Mercurial > repos > iuc > medaka_variant_pipeline
changeset 12:597407d61386 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
| author | iuc |
|---|---|
| date | Fri, 17 Sep 2021 20:22:27 +0000 |
| parents | 11fedf536104 |
| children | 3fbefde449bc |
| files | convert_VCF_info_fields.py test-data/ref.fasta |
| diffstat | 2 files changed, 131 insertions(+), 71 deletions(-) [+] |
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--- a/convert_VCF_info_fields.py Sun Sep 12 20:35:06 2021 +0000 +++ b/convert_VCF_info_fields.py Fri Sep 17 20:22:27 2021 +0000 @@ -7,11 +7,11 @@ # 10/21/2020 - Nathan P. Roach, natproach@gmail.com +import re import sys from collections import OrderedDict from math import log10 -import scipy import scipy.stats @@ -33,84 +33,144 @@ def annotateVCF(in_vcf_filepath, out_vcf_filepath): + """Postprocess output of medaka tools annotate. + + Splits multiallelic sites into separate records. + Replaces medaka INFO fields that might represent information of the ref + and multiple alternate alleles with simple ref, alt allele counterparts. + """ + 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=0.2\n") - if line[0:2] == "##": - if line[0:11] == "##INFO=<ID=": - id_ = line[11:].split(',')[0] - if id_ in to_skip: + # medaka INFO fields that do not make sense after splitting of + # multi-allelic records + # DP will be overwritten with the value of DPSP because medaka tools + # annotate currently only calculates the latter correctly + # (https://github.com/nanoporetech/medaka/issues/192). + # DPS, which is as unreliable as DP, gets skipped and the code + # calculates the spanning reads equivalent DPSPS instead. + to_skip = {'SC', 'SR', 'AR', 'DP', 'DPSP', 'DPS'} + struct_meta_pat = re.compile('##(.+)=<ID=([^,]+)(,.+)?>') + header_lines = [] + contig_ids = set() + contig_ids_simple = set() + # parse the metadata lines of the input VCF and drop: + # - duplicate lines + # - INFO lines declaring keys we are not going to write + # - redundant contig information + while True: + line = in_vcf.readline() + if line[:2] != '##': + assert line.startswith('#CHROM') + break + if line in header_lines: + # the annotate tool may generate lines already written by + # medaka variant again (example: medaka version line) + continue + match = struct_meta_pat.match(line) + if match: + match_type, match_id, match_misc = match.groups() + if match_type == 'INFO': + if match_id == 'DPSP': + line = line.replace('DPSP', 'DP') + elif match_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: + elif match_type == 'contig': + contig_ids.add(match_id) + if not match_misc: + # the annotate tools writes its own contig info, + # which is redundant with contig info generated by + # medaka variant, but lacks a length value. + # We don't need the incomplete line. + contig_ids_simple.add(match_id) + continue + header_lines.append(line) + # Lets check the above assumption about each ID-only contig line + # having a more complete counterpart. + assert not (contig_ids_simple - contig_ids) + header_lines.insert(1, '##convert_VCF_info_fields=0.2\n') + header_lines += [ + '##INFO=<ID=DPSPS,Number=2,Type=Integer,Description="Depth of spanning reads by strand">\n', + '##INFO=<ID=AF,Number=1,Type=Float,Description="Spanning Reads Allele Frequency">\n', + '##INFO=<ID=FAF,Number=1,Type=Float,Description="Forward Spanning Reads Allele Frequency">\n', + '##INFO=<ID=RAF,Number=1,Type=Float,Description="Reverse Spanning Reads Allele Frequency">\n', + '##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias of spanning reads at this position">\n', + '##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', + '##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', + line + ] + + with open(out_vcf_filepath, 'w') as out_vcf: + out_vcf.writelines(header_lines) + for line in in_vcf: 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 = scipy.stats.fisher_exact(dp2x2) - sb = pval_to_phredqual(p_val) + if len(sr_list) != len(sc_list): + print( + 'WARNING - SR and SC are different lengths, ' + 'skipping variant' + ) + print(line.strip()) # Print the line for debugging purposes + continue + 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 = scipy.stats.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)) + as_ = ( + sc_list[ref_fwd], + sc_list[ref_rev], + sc_list[i], + sc_list[i + 1] + ) - 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 + info = [] + for code in info_dict: + if code in to_skip: + continue + val = info_dict[code] + info.append("%s=%s" % (code, val)) + + info.append('DP=%d' % dpsp) + 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('\t'.join(fields)) in_vcf.close() - out_vcf.close() if __name__ == "__main__":
--- a/test-data/ref.fasta Sun Sep 12 20:35:06 2021 +0000 +++ b/test-data/ref.fasta Fri Sep 17 20:22:27 2021 +0000 @@ -1,2 +1,2 @@ >NC_045512.2 -ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +attaaaggtttataccttcccaggtaacaaaccaaccaactttcgatctcttgtagatctgttctctaaacgaactttaaaatctgtgtggctGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC