Merge pull request #3 from genotoul-bioinfo/dev

Fix final bins output format and add usage in README

README.md

@@ -98,6 +98,62 @@ singularity exec binette.sif binette -h
 
 # Usage 
 
+## Input Formats
+
+Binette supports two input formats for bin sets: 
+
+1. **Contig2bin Tables:** You can provide bin sets using contig2bin tables, which establish the relationship between each contig and its corresponding bin. In this format, you need to specify the `--contig2bin_tables` argument. 
+
+For example, consider the following two `contig2bin_tables`:
+
+- `bin_set1.tsv`:
+
+    ```tsv
+    contig_1   binA
+    contig_8   binA
+    contig_15  binB
+    contig_9   binC
+    ```
+    
+- `bin_set2.tsv`:
+
+    ```tsv
+    contig_1   bin.0
+    contig_8   bin.0
+    contig_15  bin.1
+    contig_9   bin.2
+    contig_10  bin.0
+    ```
+    
+    The `binette` command to process this input would be:
+    
+    ```bash
+    binette --contig2bin_tables bin_set1.tsv bin_set2.tsv --contigs assembly.fasta
+    ```
+
+2. **Bin Directories:** Alternatively, you can use bin directories, where each bin is represented by a separate FASTA file. For this format, you need to provide the `--bin_dirs` argument. Here's an example of two bin directories:
+
+    ```
+    bin_set1/
+    ├── binA.fa: contains sequences of contig_1, contig_8
+    ├── binB.fa: contains sequences of contig_15
+    └── binC.fa: contains sequences of contig_9
+    ```
+    
+    ```
+    bin_set2/
+    ├── binA.fa: contains sequences of contig_1, contig_8, contig_10
+    ├── binB.fa: contains sequences of contig_15
+    └── binC.fa: contains sequences of contig_9
+    ```
+    
+    The `binette` command to process this input would be:
+    
+    ```bash
+    binette --bin_dirs bin_set1 bin_set2 --contigs assembly.fasta
+    ```
+
+In both formats, the `--contigs` argument should specify a FASTA file containing all the contigs found in the bins. Typically, this file would be the assembly FASTA file used to generate the bins. In these exemple the `assembly.fasta` file should contain at least the five contigs mentioned in the `contig2bin_tables` files or in the bin fasta files: `contig_1`, `contig_8`, `contig_15`, `contig_9`, and `contig_10`.
 
 
 # Bug reporting and feature requests
@@ -109,3 +165,4 @@ Please submit bug reports and feature requests to the issue tracker:
 # Licence
 
 This program is released as an open source software under the terms of [MIT License](https://forgemia.inra.fr/jean.mainguy/binette/-/raw/main/LICENSE).
+

binette/bin_quality.py

@@ -154,12 +154,12 @@ def add_bin_metrics(bins, contig_info, contamination_weight, threads=1):
     contig_to_length = contig_info["contig_to_length"]
 
     logging.info("Assess bin length and N50")
-    bin_and_contigsize_args = ((bin, contig_to_length) for bin in bins)
+    # bin_and_contigsize_args = ((bin, contig_to_length) for bin in bins)
 
-    with Pool(processes=threads) as pool:
-        pool.starmap(get_bin_size_and_N50, bin_and_contigsize_args)
+    # with Pool(processes=threads) as pool:
+    #     pool.starmap(get_bin_size_and_N50, bin_and_contigsize_args)
 
-    # add_bin_size_and_N50(bins, contig_to_length)
+    add_bin_size_and_N50(bins, contig_to_length)
 
     logging.info("Asses bin quality")
     assess_bins_quality_by_chunk(

binette/cds.py

@@ -62,10 +62,10 @@ def get_contig_cds_metadata_flat(contig_to_genes):
 
     contig_to_cds_count = {contig: len(genes) for contig, genes in contig_to_genes.items()}
 
-    contig_to_aa_counter = {contig: get_aa_composition(genes) for contig, genes in tqdm(contig_to_genes.items())}
+    contig_to_aa_counter = {contig: get_aa_composition(genes) for contig, genes in tqdm(contig_to_genes.items(), unit="contig")}
     logging.info("contig_to_aa_counter done. ")
 
-    contig_to_aa_length = {contig: sum(counter.values()) for contig, counter in contig_to_aa_counter.items()}
+    contig_to_aa_length = {contig: sum(counter.values()) for contig, counter in tqdm(contig_to_aa_counter.items(), unit="contig")}
     logging.info("contig_to_aa_length done. ")
 
     return contig_to_cds_count, contig_to_aa_counter, contig_to_aa_length
@@ -81,12 +81,12 @@ def get_contig_cds_metadata(contig_to_genes, threads):
         for contig, genes in tqdm(contig_to_genes.items()):
             contig_to_future[contig] = tpe.submit(get_aa_composition, genes)
 
-    contig_to_aa_counter = {contig: future.result() for contig, future in tqdm(contig_to_future.items())}
+    contig_to_aa_counter = {contig: future.result() for contig, future in tqdm(contig_to_future.items(), unit="contig")}
 
     # contig_to_aa_counter = {contig:get_aa_composition(genes) for contig, genes in tqdm(contig_to_genes.items())}
     logging.info("contig_to_aa_counter done. ")
 
-    contig_to_aa_length = {contig: sum(counter.values()) for contig, counter in contig_to_aa_counter.items()}
+    contig_to_aa_length = {contig: sum(counter.values()) for contig, counter in  tqdm(contig_to_aa_counter.items(), unit="contig")}
     logging.info("contig_to_aa_length done. ")
 
     return contig_to_cds_count, contig_to_aa_counter, contig_to_aa_length

setup.py

@@ -11,7 +11,7 @@
 
     setup(
         name="binette",
-        version="0.1.4",
+        version="0.1.5",
         author="Jean Mainguy",
         packages=find_packages(),
         entry_points={"console_scripts": ["binette = binette.binette:main"]},