Merge branch 'hotfix/1.1.0' into main

Fixed bug that added 1 to total fragment length, this will slightly increase the fpbm_br and fpbm_nbr values
Added option to analyse long read data

CHANGES.md

@@ -1,4 +1,9 @@
 
+## 1.1.0
+* Added option to analyse long read data
+* Fixed bug that added 1 to total fragment length, this will slightly increase the fpbm_br and fpbm_nbr values 
+* added option to add header line to output
+
 ## 1.0.0
 * First release to calculate TA repeats FPBM values using samtools bedcoverage data 
 

Dockerfile

@@ -3,7 +3,7 @@ USER root
 
 MAINTAINER  [email protected]
 
-ENV ANALYSE_TA_VER '1.0.0'
+ENV ANALYSE_TA_VER '1.1.0'
 
 # install system tools
 RUN apt-get -yq update
@@ -40,7 +40,7 @@ RUN pip3 install --install-option="--prefix=$CGP_OPT/python-lib" dist/$(ls -1 di
 FROM ubuntu:20.04
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Sanger Institute" \
-      version="1.0.0" \
+      version="1.1.0" \
       description="Tool to perform TA repeat bed coverage analysis"
 
 ### security upgrades and cleanup

README.md

@@ -49,6 +49,14 @@ Various exceptions can occur for malformed input files.
 
  * ```test_sample 6.12 15.8``` command line output <sample_name> <mean_fpbm_broken> <mean_fpbm_non_broken>.
 
+### outputFormat with dnovo flag set 
+* ```Applicable only to Long Read sequencing data ```
+Use of dnovo flag will classify the TA repeat regions into broken and non-broken based on the user defined dnovo_cutoff parmater.
+This  is applicable for long read data where average length of TA repeat is known for each interval
+* ```br:broken```
+* ```nbr:non_broken```
+* ```test_sample 6.12 15.8``` command line output <sample_name> <mean_fpbm_br> <mean_fpbm_nbr> <ref_br> <ref_nbr> <mean_fpbm_dnovo_br> <mean_fpbm_dnovo_br> <dnovo_br> <dnovo_nbr> <dnovo_in_ref_br> <dnovo_in_ref_nbr> <cumulative_fpbm_br> <cumulative_fpbm_nbr> <jaccard_br> <jaccard_nbr>. 
+
 ## INSTALL
 Installing via `pip install`. Simply execute with the path to the compiled 'whl' found on the [release page][analyse_ta-releases]:
 

analyse_ta/commandline.py

@@ -3,6 +3,7 @@
 import os
 import argparse
 import pkg_resources
+
 # load config and reference files....
 
 version = pkg_resources.require("analyse_ta")[0].version
@@ -11,32 +12,92 @@
 def main():  # pragma: no cover <--
     usage = "\n %prog [options] -br input_br.bedcov -nbr input_nbr.bedcov -s <sample>"
 
-    optParser = argparse.ArgumentParser(prog='analyse_ta',
-                                        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    optParser = argparse.ArgumentParser(
+        prog="analyse_ta", formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
     optional = optParser._action_groups.pop()
-    required = optParser.add_argument_group('required arguments')
+    required = optParser.add_argument_group("required arguments")
+
+    required.add_argument(
+        "-br",
+        "--file_br",
+        type=str,
+        dest="file_br",
+        required=True,
+        default=None,
+        help="broken ta repeat bed coverage file",
+    )
+    required.add_argument(
+        "-nbr",
+        "--file_nbr",
+        type=str,
+        dest="file_nbr",
+        required=True,
+        default=None,
+        help="non broken ta repeat bed coverage file",
+    )
+
+    optional.add_argument(
+        "-s",
+        "--sample_name",
+        type=str,
+        dest="sample_name",
+        required=False,
+        default="test_sample",
+        help="sample name",
+    )
+
+    optional.add_argument(
+        "-dn",
+        "--dnovo",
+        action="store_true",
+        dest="dnovo",
+        default=False,
+        help="set flag to analyse dnovo long read data",
+    )
+
+    optional.add_argument(
+        "-ah",
+        "--add_header",
+        action="store_true",
+        dest="add_header",
+        default=False,
+        help="set flag to add_header line, useful in batch mode to set for first sample",
+    )
 
-    required.add_argument("-br", "--file_br", type=str, dest="file_br", required=True,
-                          default=None, help="broken ta repeat bed coverage file")
-    required.add_argument("-nbr", "--file_nbr", type=str, dest="file_nbr", required=True,
-                          default=None, help="non broken ta repeat bed coverage file")
+    optional.add_argument(
+        "-dn_cutoff",
+        "--dnovo_cutoff",
+        type=int,
+        dest="dnovo_cutoff",
+        required=False,
+        default=2,
+        help="cut off length ratio with ref interval to flag as broken region",
+    )
 
-    optional.add_argument("-s", "--sample_name", type=str, dest="sample_name", required=False,
-                          default='test_sample', help="sample name")
-    optional.add_argument("-v", "--version", action='version', version='%(prog)s ' + version)
-    optional.add_argument("-q", "--quiet", action="store_false", dest="verbose", required=False, default=True)
+    optional.add_argument(
+        "-v", "--version", action="version", version="%(prog)s " + version
+    )
+    optional.add_argument(
+        "-q",
+        "--quiet",
+        action="store_false",
+        dest="verbose",
+        required=False,
+        default=True,
+    )
 
     optParser._action_groups.append(optional)
     if len(sys.argv) == 0:
         optParser.print_help()
         sys.exit(1)
     opts = optParser.parse_args()
     if not opts.file_nbr or not opts.file_br:
-        sys.exit('\nERROR Arguments required\n\tPlease run: analyse_ta.py --help\n')
+        sys.exit("\nERROR Arguments required\n\tPlease run: analyse_ta.py --help\n")
     # vars function returns __dict__ of Namespace instance
     processed = processcov.processBedCov(**vars(opts))
     print(processed.results)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

analyse_ta/process_bedcov.py

@@ -1,44 +1,141 @@
 import os
 import sys
 import pandas as pd
+import numpy as np
 
 
-'''
+"""
   This class claculates mean coverage for broken and non_broken TA reapeat depth output fron samtools bedcov
-'''
+"""
 
 
 class processBedCov:
     """
-        Main class , loads user defined parameters and files
+    Main class , loads user defined parameters and files
     """
 
     def __init__(self, **kwargs):
-        self.br_file = kwargs['file_br']
-        self.nbr_file = kwargs['file_nbr']
-        self.sample = kwargs.get('sample_name', 'test_sample')
+        self.br_file = kwargs["file_br"]
+        self.nbr_file = kwargs["file_nbr"]
+        self.dnovo = kwargs["dnovo"]
+        self.add_header = kwargs["add_header"]
+        self.dnovo_cutoff = kwargs["dnovo_cutoff"]
+        self.sample = kwargs.get("sample_name", "test_sample")
         # check input data ...
         self.results = self.process()
 
     def process(self):
-        mydf_br = create_df_to_merge(self.br_file, 'br')
-        mydf_nbr = create_df_to_merge(self.nbr_file, 'nbr')
+        mydf_br = create_df_to_merge(self.br_file, "br", self.dnovo_cutoff, self.dnovo)
+        mydf_nbr = create_df_to_merge(
+            self.nbr_file, "nbr", self.dnovo_cutoff, self.dnovo
+        )
         merged_df = pd.concat([mydf_nbr, mydf_br])
-        mean_fpmb_const = merged_df['frl'].sum(axis=0)
-        merged_df['fpbm'] = merged_df['frl'] / mean_fpmb_const * (10**6)
-        br_mean = merged_df.loc[merged_df.ta_type == 'br']
-        nbr_mean = merged_df.loc[merged_df.ta_type == 'nbr']
-        return f"{self.sample}\t{br_mean['fpbm'].mean(axis=0):.2f}\t{nbr_mean['fpbm'].mean(axis=0):.2f}"
+        mean_fpmb_const = merged_df["frl"].sum(axis=0)
+        merged_df["fpbm"] = merged_df["frl"] / mean_fpmb_const * (10**6)
+        br_mean = merged_df.loc[merged_df.ta_type == "br"]
+        nbr_mean = merged_df.loc[merged_df.ta_type == "nbr"]
+        header = f"sample\tfpbm_br\tfpbm_nbr\n"
+        output = ""
+        if self.add_header:
+            output = header
+        if self.dnovo:
+            if self.add_header:
+                output = output.strip()
+                output = (f"{output}\tref_br\tref_nbr\tmean_fpbm_dnovo_br\tmean_fpbm_dnovo_br\tdnovo_br\tdnovo_nbr"
+                         f"\tdnovo_in_ref_br\tdnovo_in_ref_nbr\tcumulative_fpbm_br"
+                         f"\tcumulative_fpbm_nbr\tjaccard_br\tjaccard_nbr\n")
+            br_mean_dnovo = merged_df.loc[merged_df.ta_type_dnovo == "br"]
+            nbr_mean_dnovo = merged_df.loc[merged_df.ta_type_dnovo == "nbr"]
+            br_cumulative_mean = merged_df.loc[
+                (merged_df["ta_type_dnovo"] == "br") | (merged_df["ta_type"] == "br")
+            ]
+            nbr_cumulative_mean = merged_df.loc[
+                (merged_df["ta_type_dnovo"] == "nbr") | (merged_df["ta_type"] == "nbr")
+            ]
+            num_br = len(merged_df[merged_df["ta_type"] == "br"])
+            num_nbr = len(merged_df[merged_df["ta_type"] == "nbr"])
+            num_br_dnovo = len(merged_df[merged_df["ta_type_dnovo"] == "br"])
+            num_nbr_dnovo = len(merged_df[merged_df["ta_type_dnovo"] == "nbr"])
+            br_m11 = len(
+                merged_df[
+                    (merged_df["ta_type_dnovo"] == "br") & (merged_df["ta_type"] == "br")
+                ]
+            )
+            br_m01 = len(
+                merged_df[
+                    (merged_df["ta_type_dnovo"] != "br") & (merged_df["ta_type"] == "br")
+                ]
+            )
+            br_m10 = len(
+                merged_df[
+                    (merged_df["ta_type_dnovo"] == "br") & (merged_df["ta_type"] != "br")
+                ]
+            )
+            nbr_m11 = len(
+                merged_df[
+                    (merged_df["ta_type_dnovo"] == "nbr") & (merged_df["ta_type"] == "nbr")
+                ]
+            )
+            nbr_m01 = len(
+                merged_df[
+                    (merged_df["ta_type_dnovo"] != "nbr") & (merged_df["ta_type"] == "nbr")
+                ]
+            )
+            nbr_m10 = len(
+                merged_df[
+                    (merged_df["ta_type_dnovo"] == "nbr") & (merged_df["ta_type"] != "nbr")
+                ]
+            )
 
+            jindex_br = (br_m11 / (br_m01 + br_m10 + br_m11)) * 100
+            jindex_nbr = (nbr_m11 / (nbr_m01 + nbr_m10 + nbr_m11)) * 100
 
-def create_df_to_merge(infile, ta_type):
+            return (
+                f"{output}{self.sample}\t{br_mean['fpbm'].mean(axis=0):.2f}"
+                f"\t{nbr_mean['fpbm'].mean(axis=0):.2f}\t{num_br}\t{num_nbr}"
+                f"\t{br_mean_dnovo['fpbm'].mean(axis=0):.2f}\t{nbr_mean_dnovo['fpbm'].mean(axis=0):.2f}"
+                f"\t{num_br_dnovo}\t{num_nbr_dnovo}\t{br_m11}\t{nbr_m11}"
+                f"\t{br_cumulative_mean['fpbm'].mean(axis=0):.2f}"
+                f"\t{nbr_cumulative_mean['fpbm'].mean(axis=0):.2f}\t{jindex_br:.2f}\t{jindex_nbr:.2f}"
+            )
+
+        output = f"{output}{self.sample}\t{br_mean['fpbm'].mean(axis=0):.2f}\t{nbr_mean['fpbm'].mean(axis=0):.2f}"
+        return output
+
+
+def create_df_to_merge(infile, ta_type, dnovo_cutoff, dnovo=None):
     """
-       create pandas data frame
+    create pandas data frame
     """
     if not os.path.isfile(infile):
+        print(f"File not found {infile}")
         return None
-    df = pd.read_csv(infile, compression='infer', sep="\t", low_memory=False,
-                     header=None, names=['chr', 'start', 'end', 'coverage'])
-    df['frl'] = df['coverage'] / (df['end'] - df['start']) + 1
-    df['ta_type'] = ta_type
+    df = pd.read_csv(
+        infile,
+        compression="infer",
+        sep="\t",
+        low_memory=False,
+        header=None,
+        names=["chr", "start", "end", "coverage"],
+    )
+
+    if dnovo:
+        df["frl"] = (df["coverage"] * 2) / ((df["end"] - df["start"]) + 1)
+        df["ta_type_dnovo"] = np.select(
+            [df["frl"] <= dnovo_cutoff, df["frl"] > dnovo_cutoff], ["nbr", "br"]
+        )
+        df["ta_type"] = ta_type
+
+    else:
+        df["frl"] = df["coverage"] / ((df["end"] - df["start"]) + 1)
+        df["ta_type"] = ta_type
     return df
+
+
+def _print_df(mydf, out_file):
+    if out_file:
+        mydf.to_csv(
+            out_file, sep="\t", mode="w", header=True, index=True, doublequote=False
+        )
+    else:
+        sys.exit("Outfile not provided")

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup
 
 config = {
-    'version': '1.0.0',
+    'version': '1.1.0',
     'name': 'analyse_ta',
     'description': 'Tool to analyse TA repeats bed coverage...',
     'author': 'Shriram Bhosle',

test/test_ta.py

@@ -13,11 +13,26 @@ class TestClass():
   test_dir = configdir + '/data/'
   options = {'file_br': test_dir + 'test_br.bedcov',
                    'file_nbr': test_dir + 'test_nbr.bedcov',
+                   'dnovo':False,
+                   'add_header':True,
+                   'dnovo_cutoff':2,
+                   'sample_name': 'my_test_sample',
+                   }
+  options_ta_ext = {'file_br': test_dir + 'test_br.bedcov',
+                   'file_nbr': test_dir + 'test_nbr.bedcov',
+                   'dnovo':True,
+                   'add_header':False,
+                   'dnovo_cutoff':10,
                    'sample_name': 'my_test_sample',
                    }
   processed=processcov.processBedCov(**options)
+  processed_ta_ext=processcov.processBedCov(**options_ta_ext)
   # celline output
   def test_bedcov(self):
       f=self.processed
-      assert f.results == "my_test_sample\t35.23\t80.85"
+      assert f.results == "sample\tfpbm_br\tfpbm_nbr\nmy_test_sample\t33.04\t82.05"
+
+  def test_ta_ext(self):
+      f_ext=self.processed_ta_ext
+      assert f_ext.results == "my_test_sample\t33.04\t82.05\t5434\t10000\t79.39\t14.36\t11970\t3464\t2776\t806\t67.53\t67.78\t18.98\t6.37"