changeset 7:fbf007713188 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_VCF_info_fields.py	Wed Feb 10 08:28:25 2021 +0000
@@ -0,0 +1,112 @@
+#!/usr/bin/env python3
+
+# Takes in VCF file annotated with medaka tools annotate and converts
+#
+# Usage statement:
+# python convert_VCF_info_fields.py in_vcf.vcf out_vcf.vcf
+
+# 10/21/2020 - Nathan P. Roach, [e-mail]
+
+import sys
+from collections import OrderedDict
+from math import log10
+
+from scipy.stats import fisher_exact
+
+
+def pval_to_phredqual(pval):
+    return round(-10 * log10(pval))
+
+
+def parseInfoField(info):
+    info_fields = info.split(';')
+    info_dict = OrderedDict()
+    for info_field in info_fields:
+        code, val = info_field.split('=')
+        info_dict[code] = val
+    return info_dict
+
+
+def annotateVCF(in_vcf_filepath, out_vcf_filepath):
+    in_vcf = open(in_vcf_filepath, 'r')
+    out_vcf = open(out_vcf_filepath, 'w')
+    to_skip = set(['SC', 'SR'])
+    for i, line in enumerate(in_vcf):
+        if i == 1:
+            out_vcf.write("##convert_VCF_info_fields=0.1\n")
+        if line[0:2] == "##":
+            if line[0:11] == "##INFO=<ID=":
+                id_ = line[11:].split(',')[0]
+                if id_ in to_skip:
+                    continue
+            out_vcf.write(line)
+        elif line[0] == "#":
+            out_vcf.write('##INFO=<ID=DPSPS,Number=2,Type=Integer,Description="Spanning Reads Allele Frequency By Strand">\n')
+            out_vcf.write('##INFO=<ID=AF,Number=1,Type=Float,Description="Spanning Reads Allele Frequency">\n')
+            out_vcf.write('##INFO=<ID=FAF,Number=1,Type=Float,Description="Forward Spanning Reads Allele Frequency">\n')
+            out_vcf.write('##INFO=<ID=RAF,Number=1,Type=Float,Description="Reverse Spanning Reads Allele Frequency">\n')
+            out_vcf.write('##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias of spanning reads at this position">\n')
+            out_vcf.write('##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases in spanning reads">\n')
+            out_vcf.write('##INFO=<ID=AS,Number=4,Type=Integer,Description="Total alignment score to ref and alt allele of spanning reads by strand (ref fwd, ref rev, alt fwd, alt rev) aligned with parasail match 5, mismatch -4, open 5, extend 3">\n')
+            out_vcf.write(line)
+        else:
+            fields = line.split('\t')
+            info_dict = parseInfoField(fields[7])
+            sr_list = [int(x) for x in info_dict["SR"].split(',')]
+            sc_list = [int(x) for x in info_dict["SC"].split(',')]
+            if len(sr_list) == len(sc_list):
+                variant_list = fields[4].split(',')
+                dpsp = int(info_dict["DPSP"])
+                ref_fwd, ref_rev = 0, 1
+                dpspf, dpspr = (int(x) for x in info_dict["AR"].split(','))
+                for i in range(0, len(sr_list), 2):
+                    dpspf += sr_list[i]
+                    dpspr += sr_list[i + 1]
+                for j, i in enumerate(range(2, len(sr_list), 2)):
+                    dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1])
+                    dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
+                    _, p_val = fisher_exact(dp2x2)
+                    sb = pval_to_phredqual(p_val)
+
+                    as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1])
+
+                    info = []
+                    for code in info_dict:
+                        if code in to_skip:
+                            continue
+                        val = info_dict[code]
+                        info.append("%s=%s" % (code, val))
+
+                    info.append("DPSPS=%d,%d" % (dpspf, dpspr))
+
+                    if dpsp == 0:
+                        info.append("AF=NaN")
+                    else:
+                        af = dp4[2] + dp4[3] / dpsp
+                        info.append("AF=%.6f" % (af))
+                    if dpspf == 0:
+                        info.append("FAF=NaN")
+                    else:
+                        faf = dp4[2] / dpspf
+                        info.append("FAF=%.6f" % (faf))
+                    if dpspr == 0:
+                        info.append("RAF=NaN")
+                    else:
+                        raf = dp4[3] / dpspr
+                        info.append("RAF=%.6f" % (raf))
+                    info.append("SB=%d" % (sb))
+                    info.append("DP4=%d,%d,%d,%d" % (dp4))
+                    info.append("AS=%d,%d,%d,%d" % (as_))
+                    new_info = ';'.join(info)
+                    fields[4] = variant_list[j]
+                    fields[7] = new_info
+                    out_vcf.write("%s" % ("\t".join(fields)))
+            else:
+                print("WARNING - SR and SC are different lengths, skipping variant")
+                print(line.strip())  # Print the line for debugging purposes
+    in_vcf.close()
+    out_vcf.close()
+
+
+if __name__ == "__main__":
+    annotateVCF(sys.argv[1], sys.argv[2])