/simple
-RUN mkdir $ROOT_DIR
-COPY . $ROOT_DIR
-
-RUN cd $ROOT_DIR && \
-    pip install -i $PYPI fastapi uvicorn pydantic jinja2 && \
-    pip install -r requirements.txt && ls -l $ROOT_DIR
+RUN cd $ROOT_DIR && pip install -i $PYPI fastapi uvicorn pydantic jinja2
 
 ENTRYPOINT ["python", "/opt/sashimi/server.py", "--host", "0.0.0.0"]

WebDockerfile

@@ -10,7 +10,10 @@ conda install sashimi-py
 git clone from https://github.com/ygidtu/sashimipy sashimi
 cd sashimi
 
-conda create env -n sashimi meta.yaml
+conda env create -n sashimi -f environment.yaml
+# or
+conda env create -n sashimi -c conda-forge -c bioconda  -f requirements.txt
+conda activate sashimi && python setup.py install
 ```
 
 ### via PyPI

docs/installation.md

@@ -0,0 +1,25 @@
+channels:
+  - conda-forge
+  - bioconda
+  - default
+
+dependencies:
+  - python
+  - pysam
+  - filetype
+  - pybigwig
+  - click-option-group
+  - cairocffi
+  - hicmatrix
+  - matplotlib-base
+  - seaborn-base
+  - click
+  - numpy
+  - requests
+  - xmltodict
+  - pandas
+  - loguru
+  - adjusttext
+  - pip
+  - pip:
+      - -e .

environment.yaml

@@ -1,47 +1,48 @@
-asciitree>=0.3.3
-cairocffi>=1.4.0
-certifi>=2022.9.24 ; python_version >= '3.6'
-cffi>=1.15.1
-charset-normalizer>=2.1.1 ; python_full_version >= '3.6.0'
-click>=8.1.3
-click-option-group>=0.5.5
-contourpy>=1.0.6 ; python_version >= '3.7'
-cooler>=0.8.11
-cycler>=0.11.0 ; python_version >= '3.6'
-cytoolz>=0.10.1
-dill>=0.3.6 ; python_version >= '3.7'
-filetype>=1.2.0
-fonttools>=4.38.0 ; python_version >= '3.7'
-h5py>=3.7.0 ; python_version >= '3.7'
-hicmatrix>=15
-idna>=3.4 ; python_version >= '3.5'
-intervaltree>=3.1.0
-kiwisolver>=1.4.4 ; python_version >= '3.7'
-loguru>=0.6.0
-matplotlib>=3.6.2
-multiprocess>=0.70.14 ; python_version >= '3.7'
-numexpr>=2.8.4 ; python_version >= '3.7'
-numpy>=1.23.4
-packaging>=21.3 ; python_version >= '3.6'
-pandas>=1.5.1
-pillow>=9.3.0 ; python_version >= '3.7'
-pybigwig>=0.3.18
-pycparser>=2.21
-pyfaidx>=0.7.1
-pypairix>=0.3.7
-pyparsing>=3.0.9 ; python_full_version >= '3.6.8'
-pysam>=0.20.0
-python-dateutil>=2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pytz>=2022.6
-pyyaml>=6.0 ; python_version >= '3.6'
-requests>=2.28.1
-scipy>=1.9.3
-seaborn>=0.12.1
-setuptools>=65.5.1 ; python_version >= '3.7'
-simplejson>=3.18.0 ; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
-six>=1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-sortedcontainers>=2.4.0
-tables>=3.7.0 ; python_version >= '3.6'
-toolz>=0.12.0 ; python_version >= '3.5'
-urllib3>=1.26.12 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' and python_version < '4'
-xmltodict>=0.13.0
+adjusttext
+asciitree
+cairocffi
+certifi
+cffi
+charset-normalizer
+click
+click-option-group
+contourpy
+cooler
+cycler
+cytoolz
+dill
+filetype
+fonttools
+h5py
+hicmatrix
+idna
+intervaltree
+kiwisolver
+loguru
+matplotlib
+multiprocess
+numexpr
+numpy
+packaging
+pandas
+pillow
+pybigwig
+pycparser
+pyfaidx
+pypairix
+pyparsing
+pysam
+python-dateutil
+pytz
+pyyaml
+requests
+scipy
+seaborn
+setuptools
+simplejson
+six
+sortedcontainers
+tables
+toolz
+urllib3
+xmltodict

meta.yaml

@@ -24,7 +24,7 @@ def __init__(self, chromosome, start, end, strand: str = "+"):
         :param strand: the strand of the given junction.
         """
         self.chromosome = chromosome
-        self.start = int(start) + 1
+        self.start = int(start)
         self.end = int(end)
         self.strand = strand
 
@@ -61,7 +61,7 @@ def __hash__(self):
         generate hash
         :return:
         """
-        return hash((self.chromosome, self.start, self.end))
+        return hash((self.chromosome, self.start, self.end, self.strand))
 
     def __str__(self):
         u"""