Bug fixes and improvements (#4)

* Change from minimap2 to winnowmap

- winnowmap performs better in repeat regions as shown in the paper https://doi.org/10.1093/bioinformatics/btaa435

* Add new error catch

* Add script to check if magnipore positions are within annotated regions

* add (0-based) information to readmes

* - changed default parameters for winnowmap
- fixed bug that doubled the read counts
- minor bug fixes

Author: JannesSP

README.md

@@ -31,14 +31,6 @@ mamba create -n magnipore -c jannessp magnipore
 conda activate magnipore
 ```
 
-*Alternatively you can create a conda environment using the [conda_env.yml](conda.recipe/conda_env.yml) and mamba.*
-```bash
-conda install mamba
-mamba env create -f conda/conda_env.yml
-conda activate magnipore
-git clone https://github.com/JannesSP/magnipore.git
-```
-
 If you want to basecall your ONT data you also need a Guppy version from [Oxford Nanopore Technologies](https://community.nanoporetech.com).
 
 ---
@@ -67,7 +59,7 @@ Conda Dependencies
 - matplotlib>=3.6.2
 - numpy>=1.23
 - scipy>=1.9
-- minimap2>=2.24
+- winnowmap>=2.0
 - pandas>=1.5
 - seaborn>=0.12
 - psutil>=5.9
@@ -173,7 +165,7 @@ The .magnipore file is a TSV containing the following columns.
 - bayesian_p : p-value for the signal comparison
 - signal_type : classification into "mod" for modification and "mut" for mutation
 - ref_1 : contig name of sample 1
-- pos_1 : position in contig of sample 1
+- pos_1 : position in contig of sample 1 (0-based)
 - base_1 : base at the position of sample 1
 - motif_1 : motif around the base at the position of sample 1
 - signal_mean_1 : mean of the signal distribution at the position of sample 1
@@ -205,31 +197,34 @@ Errors of first sample:
 - 119: Cannot basecall .slow5/.blow5 with guppy
 - 120: Could not find raw data or unknown file format
 - 121: Guppy basecalling failed
-- 122: minimap2 mapping failed
+- 122: mapping failed
 - 123: Samtools indexing failed
 - 124: f5c index failed
 - 125: f5c eventalign failed
 - 126: Could not find provided fastq files
+- 127: f5c eventalign file is empty
 ---
 Errors of second sample
 - 219: Cannot basecall .slow5/.blow5 with guppy
 - 220: Could not find raw data or unknown file format
 - 221: Guppy basecalling failed
-- 222: minimap2 mapping failed
+- 222: mapping failed
 - 223: Samtools indexing failed
 - 224: f5c index failed
 - 225: f5c eventalign failed
 - 226: Could not find provided fastq files
+- 227: f5c eventalign file is empty
 
 ### If Subscript Nanosherlock is Executed Separately
 
 The -e parameter of nanosherlock specifies the leading number of the error code. Default is 0.
 - 019: Cannot basecall .slow5/.blow5 with guppy
 - 020: Could not find raw data or unknown file format 
 - 021: Guppy basecalling failed
-- 022: minimap2 mapping failed
+- 022: mapping failed
 - 023: Samtools indexing failed
 - 024: f5c index failed
 - 025: f5c eventalign failed
 - 026: Could not find provided fastq files
+- 027: f5c eventalign file is empty
   </details>

README.rst

@@ -10,16 +10,6 @@ for **linux-64 and osx-64**.
    mamba create -n magnipore -c jannessp magnipore
    conda activate magnipore
 
-Alternatively you can create a conda environment using
-the `conda_env.yml <conda.recipe/conda_env.yml>`__ and mamba.
-
-.. code:: bash
-
-   conda install mamba
-   mamba env create -f conda/conda_env.yml
-   conda activate magnipore
-   git clone https://github.com/JannesSP/magnipore.git
-
 If you want to basecall your ONT data you also need a Guppy version from
 `Oxford Nanopore Technologies <https://community.nanoporetech.com>`__.
 
@@ -54,7 +44,7 @@ Conda Dependencies:
 - matplotlib>=3.6.2
 - numpy>=1.23
 - scipy>=1.9
-- minimap2>=2.24
+- winnowmap>=2.0
 - pandas>=1.5
 - seaborn>=0.12
 - psutil>=5.9
@@ -169,7 +159,7 @@ The .magnipore file is a TSV containing the following columns.
 -  signal_type : classification into “mod” for modification and “mut”
    for mutation
 -  ref_1 : contig name of sample 1
--  pos_1 : position in contig of sample 1
+-  pos_1 : position in contig of sample 1 (0-based)
 -  base_1 : base at the position of sample 1
 -  motif_1 : motif around the base at the position of sample 1
 -  signal_mean_1 : mean of the signal distribution at the position of
@@ -208,22 +198,24 @@ Error Codes Explanation
 -  119: Cannot basecall other .slow5/.blow5 with guppy
 -  120: Could not find raw data or unknown file format
 -  121: Guppy basecalling failed
--  122: minimap2 mapping failed
+-  122: mapping failed
 -  123: Samtools indexing failed
 -  124: f5c index failed
 -  125: f5c eventalign failed
 -  126: Could not find provided fastq files
+-  127: f5c eventalign file is empty
 
    Errors of second sample
 
 -  219: Cannot basecall other .slow5/.blow5 with guppy
 -  220: Could not find raw data or unknown file format
 -  221: Guppy basecalling failed
--  222: minimap2 mapping failed
+-  222: mapping failed
 -  223: Samtools indexing failed
 -  224: f5c index failed
 -  225: f5c eventalign failed
 -  226: Could not find provided fastq files
+-  227: f5c eventalign file is empty
 
 If Subscript Nanosherlock is Executed Separately
 ------------------------------------------------
@@ -234,8 +226,9 @@ error code. Default is 0.
 - 019: Cannot basecall other .slow5/.blow5 with guppy
 - 020: Could not find raw data or unknown file format
 - 021: Guppy basecalling failed
-- 022: minimap2 mapping failed
+- 022: mapping failed
 - 023: Samtools indexing failed
 - 024: f5c index failed
 - 025: f5c eventalign failed 
-- 026: Could not find provided fastq files
+- 026: Could not find provided fastq files
+- 027: f5c eventalign file is empty