Merge pull request #47 from ygidtu/dev

update web to v0.0.5, fix several bugs, update docs

Author: ygidtu

WebDockerfile

@@ -9,4 +9,4 @@ RUN cd $ROOT_DIR && \
     pip install -i $PYPI fastapi uvicorn pydantic jinja2 && \
     pip install -r requirements.txt && ls -l $ROOT_DIR
 
-ENTRYPOINT ["python", "/opt/sashimi/server.py"]
+ENTRYPOINT ["python", "/opt/sashimi/server.py", "--host", "0.0.0.0"]

docs/imgs/web/add.png

@@ -69,9 +69,9 @@ docker run --rm -v $PWD:$PWD --user $(id -u):$(id -g) ygidtu/sashimi --help
 
 - `-v`, `--volumn`: mount the working directory to docker container
 - `--user`: prevent docker read and write file using root privileges
-- the rest usage please check [Command line usage](./command_line_usage.md)
+- the rest usage please check [Command line usage](./command.md)
 
-**Note: ** detailed command line usage please check [Command line Usage](./command_line_usage.md)
+**Note: ** detailed command line usage please check [Command line Usage](./command.md)
 
 
 ## Build Web interface from source
@@ -101,6 +101,8 @@ python server.py --help
 ```bash
 docker pull ygidtu/sashimiweb
 
-export PORT=8080  # the port your are trying to exposed
-docker run --rm -v $PWD:$PWD --user $(id -u):$(id -g) -p $PORT:5000 ygidtu/sashimiweb
+docker run --name sashimiweb \
+  --rm -v $PWD:$PWD \
+  -p 5000:5000 \
+  ygidtu/sashimiweb 
 ```

docs/imgs/web/draw.png

@@ -6,7 +6,9 @@
 
 #### 1. requirements
 
-Except the sashimi, we still required `fastapi`, `uvicorn` and `pydantic`
+Except the sashimi, we required `fastapi`, `uvicorn` and `pydantic` and `nodejs`
+
+The deployment please check the [Build Web interface from source](./installation.md)
 
 ## Usage
 

docs/imgs/web/main.png

@@ -55,10 +55,12 @@ def __init__(self,
 
     @property
     def wiggle(self) -> np.array:
-        if self.plus is None or np.sum(self.plus) == 0:
+        if (self.plus is None or np.sum(self.plus) == 0) and self.minus is not None:
             return self.minus
-        elif self.minus is None or np.sum(self.minus) == 0:
-            return self.plus
+
+        if self.plus is not None and self.minus is not None:
+            return self.plus + self.minus
+
         return self.plus
 
     def __add__(self, other):

docs/imgs/web/preview.png

@@ -564,7 +564,8 @@ def main(**kwargs):
                                       n_y_ticks=kwargs["n_y_ticks"],
                                       show_y_label=not kwargs["hide_y_label"],
                                       show_site_plot=kwargs["show_site"],
-                                      strand_choice=kwargs["site_strand"])
+                                      strand_choice=kwargs["site_strand"],
+                                      density_by_strand=kwargs["density_by_strand"],)
             elif key == "heatmap":
                 for f in process_file_list(kwargs[key], key):
                     if barcodes and f.label in barcodes.keys() and f.category in ["bam", "atac"]:

docs/installation.md

@@ -53,7 +53,8 @@ def create(cls,
                barcodes: Optional[Set[str]] = None,
                barcode_tag: str = "CB",
                umi_tag: str = "UB",
-               library: str = "fru"
+               library: str = "fru",
+               density_by_strand: bool = False
                ):
         u"""
 
@@ -88,7 +89,8 @@ def create(cls,
             barcodes=barcode,
             barcode_tag=barcode_tag,
             umi_tag=umi_tag,
-            library=library
+            library=library,
+            density_by_strand=density_by_strand
         )
 
     def __hash__(self):
@@ -282,11 +284,11 @@ def load(self,
             spanned_junctions_plus, spanned_junctions_minus = {}, {}
 
         self.data = ReadDepth(
-            plus,
+            plus if self.density_by_strand else plus + minus,
             junctions_dict=filtered_junctions,
             site_plus=site_plus,
             site_minus=site_minus,
-            minus=minus,
+            minus=minus if self.density_by_strand else None,
             junction_dict_plus=spanned_junctions_plus,
             junction_dict_minus=spanned_junctions_minus,
             strand_aware=False if self.library == "fru" else True)