levseq 1.0.0__tar.gz → 1.0.2__tar.gz

{levseq-1.0.0/levseq.egg-info → levseq-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: levseq
-Version: 1.0.0
+Version: 1.0.2
 Home-page: https://github.com/fhalab/levseq/
 Author: Yueming Long, Emreay Gursoy, Ariane Mora
 Author-email: ylong@caltech.edu
@@ -54,7 +54,7 @@ Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore tech
 
 - Data to reproduce the results and to test are available on zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13694463.svg)](https://doi.org/10.5281/zenodo.13694463)
 
-- A dockerized website and database for labs to locally host and visualize their data: https://github.com/fhalab/LevSeq_VDB/
+- A dockerized website and database for labs to locally host and visualize their data: website is available at: https://levseq.caltech.edu/ and code to host locally at: https://github.com/fhalab/LevSeq_VDB/
 
 ## Setup
 
@@ -90,7 +90,7 @@ git clone https://github.com/fhalab/LevSeq.git
 ```
 
 ```
-conda create --name levseq python=3.8
+conda create --name levseq python=3.8 -y
 ```
 
 ```
@@ -100,7 +100,7 @@ conda activate levseq
 From the LevSeq folder, install the package using pip:
 
 ```
-pip install releases/levseq-0.1.0.tar.gz
+pip install levseq
 ```
 #### Dependencies 
 
@@ -116,15 +116,18 @@ conda install -c bioconda -c conda-forge minimap2
 ```
 or for mac users you can use: `brew install minimap2`
 Once dependencies are all installed, you can run LevSeq using command line.
-3. GCC
-For Mac M1 users: installation via homebrew
+3. GCC version 13 and 14 are both needed
+For Mac M chip users: installation via homebrew
 ```
-brew install gcc
+brew install gcc@14
+brew install gcc@13
 ```
 For Linux users: installation via conda 
 ```
-conda install conda-forge::gcc
+conda install conda-forge::gcc=14
+conda install conda-forge::gcc=13
 ```
+
 ### Usage
 #### Command Line Interface
 LevSeq can be run using the command line interface. Here's the basic structure of the command:

{levseq-1.0.0 → levseq-1.0.2}/README.md

@@ -8,7 +8,7 @@ Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore tech
 
 - Data to reproduce the results and to test are available on zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13694463.svg)](https://doi.org/10.5281/zenodo.13694463)
 
-- A dockerized website and database for labs to locally host and visualize their data: https://github.com/fhalab/LevSeq_VDB/
+- A dockerized website and database for labs to locally host and visualize their data: website is available at: https://levseq.caltech.edu/ and code to host locally at: https://github.com/fhalab/LevSeq_VDB/
 
 ## Setup
 
@@ -44,7 +44,7 @@ git clone https://github.com/fhalab/LevSeq.git
 ```
 
 ```
-conda create --name levseq python=3.8
+conda create --name levseq python=3.8 -y
 ```
 
 ```
@@ -54,7 +54,7 @@ conda activate levseq
 From the LevSeq folder, install the package using pip:
 
 ```
-pip install releases/levseq-0.1.0.tar.gz
+pip install levseq
 ```
 #### Dependencies 
 
@@ -70,15 +70,18 @@ conda install -c bioconda -c conda-forge minimap2
 ```
 or for mac users you can use: `brew install minimap2`
 Once dependencies are all installed, you can run LevSeq using command line.
-3. GCC
-For Mac M1 users: installation via homebrew
+3. GCC version 13 and 14 are both needed
+For Mac M chip users: installation via homebrew
 ```
-brew install gcc
+brew install gcc@14
+brew install gcc@13
 ```
 For Linux users: installation via conda 
 ```
-conda install conda-forge::gcc
+conda install conda-forge::gcc=14
+conda install conda-forge::gcc=13
 ```
+
 ### Usage
 #### Command Line Interface
 LevSeq can be run using the command line interface. Here's the basic structure of the command:

{levseq-1.0.0 → levseq-1.0.2}/levseq/__init__.py

@@ -18,7 +18,7 @@
 __title__ = 'levseq'
 __description__ = 'LevSeq nanopore sequencing'
 __url__ = 'https://github.com/fhalab/levseq/'
-__version__ = '1.0.0'
+__version__ = '1.0.2'
 __author__ = 'Yueming Long, Emreay Gursoy, Ariane Mora'
 __author_email__ = 'ylong@caltech.edu'
 __license__ = 'GPL3'

{levseq-1.0.0 → levseq-1.0.2}/levseq/run_levseq.py

@@ -248,8 +248,8 @@ def demux_fastq(file_to_fastq, result_folder, barcode_path):
         raise FileNotFoundError(f"Executable not found: {executable_path}")
 
     # Get min and max sequence length if user specified, otherwise use default
-    seq_min = 800 
-    seq_max = 5000
+    seq_min = 150 
+    seq_max = 10000
 
     # Use subprocess to run the executable
     prompt = f"{executable_path} -f {file_to_fastq} -d {result_folder} -b {barcode_path} -w 100 -r 100 -m {seq_min} -x {seq_max}"

{levseq-1.0.0 → levseq-1.0.2}/levseq/visualization.py

@@ -135,6 +135,19 @@ def _make_platemap(df, title, cmap=None):
 
     Called via `generate_platemaps`; see docs there.
     """
+    # Handle empty dataframe case
+    if df.empty:
+        # Create a dummy plot with a message
+        empty_df = pd.DataFrame({
+            'Row': list('ABCDEFGH'),
+            'Column': [str(i) for i in range(1, 13)],
+            'logseqdepth': [0] * 96,
+            'Mutations': [''] * 96,
+            'Alignment Count': [0] * 96,
+            'Alignment Probability': [0] * 96
+        })
+        df = empty_df
+
     # Convert SeqDepth to log for easier visualization.
     df["logseqdepth"] = np.log(
         df["Alignment Count"],
@@ -149,28 +162,30 @@ def _make_platemap(df, title, cmap=None):
     # Set some base opts
     opts = dict(invert_yaxis=True, title=title, show_legend=True)
 
-    # logseqdepth heatmap
-    seq_depth_cmap = list(reversed(cc.CET_D9))
-
-    # Set the center
-    center = np.log(10)
-
-    add_min = False
-    if df["logseqdepth"].min() >= center:
-        add_min = True
-
-    # Adjust if it is greater than max of data (avoids ValueError)
-    if df["logseqdepth"].max() <= center:
-        # Adjust the center
-        center = df["logseqdepth"].median()
-
-    # center colormap
-    if not add_min:
-        color_levels = ns.viz._center_colormap(df["logseqdepth"], center)
+    # Set the center and handle empty or zero-only data
+    if df["logseqdepth"].max() <= 0:
+        # For empty data, create minimal valid range
+        df["logseqdepth"] = 1  # Set to constant value
+        color_levels = [0.9, 1, 1.1]  # Create minimal valid range
+        seq_depth_cmap = ['#f7f7f7', '#f7f7f7']  # Use same color for uniform appearance
     else:
-        color_levels = ns.viz._center_colormap(
-            list(df["logseqdepth"]) + [np.log(1)], center
-        )
+        # Regular case with actual data
+        seq_depth_cmap = list(reversed(cc.CET_D9))
+        center = np.log(10)
+        add_min = False
+        
+        if df["logseqdepth"].min() >= center:
+            add_min = True
+
+        if df["logseqdepth"].max() <= center:
+            center = df["logseqdepth"].median()
+
+        if not add_min:
+            color_levels = ns.viz._center_colormap(df["logseqdepth"], center)
+        else:
+            color_levels = ns.viz._center_colormap(
+                list(df["logseqdepth"]) + [np.log(1)], center
+            )
 
     # Get heights
     n_rows = len(df["Row"].unique())
@@ -271,7 +286,9 @@ def _make_platemap(df, title, cmap=None):
 
     # Use in apply statement for residue labels
     def split_variant_labels(mutation_string):
-
+        if pd.isna(mutation_string) or mutation_string == '':
+            return ''
+            
         num_mutations = len(mutation_string.split("_"))
 
         if num_mutations > 4:
@@ -287,7 +304,7 @@ def _make_platemap(df, title, cmap=None):
 
     # Set the font size based on if #PARENT# is in a well and num of mutations
     max_num_mutations = _df["Labels"].apply(lambda x: len(x.split("\n"))).max()
-    has_parent = "#PARENT#" in _df["Labels"]
+    has_parent = "#PARENT#" in _df["Labels"].values
 
     if max_num_mutations > 3 or has_parent:
         label_fontsize = "8pt"
@@ -299,12 +316,14 @@ def _make_platemap(df, title, cmap=None):
         ["Column", "Row"],
         "Labels",
     ).opts(text_font_size=label_fontsize, **opts, text_color="#000000")
+    
     # return formatted final plot
     return (hm * boxes * labels).opts(
         frame_height=550, frame_width=550 * 3 // 2, border=50, show_legend=True
     )
 
 
+
 # Main function to return heatmap with or without alignment
 def generate_platemaps(
     max_combo_data,

{levseq-1.0.0 → levseq-1.0.2/levseq.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: levseq
-Version: 1.0.0
+Version: 1.0.2
 Home-page: https://github.com/fhalab/levseq/
 Author: Yueming Long, Emreay Gursoy, Ariane Mora
 Author-email: ylong@caltech.edu
@@ -54,7 +54,7 @@ Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore tech
 
 - Data to reproduce the results and to test are available on zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13694463.svg)](https://doi.org/10.5281/zenodo.13694463)
 
-- A dockerized website and database for labs to locally host and visualize their data: https://github.com/fhalab/LevSeq_VDB/
+- A dockerized website and database for labs to locally host and visualize their data: website is available at: https://levseq.caltech.edu/ and code to host locally at: https://github.com/fhalab/LevSeq_VDB/
 
 ## Setup
 
@@ -90,7 +90,7 @@ git clone https://github.com/fhalab/LevSeq.git
 ```
 
 ```
-conda create --name levseq python=3.8
+conda create --name levseq python=3.8 -y
 ```
 
 ```
@@ -100,7 +100,7 @@ conda activate levseq
 From the LevSeq folder, install the package using pip:
 
 ```
-pip install releases/levseq-0.1.0.tar.gz
+pip install levseq
 ```
 #### Dependencies 
 
@@ -116,15 +116,18 @@ conda install -c bioconda -c conda-forge minimap2
 ```
 or for mac users you can use: `brew install minimap2`
 Once dependencies are all installed, you can run LevSeq using command line.
-3. GCC
-For Mac M1 users: installation via homebrew
+3. GCC version 13 and 14 are both needed
+For Mac M chip users: installation via homebrew
 ```
-brew install gcc
+brew install gcc@14
+brew install gcc@13
 ```
 For Linux users: installation via conda 
 ```
-conda install conda-forge::gcc
+conda install conda-forge::gcc=14
+conda install conda-forge::gcc=13
 ```
+
 ### Usage
 #### Command Line Interface
 LevSeq can be run using the command line interface. Here's the basic structure of the command: