added documentation

SVTools.py

@@ -1,4 +1,5 @@
 class SVariant:
+    """Class representing structural variant."""
     def __init__(self, tool, line=None, chrom=None, pos=None, id=None, ref=None, end=None, gt=None, svlen=None, svtype=None, cipos1=None, cipos2=None, ciend1=None, ciend2=None, algorithms=None):
         self.tool = tool
         if(line is not None):
@@ -19,6 +20,11 @@ def __init__(self, tool, line=None, chrom=None, pos=None, id=None, ref=None, end
             self.used = False
             self.algorithms = algorithms
     def printVcfLine(self):
+        """Creates a line for the entry in VCF file for particular SV.
+
+        Returns:
+            str: Line entry for VCF file.
+        """
         sv_len = self.svlen
         end = self.end
         if(self.svtype == "INS" or self.svtype == "DUP"):
@@ -28,6 +34,11 @@ def printVcfLine(self):
         return '\t'.join((self.chrom, str(self.pos), self.id, self.ref, "<"+self.svtype+">",
                  ".", "PASS", "END="+str(end)+";SVLEN="+str(sv_len)+";SVTYPE="+self.svtype+";ALGORITHM="+self.algorithms+";CIPOS="+str(self.cipos1)+","+str(self.cipos2)+";CIEND="+str(self.ciend1)+","+str(self.ciend2), "GT", self.gt, "\n"))
     def parse_line(self, line):
+        """Parses a line from VCF file, and uses that information for the SVariant initialisation.
+
+        Args:
+            line (str): Line from the VCF file.
+        """
         values = line.split("\t")
         self.chrom = values[0]
         self.pos = int(values[1])
@@ -64,6 +75,14 @@ def parse_line(self, line):
 
         self.used = False
     def parse_type(self, svtype):
+        """Parses type of the SV.
+
+        Args:
+            svtype (str): Type from the INFO field.
+
+        Returns:
+            _type_: Uniform type of SV.
+        """
         if "del" in svtype.casefold():
             return "DEL"
         if "inv" in svtype.casefold():
@@ -78,8 +97,17 @@ def parse_type(self, svtype):
             return "CNV"
         return "UNK"
     def print_sv(self):
+        """Print the SV in the console. Used mostly for debugging."""
         print(self.svtype + ": " + self.chrom + " " + str(self.pos) + "(" + str(self.cipos1) +", " + str(self.cipos2) + ")" + " - " + str(self.end) + "(" + str(self.cipos1) +", " + str(self.cipos2) + ")" + " LEN: " + str(self.svlen) + " GT: " + self.gt)
     def checkOverlap(self, sv2):
+        """Checks overlap between SVariants.
+
+        Args:
+            sv2 (SVariant): Variant to overlap.
+
+        Returns:
+            bool: Information whether the variants overlap or not.
+        """
         if(self.chrom != sv2.chrom):
             return False
         # bear in mind that cipos first coord is negative, hence just addition (example cipos=-10,10)
@@ -104,11 +132,18 @@ def checkOverlap(self, sv2):
         return False
 
 class SVTool:
+    """Class for storing the SV callers."""
     max_conf = 200 # max confidence interval length
+    """Maximum confidence interval."""
     def __init__(self, filename):
         self.tool = filename.split("/")[-1].split(".")[0]
         self.parse_file(filename)
     def parse_file(self, filename):
+        """Function for parsing the VCF file.
+
+        Args:
+            filename (str): Name of the VCF file for particular tool.
+        """
         self.sv_list = list()
         with open(filename) as file:
             for line in file:

charles_filter_n.py

@@ -1,32 +1,41 @@
+"""Script for generating accuracy metrics between the gold set and the SVs created by ConsensuSV."""
+
 import re
 import argparse
 import os
-
 from subprocess import Popen, PIPE
-parser = argparse.ArgumentParser(description='Extracts sample.')
 
+parser = argparse.ArgumentParser(description='Extracts sample.')
+"""Parser for the arguments to the script."""
 parser.add_argument('-s', '--samples', help='Samples name to compare (comma-separated).', required=True)
 parser.add_argument('-o', '--outputs', help='Our files (generated by consensuSV, comma-separated).', required=True)
 
 args = parser.parse_args()
+"""Arguments to the script."""
 
 
 
 our_callers = set(['lumpy', 'VH', 'wham', 'Manta', 'Delly']) # + cnvnator, breakseq, breakdancer
+"""Callers used in gold set & our tool (intersection)."""
+
 samples = args.samples.split(',')
-outputs = args.outputs.split(',')
+"""Samples to compare."""
 
+outputs = args.outputs.split(',')
+"""Output files from ConsensuSV."""
 if os.path.exists('charles_pass'):
     os.remove('charles_pass')
 if os.path.exists('charles_pass'):
     os.remove('charles_pass')
 
 i = 0
+"""Iterator"""
 for sample in samples:
     open('charles_pass','w').writelines([ line for line in open('ALL_Illumina_Integrate_20170206.vcf') if 'PASS' in line or '#' in line])
     open('charles_pass2','w').writelines([ line for line in open('charles_pass') if sample in line or '#' in line])
 
     full_text = ""
+    """Full text from gold set."""
     with open('charles_pass2', 'r') as f:
         for line in f:
             if not('#' in line):

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/build/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 282ead6f489089e892512bba2a5c5ccd
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_sources/autoapi/SVTools/index.rst.txt

@@ -0,0 +1,87 @@
+:py:mod:`SVTools`
+=================
+
+.. py:module:: SVTools
+
+
+Module Contents
+---------------
+
+Classes
+~~~~~~~
+
+.. autoapisummary::
+
+   SVTools.SVariant
+   SVTools.SVTool
+
+
+
+
+.. py:class:: SVariant(tool, line=None, chrom=None, pos=None, id=None, ref=None, end=None, gt=None, svlen=None, svtype=None, cipos1=None, cipos2=None, ciend1=None, ciend2=None, algorithms=None)
+
+   Class representing structural variant.
+
+   .. py:method:: printVcfLine(self)
+
+      Creates a line for the entry in VCF file for particular SV.
+
+      Returns:
+          str: Line entry for VCF file.
+
+
+   .. py:method:: parse_line(self, line)
+
+      Parses a line from VCF file, and uses that information for the SVariant initialisation.
+
+      Args:
+          line (str): Line from the VCF file.
+
+
+   .. py:method:: parse_type(self, svtype)
+
+      Parses type of the SV.
+
+      Args:
+          svtype (str): Type from the INFO field.
+
+      Returns:
+          _type_: Uniform type of SV.
+
+
+   .. py:method:: print_sv(self)
+
+      Print the SV in the console. Used mostly for debugging.
+
+
+   .. py:method:: checkOverlap(self, sv2)
+
+      Checks overlap between SVariants.
+
+      Args:
+          sv2 (SVariant): Variant to overlap.
+
+      Returns:
+          bool: Information whether the variants overlap or not.
+
+
+
+.. py:class:: SVTool(filename)
+
+   Class for storing the SV callers.
+
+   .. py:attribute:: max_conf
+      :annotation: = 200
+
+      Maximum confidence interval.
+
+
+   .. py:method:: parse_file(self, filename)
+
+      Function for parsing the VCF file.
+
+      Args:
+          filename (str): Name of the VCF file for particular tool.
+
+
+

docs/build/html/_sources/autoapi/charles_filter_n/index.rst.txt

@@ -0,0 +1,56 @@
+:py:mod:`charles_filter_n`
+==========================
+
+.. py:module:: charles_filter_n
+
+.. autoapi-nested-parse::
+
+   Script for generating accuracy metrics between the gold set and the SVs created by ConsensuSV.
+
+
+
+Module Contents
+---------------
+
+.. py:data:: parser
+   
+
+   Parser for the arguments to the script.
+
+
+.. py:data:: args
+   
+
+   Arguments to the script.
+
+
+.. py:data:: our_callers
+   
+
+   Callers used in gold set & our tool (intersection).
+
+
+.. py:data:: samples
+   
+
+   Samples to compare.
+
+
+.. py:data:: outputs
+   
+
+   Output files from ConsensuSV.
+
+
+.. py:data:: i
+   :annotation: = 0
+
+   Iterator
+
+
+.. py:data:: full_text
+   :annotation: = 
+
+   Full text from gold set.
+
+

docs/build/html/_sources/autoapi/conf/index.rst.txt

@@ -0,0 +1,59 @@
+:py:mod:`conf`
+==============
+
+.. py:module:: conf
+
+
+Module Contents
+---------------
+
+.. py:data:: project
+   :annotation: = ConsensuSV-core
+
+
+
+.. py:data:: copyright
+   :annotation: = 2022, Mateusz Chiliński, Dariusz Plewczyński
+
+
+
+.. py:data:: author
+   :annotation: = Mateusz Chiliński, Dariusz Plewczyński
+
+
+
+.. py:data:: release
+   :annotation: = 1.7
+
+
+
+.. py:data:: extensions
+   :annotation: = ['autoapi.extension']
+
+
+
+.. py:data:: autoapi_dirs
+   :annotation: = ['../../']
+
+
+
+.. py:data:: templates_path
+   :annotation: = ['_templates']
+
+
+
+.. py:data:: exclude_patterns
+   :annotation: = []
+
+
+
+.. py:data:: html_theme
+   :annotation: = sphinx_rtd_theme
+
+
+
+.. py:data:: html_static_path
+   :annotation: = ['_static']
+
+
+

docs/build/html/_sources/autoapi/index.rst.txt

@@ -0,0 +1,16 @@
+API Reference
+=============
+
+This page contains auto-generated API reference documentation [#f1]_.
+
+.. toctree::
+   :titlesonly:
+
+   /autoapi/charles_filter_n/index
+   /autoapi/input/index
+   /autoapi/utilities/index
+   /autoapi/SVTools/index
+   /autoapi/main/index
+   /autoapi/conf/index
+
+.. [#f1] Created with `sphinx-autoapi <https://github.com/readthedocs/sphinx-autoapi>`_