update citation; crash on empty bed file

docs/index.md

@@ -3,7 +3,7 @@
 [![PyPIDownloads](https://pepy.tech/badge/scbs)](https://pepy.tech/project/methscan)
 [![GitHub](https://img.shields.io/github/v/tag/anders-biostat/MethSCAn?logo=github)](https://github.com/anders-biostat/MethSCAn)
 
-a command line tool for **S**ingle-**C**ell **An**alysis of **Meth**ylation data
+a command line tool for **S**ingle-**C**ell **An**alysis of **Meth**ylation data.
 
 ## Installation
 
@@ -48,15 +48,17 @@ Lastly, you can also select two cell populations and identify differentially met
 You can find a list of the available `methscan` commands [here](commands.html).
 
 
-## bioRxiv preprint
+## Publication / Citation
 
-For a detailed explanation of the methods implemented in *MethSCAn*, please check our bioRxiv preprint.
-Note that this package was formerly known as ['scbs'](https://github.com/LKremer/scbs) and later renamed to *MethSCAn*.
+For a detailed explanation of the methods implemented in *MethSCAn*, please check out our open access article in Nature Methods:
 
 *Analyzing single-cell bisulfite sequencing data with MethSCAn*  
-Lukas PM Kremer, Martina Braun, Svetlana Ovchinnikova, Leonie Kuechenhoff, Santiago Cerrizuela, Ana Martin-Villalba, Simon Anders  
-bioRxiv 2022.06.15.496318; doi: [https://doi.org/10.1101/2022.06.15.496318](https://doi.org/10.1101/2022.06.15.496318)
+Lukas PM Kremer, Martina Braun, Svetlana Ovchinnikova, Leonie Kuechenhoff, Santiago Cerrizuela, Ana Martin-Villalba, Simon Anders.  
+Nature Methods, 2024
+doi: [https://doi.org/10.1038/s41592-024-02347-x](https://doi.org/10.1038/s41592-024-02347-x)
 
+Please cite this article if you used MethSCAn in your research.  
+Note that this package was formerly known as ['scbs'](https://github.com/LKremer/scbs) and later renamed to *MethSCAn*.
 
 ## Hardware requirements
 

methscan/cli.py

@@ -86,50 +86,48 @@ def _set_n_threads(ctx, param, value):
     help_options_color="green",
     help=f"""
 \b
- __  __      _   _     ____   ____    _           \b
-|  \/  | ___| |_| |__ / ___| / ___|  / \   _ __  
-| |\/| |/ _ \ __| '_ \\\\___ \| |     / _ \ | '_ \  \b
-| |  | |  __/ |_| | | |___) | |___ / ___ \| | | |
-|_|  |_|\___|\__|_| |_|____/ \____/_/   \_\_| |_| {VERSION_STR}
+ __  __      _   _     ____   ____    _  \b
+|  \\/  | ___| |_| |__ / ___| / ___|  / \\   _ __
+| |\\/| |/ _ \\ __| '_ \\\\___ \\| |     / _ \\ | '_ \\  \b
+| |  | |  __/ |_| | | |___) | |___ / ___ \\| | | |
+|_|  |_|\\___|\\__|_| |_|____/ \\____/_/   \\_\\_| |_| {VERSION_STR}
 
 
-    Below you find a list of all available commands.
+  Below you find a list of all available commands.
 To find out what they do and how to use them, check their help like this:
 
-    {style("methscan [command] --help", fg="blue")}
+  {style("methscan [command] --help", fg="blue")}
 
-    To use stdin or stdout, use the dash character
-{style("-", fg="blue")} instead of a file path.
-    """,
+\b
+  For documentation and a usage tutorial, go to 
+  {style("https://anders-biostat.github.io/MethSCAn/", fg="blue")}.""",
 )
 @click.version_option(version=__version__)
 @click.version_option(
     "cite",
     "--cite",
     help="Show publication reference and exit.",
     message=(
-        """If you used MethSCAn in your research, please cite:
+        f"""If you used MethSCAn in your research, please cite:
 
-Analyzing single-cell bisulfite sequencing data with MethSCAn
+{style("Analyzing single-cell bisulfite sequencing data with MethSCAn",
+       fg="bright_white", bold=True)}
 Lukas PM Kremer, Martina M Braun, Svetlana Ovchinnikova, Leonie Küchenhoff, """
-        """Santiago Cerrizuela, Ana Martin-Villalba, Simon Anders
-bioRxiv, 2022
-
-doi / link: https://doi.org/10.1101/2022.06.15.496318
-
+        f"""Santiago Cerrizuela, Ana Martin-Villalba, Simon Anders
+Nature Methods, 2024
+doi: {style("https://doi.org/10.1038/s41592-024-02347-x", fg="blue")}
+"""
+"""
 BibTeX entry:
-
 @article{kremer2024,
   title={Analyzing single-cell bisulfite sequencing data with {MethSCAn}},
   author={Kremer, Lukas PM and Braun, Martina M and Ovchinnikova, Svetlana and """
         """K{\"u}chenhoff, Leonie and Cerrizuela, Santiago and """
         """Martin-Villalba, Ana and Anders, Simon},
-  journal={bioRxiv},
-  year={2022},
-  doi = {10.1101/2022.06.15.496318},
-  publisher={Cold Spring Harbor Laboratory}
-}
-"""
+  journal={Nature Methods},
+  year={2024},
+  doi={10.1038/s41592-024-02347-x}
+}"""
     ),
 )
 def cli():

methscan/utils.py

@@ -32,11 +32,13 @@ def _get_filepath(f):
 def _iter_bed(file_obj, strand_col_i=None, keep_cols=False):
     is_rev_strand = False
     other_columns = False
+    is_empty = True
     if strand_col_i is not None:
         strand_col_i -= 1  # CLI is 1-indexed
     for line in file_obj:
         if line.startswith("#") or not line.strip():
             continue  # skip comments
+        is_empty = False
         values = line.strip().split("\t")
         if strand_col_i is not None:
             strand_val = values[strand_col_i]
@@ -53,6 +55,8 @@ def _iter_bed(file_obj, strand_col_i=None, keep_cols=False):
             other_columns = values[3:]
         # yield chrom, start, end, and whether the feature is on the minus strand
         yield values[0], int(values[1]), int(values[2]), is_rev_strand, other_columns
+    if is_empty:
+        raise Exception("The BED file you have provided is empty.")
 
 
 def _parse_cell_names(data_dir):