diff mut2sscs.py @ 0:e5953c54cfb5 draft

planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mut2sscs.py	Sun Oct 04 17:19:39 2020 +0000
@@ -0,0 +1,133 @@
+#!/usr/bin/env python
+
+"""mut2sscs.py
+
+Author -- Gundula Povysil
+Contact -- [e-mail]
+
+Takes a tabular file with mutations from DCS and a BAM file of SSCS as input
+and extracts all tags of reads that carry the mutation.
+Calculates statistics about number of ab/ba/duplex per mutation.
+
+=======  ==========  =================  ================================
+Version  Date        Author             Description
+0.2.1    2019-10-27  Gundula Povysil    -
+=======  ==========  =================  ================================
+
+USAGE: python mut2sscs.py DCS_Mutations.tabular SSCS.bam SSCS_counts.json
+
+"""
+
+from __future__ import division
+
+import argparse
+import json
+import os
+import sys
+
+import numpy as np
+import pysam
+
+
+def make_argparser():
+    parser = argparse.ArgumentParser(description='Takes a tabular file with mutations and a BAM file as input and prints all tags of reads that carry the mutation to a user specified output file.')
+    parser.add_argument('--mutFile',
+                        help='TABULAR file with DCS mutations.')
+    parser.add_argument('--bamFile',
+                        help='BAM file with aligned SSCS reads.')
+    parser.add_argument('--outputJson',
+                        help='Output JSON file to store SSCS counts.')
+    return parser
+
+
+def mut2sscs(argv):
+    parser = make_argparser()
+    args = parser.parse_args(argv[1:])
+
+    file1 = args.mutFile
+    file2 = args.bamFile
+    sscs_counts_json = args.outputJson
+
+    if os.path.isfile(file1) is False:
+        sys.exit("Error: Could not find '{}'".format(file1))
+
+    if os.path.isfile(file2) is False:
+        sys.exit("Error: Could not find '{}'".format(file2))
+
+    # 1. read mut file
+    with open(file1, 'r') as mut:
+        mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype=str)
+
+    # 2 read SSCS bam file
+    # pysam.index(file2)
+    bam = pysam.AlignmentFile(file2, "rb")
+
+    # get tags
+    mut_pos_dict = {}
+    ref_pos_dict = {}
+    if mut_array.shape == (1,13):
+        mut_array = mut_array.reshape((1, len(mut_array)))
+
+    for m in range(0, len(mut_array[:, 0])):
+        print(str(m + 1) + " of " + str(len(mut_array[:, 0])))
+        chrom = mut_array[m, 1]
+        stop_pos = mut_array[m, 2].astype(int)
+        chrom_stop_pos = str(chrom) + "#" + str(stop_pos)
+        ref = mut_array[m, 9]
+        alt = mut_array[m, 10]
+
+        for pileupcolumn in bam.pileup(chrom.tostring(), stop_pos - 2, stop_pos, max_depth=1000000000):
+            if pileupcolumn.reference_pos == stop_pos - 1:
+                count_alt = 0
+                count_ref = 0
+                count_indel = 0
+                print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups),
+                      "difference= ", len(pileupcolumn.pileups) - pileupcolumn.n)
+                for pileupread in pileupcolumn.pileups:
+                    if not pileupread.is_del and not pileupread.is_refskip:
+                        tag = pileupread.alignment.query_name
+                        abba = tag[-2:]
+                        # query position is None if is_del or is_refskip is set.
+                        if pileupread.alignment.query_sequence[pileupread.query_position] == alt:
+                            count_alt += 1
+                            if chrom_stop_pos in mut_pos_dict:
+                                if abba in mut_pos_dict[chrom_stop_pos]:
+                                    mut_pos_dict[chrom_stop_pos][abba] += 1
+                                else:
+                                    mut_pos_dict[chrom_stop_pos][abba] = 1
+                            else:
+                                mut_pos_dict[chrom_stop_pos] = {}
+                                mut_pos_dict[chrom_stop_pos][abba] = 1
+                        elif pileupread.alignment.query_sequence[pileupread.query_position] == ref:
+                            count_ref += 1
+                            if chrom_stop_pos in ref_pos_dict:
+                                if abba in ref_pos_dict[chrom_stop_pos]:
+                                    ref_pos_dict[chrom_stop_pos][abba] += 1
+                                else:
+                                    ref_pos_dict[chrom_stop_pos][abba] = 1
+                            else:
+                                ref_pos_dict[chrom_stop_pos] = {}
+                                ref_pos_dict[chrom_stop_pos][abba] = 1
+                        else:
+                            count_indel += 1
+
+                print("coverage at pos %s = %s, ref = %s, alt = %s, indel = %s,\n" %
+                      (pileupcolumn.pos, count_ref + count_alt, count_ref, count_alt, count_indel))
+
+        # if mutation is in DCS file but not in SSCS, then set counts to NA
+        if chrom_stop_pos not in mut_pos_dict.keys():
+            mut_pos_dict[chrom_stop_pos] = {}
+            mut_pos_dict[chrom_stop_pos]["ab"] = 0
+            mut_pos_dict[chrom_stop_pos]["ba"] = 0
+            ref_pos_dict[chrom_stop_pos] = {}
+            ref_pos_dict[chrom_stop_pos]["ab"] = 0
+            ref_pos_dict[chrom_stop_pos]["ba"] = 0
+    bam.close()
+
+    # save counts
+    with open(sscs_counts_json, "w") as f:
+        json.dump((mut_pos_dict, ref_pos_dict), f)
+
+
+if __name__ == '__main__':
+    sys.exit(mut2sscs(sys.argv))