methplotlib 0.20.1__tar.gz → 0.23.0__tar.gz

methplotlib-0.23.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Wouter De Coster
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

methplotlib-0.23.0/PKG-INFO

@@ -0,0 +1,117 @@
+Metadata-Version: 2.4
+Name: methplotlib
+Version: 0.23.0
+Summary: Plot nucleotide modification data from nanopore sequencing
+Home-page: https://github.com/wdecoster/methplotlib
+Author: Wouter De Coster
+Author-email: decosterwouter@gmail.com
+License: MIT
+Keywords: nanopore methylation modification
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: plotly>=4.9.0
+Requires-Dist: numpy>=1.16.5
+Requires-Dist: pandas>=0.23.4
+Requires-Dist: pyranges>=0.0.77
+Requires-Dist: fisher>=0.1.9
+Requires-Dist: scikit-learn
+Requires-Dist: pyfaidx
+Requires-Dist: biopython
+Requires-Dist: pysam
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/methplotlib/badges/version.svg)](https://anaconda.org/bioconda/methplotlib)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/methplotlib/badges/license.svg)](https://anaconda.org/bioconda/methplotlib)
+
+# METHPLOTLIB
+
+This script generates a browser view on a window using data from  
+i) [nanopolish](https://github.com/jts/nanopolish), either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py). The methylation calls can additionally be phased using scripts/annotate_calls_by_phase.py and scripts/split_calls_by_phase.py  
+ii) [nanocompore](https://github.com/tleonardi/nanocompore)  
+iii) in ont-cram format with MM/ML tags according to the SAM specifications  
+iv) in bedgraph format, with 4 columns (chromosome, start, end, value) or the 5 columns written by `modkit pileup --bedgraph`  
+v) in bedMethyl format, as written by [modkit](https://github.com/nanoporetech/modkit) `pileup` (18 columns, with or without `--only-tabs`) or by `modbam2bed --extended` (14 columns). Files containing multiple modifications (e.g. 5mC and 5hmC) do not have to be split up: each modification gets its own track, and `--mods` can be used to restrict to some of them  
+
+## INSTALLATION
+
+Creating a new conda environment:  
+`conda create -n methplotlib methplotlib`
+
+Or using pip:  
+`pip install methplotlib`
+
+
+
+## USAGE
+```
+methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES
+                   [NAMES ...] -w WINDOW [-g GTF] [-b BED] [-f FASTA]
+                   [--simplify] [--split] [--static STATIC] [--smooth SMOOTH]
+                   [--dotsize DOTSIZE] [--example] [-o OUTFILE] [-q QCFILE]
+
+plotting nanopolish methylation calls or frequency
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -v, --version         Print version and exit.
+  -m, --methylation METHYLATION [METHYLATION ...]
+                        data in nanopolish, nanocompore, ont-cram or bedgraph
+                        format
+  -n, --names NAMES [NAMES ...]
+                        names of datasets in --methylation
+  -w, --window WINDOW   window (region) to which the visualisation has to be restricted
+  -g, --gtf GTF         add annotation based on a gtf file
+  -b, --bed BED         add annotation based on a bed file
+  -f, --fasta FASTA     required when --window is an entire chromosome, contig or transcript
+  --simplify            simplify annotation track to show genes rather than transcripts
+  --split               split, rather than overlay the methylation tracks
+  --static              Make a static image of the browser window (filename)
+  --binary              Make the nanopolish plot ignorning log likelihood nuances
+  --smooth              Rolling window size for averaging frequency values (int)
+  --dotsize             Control the size of dots in the per read plots (int)
+  --example             Show example command and exit.
+  -o, --outfile OUTFILE File to write results to. Default:
+                        methylation_browser_{chr}_{start}_{end}.html. Use
+                        {region} as a shorthand for {chr}_{start}_{end} in the
+                        filename. Missing paths will be created.
+  -q, --qcfile QCFILE   File to write the qc report to. Default: The path in
+                        outfile prefixed with qc_, default is qc_report_methyl
+                        ation_browser_{chr}_{start}_{end}.html. Use {region}
+                        as a shorthand for {chr}_{start}_{end} in the
+                        filename. Missing paths will be created.
+
+```
+
+## Snakemake workflow
+For streamlining nanopolish a Snakefile is included (using snakemake). The workflow uses a config file, of which an example is in this repository.
+
+## Example data
+The `examples` folder contains calls and frequencies for the human ACTB gene from PromethION sequencing of NA19240. An example command is available.
+
+## Companion scripts
+The `scripts` folder contains scripts for phasing modification calls in haplotypes based on [WhatsHap](https://whatshap.readthedocs.io/en/latest/) phasing, allele specific modification testing for phased data and differential modification testing across subjects.
+
+## TO DO - CONTRIBUTIONS WELCOME
+- Outlier detection (in windows) across samples

{methplotlib-0.20.1 → methplotlib-0.23.0}/README.md

@@ -1,19 +1,25 @@
-[![Build Status](https://travis-ci.com/wdecoster/methplotlib.svg?branch=master)](https://travis-ci.com/wdecoster/methplotlib)
-[![Anaconda-Server Badge](https://anaconda.org/bioconda/methplotlib/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)
 [![Anaconda-Server Badge](https://anaconda.org/bioconda/methplotlib/badges/version.svg)](https://anaconda.org/bioconda/methplotlib)
 [![Anaconda-Server Badge](https://anaconda.org/bioconda/methplotlib/badges/license.svg)](https://anaconda.org/bioconda/methplotlib)
 
 # METHPLOTLIB
 
 This script generates a browser view on a window using data from  
-i) [nanopolish](https://github.com/jts/nanopolish), either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py). The methylation calls can additionally be phased using scripts/annotate_calls_by_phase.and scripts/split_calls_by_phase.py  
+i) [nanopolish](https://github.com/jts/nanopolish), either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py). The methylation calls can additionally be phased using scripts/annotate_calls_by_phase.py and scripts/split_calls_by_phase.py  
 ii) [nanocompore](https://github.com/tleonardi/nanocompore)  
-iii) in ont-cram format with MM/MP tags according to the SAM specifications and converted using e.g. [this script](https://github.com/kpalin/gcf52ref/blob/f5_to_usam/scripts/extract_methylation_fast5_to_sam.py)  
-iv) in bedgraph format  
+iii) in ont-cram format with MM/ML tags according to the SAM specifications  
+iv) in bedgraph format, with 4 columns (chromosome, start, end, value) or the 5 columns written by `modkit pileup --bedgraph`  
+v) in bedMethyl format, as written by [modkit](https://github.com/nanoporetech/modkit) `pileup` (18 columns, with or without `--only-tabs`) or by `modbam2bed --extended` (14 columns). Files containing multiple modifications (e.g. 5mC and 5hmC) do not have to be split up: each modification gets its own track, and `--mods` can be used to restrict to some of them  
 
 ## INSTALLATION
+
+Creating a new conda environment:  
+`conda create -n methplotlib methplotlib`
+
+Or using pip:  
 `pip install methplotlib`
 
+
+
 ## USAGE
 ```
 methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES

{methplotlib-0.20.1 → methplotlib-0.23.0}/methplotlib/annotation.py

@@ -31,11 +31,14 @@ def good_record(line, chromosome):
     """
     Filtering on the gtf lines
     by checking for right chromosome and right feature type
+
+    The chromosome has to match the entire field, as a prefix match would
+    e.g. also accept chr10 up to chr19 and chr1_KI270706v1_random for chr1
     """
-    if line.startswith(str(chromosome)) and line.split("\t")[2] in ["exon", "gene"]:
-        return True
-    else:
+    if line.startswith("#"):
         return False
+    fields = line.split("\t")
+    return len(fields) > 2 and fields[0] == str(chromosome) and fields[2] in ["exon", "gene"]
 
 
 def get_features(gtfline, type="gtf"):
@@ -54,8 +57,10 @@ def parse_attributes(attributes, type="gtf"):
     """
     attribute_delimiter = {"gtf": "; ", "gff": ";"}
     kv_delimiter = {"gtf": " ", "gff": "="}
+    # the last attribute of a record keeps the trailing delimiter,
+    # which would otherwise end up in the name shown when hovering
     info = {
-        i.split(kv_delimiter[type])[0]: i.split(kv_delimiter[type])[1].replace('"', "")
+        i.split(kv_delimiter[type])[0]: i.split(kv_delimiter[type])[1].replace('"', "").rstrip(";")
         for i in attributes.split(attribute_delimiter[type])
         if i.startswith(("gene_name", "transcript_id", "locus_tag"))
     }
@@ -67,17 +72,19 @@ def parse_attributes(attributes, type="gtf"):
 
 def transcripts_in_window(df, window, feature="transcript"):
     """
-    Return the transcript names for which
-    either the end or the begin of an exon is within the window
+    Return the transcript names of the exons overlapping the window
+
+    Testing for overlap rather than for a begin or end within the window,
+    as otherwise a feature spanning the entire window would be missed
     """
     return df.loc[
-        df["begin"].between(window.begin, window.end) | df["end"].between(window.begin, window.end),
+        (df["begin"] <= window.end) & (df["end"] >= window.begin),
         feature,
     ].unique()
 
 
 def assign_colors_to_genes(transcripts):
-    genes = set([t.gene for t in transcripts])
+    genes = dict.fromkeys([t.gene for t in transcripts])
     colordict = {g: c for g, c in zip(genes, plcolors * 100)}
     for t in transcripts:
         t.color = colordict[t.gene]
@@ -90,12 +97,24 @@ def parse_annotation(gtff, window, simplify=False):
     """
     type = annot_file_sniffer(gtff)
     logging.info(f"Parsing {type} file...")
+    chromosomes_seen = set()
+    records = []
+    for line in open_gtf(gtff):
+        if good_record(line, window.chromosome):
+            records.append(get_features(line, type=type))
+        elif line.strip() and not line.startswith("#"):
+            chromosomes_seen.add(line.split("\t")[0])
+    if not records and chromosomes_seen:
+        sys.stderr.write(
+            f"\nWARNING: no exons or genes of chromosome '{window.chromosome}' "
+            f"in {gtff}.\n"
+            f"The annotation contains {len(chromosomes_seen)} chromosomes, "
+            f"such as {', '.join(sorted(chromosomes_seen)[:5])}.\n"
+            "Do the chromosome names in --window match those in your annotation "
+            "(e.g. '15' versus 'chr15')?\n"
+        )
     df = pd.DataFrame(
-        data=[
-            get_features(line, type=type)
-            for line in open_gtf(gtff)
-            if good_record(line, window.chromosome)
-        ],
+        data=records,
         columns=["chromosome", "begin", "end", "strand", "gene", "transcript"],
     )
     logging.info("Loaded GTF file, processing...")