Merge branch 'master' into dev

.gitattributes

@@ -1 +1,3 @@
-/src/meta_tran_sim/data/* filter=lfs diff=lfs merge=lfs -text
+src/marbel/data/deduplicated_pangenome_EDGAR_Microbiome_JLAB2.fas.bgz filter=lfs diff=lfs merge=lfs -text
+src/marbel/data/deduplicated_pangenome_EDGAR_Microbiome_JLAB2.fas.bgz.bio_index filter=lfs diff=lfs merge=lfs -text
+src/marbel/data/orthologues_processed_combined_all.parquet filter=lfs diff=lfs merge=lfs -text

README.md

@@ -1,4 +1,4 @@
-# meta_tran_sim_dev (Meta Transcriptomic Simulation)
+# marbel (MetAtranscriptomic Reference Builder Evaluation Library)
 
 This project generates an in silico metatranscriptomic dataset based on specified parameters.
 
@@ -35,7 +35,7 @@ BiocManager::install("polyester")
 
 ```
 
-Install the package: 
+Install the package:
 
 ```
 pip install -e .
@@ -46,36 +46,41 @@ pip install -e .
 To get help on how to use the script, run:
 
 ```sh
-meta-tran-sim --help
+marbel --help
 ```
 
 ### Command Line Arguments
 
 ```
-Usage: meta-tran-sim [OPTIONS] [N_SPECIES] [N_ORTHOGROUPS] [N_SAMPLES]...
-
-Arguments:
-  n_species         [N_SPECIES]      Number of species to be drawn for the metatranscriptomic in silico dataset [default: 20]
-  n_orthogroups     [N_ORTHOGROUPS]  Number of orthologous groups to be drawn for the metatranscriptomic in silico dataset [default: 1000]
-  n_samples          [N_SAMPLES]...    Number of samples to be created for the metatranscriptomic in silico dataset. The first number is the number of samples for group 1 and
-                                     the second number is the number of samples for group 2 [default: 10, 10]
+Usage: marbel [OPTIONS] 
 Options:
-  --version                        Show the version and exit.
-  --help                           Show this message and exit.
+ --n-species                 INTEGER                 Number of species to be drawn for the metatranscriptomic in silico dataset [default: 20]
+ --n-orthogroups             INTEGER                 Number of orthologous groups to be drawn for the metatranscriptomic in silico dataset [default: 1000]
+ --n-samples                 <INTEGER INTEGER>...    Number of samples to be created for the metatranscriptomic in silico datasetthe first number is the number of samples for group 1 and the second is the number of samples for group 2 [default: 10, 10]  
+  --outdir                   TEXT    Output directory for the metatranscriptomic in silico dataset [default: simulated_reads]
+  --max-phylo-distance        TEXT    Maximum mean phylogenetic distance for orthologous groups. Specify stricter limit to avoid groups with a more diverse phylogenetic distance. [default: None]
+  --min-identity              FLOAT   Minimum mean sequence identity score for orthologous groups. Specify for more stringent identity requirements. [default: None]
+  --deg-ratio                <FLOAT FLOAT>... Ratio of up- and down-regulated genes. The first value is the ratio of up-regulated genes, the second represents the ratio of down-regulated genes [default: 0.1, 0.1]
+  --seed                      INTEGER Seed for sampling. Set for reproducibility [default: None]
+  --read-length               INTEGER Read length for the generated reads [default: 100]
+  --output-format             [fastq.gz|fastq|fasta] Output format for the reads [default: fastq.gz]
+  --version                           Show the version and exit.
+  --help                              Show this message and exit.
+
 ```
 
 ## Examples
 
 ### Running with Default Parameters
 
 ```sh
-meta-tran-sim
+marbel
 ```
 
 ### Specifying Number of Species, Orthogroups, and Samples
 
 ```sh
-meta-tran-sim --n-species 30 --n-orthogroups 1500 --n-samples 15 20
+marbel --n-species 30 --n-orthogroups 1500 --n-samples 15 20
 ```
 
 This command will generate a dataset with:

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-requirements-txt"]
 build-backend = "hatchling.build"
 
 [project]
-name = "meta_tran_sim"
+name = "marbel"
 version = "0.0.1"
 authors = [
   { name="Timo Wentong Lin", email="ge2317@uni-giessen.de" },
@@ -26,18 +26,18 @@ dynamic = ["dependencies"]
 "Bug Tracker" = "https://github.com/jlab/meta_tran_sim_dev/issues" 
 
 [project.scripts]
-meta-tran-sim = "meta_tran_sim.meta_tran_sim:main"
+marbel= "marbel.meta_tran_sim:app"
 
 [tool.hatch.metadata.hooks.requirements_txt]
 files = ["requirements.txt"]
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/meta_tran_sim"]
+packages = ["src/marbel"]
 
 [tool.hatch.build]
 include = [
-    "src/meta_tran_sim/data/deduplicated_pangenome_EDGAR_Microbiome_JLAB2.fas.bgz",
-    "src/meta_tran_sim/data/deduplicated_pangenome_EDGAR_Microbiome_JLAB2.fas.bgz.bio_index",
-    "src/meta_tran_sim/data/orthologues_processed_combined_all.parquet",
-    "src/meta_tran_sim/data/EDGAR_all_species.newick",
+    "src/marbel/data/deduplicated_pangenome_EDGAR_Microbiome_JLAB2.fas.bgz",
+    "src/marbel/data/deduplicated_pangenome_EDGAR_Microbiome_JLAB2.fas.bgz.bio_index",
+    "src/marbel/data/orthologues_processed_combined_all.parquet",
+    "src/marbel/data/EDGAR_all_species.newick",
 ]