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Ensure consistent MH frequencies #150

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Oct 23, 2023
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Ensure consistent MH frequencies #150

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4bd3df8
Ensure consistent mh frequencies
Oct 23, 2023
b98aaaf
Update change log and docs
Oct 23, 2023
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,9 @@ This project adheres to [Semantic Versioning](http://semver.org/).
### Changed
- Merged RSIDs resolved during database build now propagated to the final marker definition (see #149).

### Fixed
- Added manual and automated fixes to ensure frequencies are formatted correcly and matche to the correct marker definition (see #150).


## [0.10.1] 2023-10-13

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2 changes: 1 addition & 1 deletion dbbuild/build-summary.txt
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Expand Up @@ -3034,7 +3034,7 @@ Marker mh11KK-040 as defined in Staadig2021 was defined previously and is redund
- 59 marker definitions based on 658 SNPs
[Byrska-Bishop2022]
- 31 population samples
- frequencies for 59232 distinct haplotypes in 31 populations; 856064 total frequencies
- frequencies for 59233 distinct haplotypes in 31 populations; 856067 total frequencies
[Fan2022]
- 22 marker definitions based on 338 SNPs and 25 indels
[Yu2022G1]
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22 changes: 19 additions & 3 deletions dbbuild/build.py
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Expand Up @@ -30,9 +30,9 @@ def main(
index.update_marker_names()
index.markers.to_csv("marker.csv", index=False)
index.indels.to_csv("indels.csv", index=False)
index.frequencies.to_csv(
"frequency.csv.gz", index=False, float_format="%.5f", compression="gzip"
)
frequencies = index.frequencies
frequencies = cleanup_frequencies(frequencies)
frequencies.to_csv("frequency.csv.gz", index=False, float_format="%.5f", compression="gzip")
index.populations.to_csv("population.csv", index=False)
index.merges.to_csv("merged.csv", index=False)
repeats = flag_repeats(Path(rmsk_path) / "rmsk.txt.gz", "marker.csv", delta=25)
Expand Down Expand Up @@ -60,6 +60,22 @@ def validate_paths(dbsnp_path, rmsk_path, chain_path):
raise FileNotFoundError(",".join(missing))


def cleanup_frequencies(freq):
freq["NumVars"] = freq.Allele.apply(lambda x: x.count("|") + 1)
freq.loc[(freq.Marker == "mh01NK-001") & (freq.Source == "Kidd2018"), "Marker"] = "mh01NH-01.v2"
freq.loc[(freq.Marker == "mh01NK-001") & (freq.Source == "Turchi2019"), "Marker"] = "mh01NH-01.v2"
freq.loc[(freq.Marker == "mh01NK-001") & (freq.Source == "Gandotra2020"), "Marker"] = "mh01NH-01.v2"
freq.loc[(freq.Marker == "mh01NK-001") & (freq.Source == "Staadig2021"), "Marker"] = "mh01NH-01.v1"
freq.loc[(freq.Marker.str.startswith(("mh05KK-023", "mh05KK-020"))) & (freq.Source == "Kidd2018") & (freq.NumVars == 3), "Marker"] = "mh05KK-023.v1"
freq.loc[(freq.Marker.str.startswith(("mh05KK-023", "mh05KK-020"))) & (freq.Source == "Kidd2018") & (freq.NumVars == 4), "Marker"] = "mh05KK-023.v2"
freq.loc[(freq.Marker.str.startswith(("mh05KK-023", "mh05KK-020"))) & (freq.Source == "Turchi2019"), "Marker"] = "mh05KK-023.v1"
freq.loc[(freq.Marker.str.startswith(("mh05KK-023", "mh05KK-020"))) & (freq.Source == "Gandotra2020"), "Marker"] = "mh05KK-023.v3"
freq.loc[(freq.Marker.str.startswith("mh05KK-120")) & (freq.Source == "Kidd2018") & (freq.NumVars == 3), "Marker"] = "mh05KK-120.v1"
freq.loc[(freq.Marker.str.startswith("mh05KK-120")) & (freq.Source == "Kidd2018") & (freq.NumVars == 4), "Marker"] = "mh05KK-120.v2"
freq = freq.drop(columns="NumVars")
return freq
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This function is the result of running that new test dozens of times. There are a handful of markers from Kidd & company that could not be rectified with a reasonable amount of effort using my automated procedure. Fortunately, a few "manual" replacements as specified here did the trick.

These issues were the result of different names being used to refer to different SNP sets at the same locus.



def get_parser():
parser = ArgumentParser(description="MicroHapDB database build procedure")
parser.add_argument("dbsnp_path")
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Binary file modified dbbuild/frequency.csv.gz
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4 changes: 2 additions & 2 deletions dbbuild/marker-aes.csv
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Expand Up @@ -36048,8 +36048,8 @@ mh06WL-017.v1,MXL,6.983
mh06WL-017.v1,PEL,7.292
mh06WL-017.v1,PJL,6.547
mh06WL-017.v1,PUR,7.729
mh06WL-017.v1,SAS,8.805
mh06WL-017.v1,STU,10.080
mh06WL-017.v1,SAS,8.806
mh06WL-017.v1,STU,10.085
mh06WL-017.v1,TSI,8.339
mh06WL-017.v1,YRI,6.634
mh06WL-017.v2,1KGP,8.679
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2 changes: 1 addition & 1 deletion dbbuild/marker.csv
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Expand Up @@ -1109,7 +1109,7 @@ mh06SCUZJ-0278537,4,130,chr6,32588674,32588803,32588674;32588684;32588765;325888
mh06SHY-003,12,91,chr6,32605762,32605852,32605762;32605766;32605777;32605783;32605785;32605788;32605797;32605821;32605825;32605844;32605851;32605852,32573539;32573543;32573554;32573560;32573562;32573565;32573574;32573598;32573602;32573621;32573628;32573629,rs602427;rs9270967;rs9270968;rs9270969;rs602457;rs573809619;rs9270970;rs9270971;rs2760993;rs9270972;rs144123929;rs602875,Wu2021
mh06WL-050,27,300,chr6,32661208,32661507,32661208;32661214;32661215;32661219;32661221;32661238;32661245;32661250;32661255;32661269;32661287;32661289;32661297;32661310;32661314;32661332;32661333;32661334;32661335;32661462;32661463;32661482;32661490;32661492;32661504;32661505;32661507,32628985;32628991;32628992;32628996;32628998;32629015;32629022;32629027;32629032;32629046;32629064;32629066;32629074;32629087;32629091;32629109;32629110;32629111;32629112;32629239;32629240;32629259;32629267;32629269;32629281;32629282;32629284,rs28724236;rs117369774;rs117656997;rs9273560;rs9273561;rs281864341;rs281864337;rs41270893;rs73729446;rs28724237;rs9273584;rs28724238;rs9273588;rs117626117;rs9273595;rs281864289;rs9273608;rs281864287;rs9273609;rs559673115;rs281864275;rs3828786;rs199987570;rs9273685;rs9273695;rs9273696;rs114262759,Yu2022G3
mh06WL-017.v2,16,100,chr6,32663167,32663266,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219,Yu2022G4
mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663288;32663293;32663298;32663302;32663303;32663327;32663332;32663336;32663342;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631065;32631070;32631075;32631079;32631080;32631104;32631109;32631113;32631119;32631129;32631130;32631133;32631142,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219;rs9274220;rs2856703;rs17843723;rs41270932;rs9274222;rs72844333;rs200098349;rs74222206;rs281863378;rs9274225;rs41270933;rs17613629;rs17613636;rs281863362;rs9274227,Yu2022G1;Yu2022G2
mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663293;32663298;32663302;32663303;32663309;32663327;32663332;32663336;32663342;32663345;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631070;32631075;32631079;32631080;32631086;32631104;32631109;32631113;32631119;32631122;32631129;32631130;32631133;32631142,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219;rs9274220;rs2856703;rs41270932;rs9274222;rs72844333;rs200098349;rs17843724;rs74222206;rs281863378;rs9274225;rs41270933;rs17613622;rs17613629;rs17613636;rs281863362;rs9274227,Yu2022G1;Yu2022G2
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The change as propagated to the marker table.

mh06LV-09,14,193,chr6,33056355,33056547,33056355;33056360;33056389;33056401;33056412;33056447;33056452;33056458;33056481;33056496;33056522;33056532;33056540;33056547,33024132;33024137;33024166;33024178;33024189;33024224;33024229;33024235;33024258;33024273;33024299;33024309;33024317;33024324,rs412735;rs570318069;rs449635;rs114484337;rs150884041;rs6457707;rs396638;rs6457708;rs12200756;rs435549;rs3130593;rs3130184;rs3130185;rs3130594,Voskoboinik2018
mh06WL-070,5,85,chr6,33893893,33893977,33893893;33893902;33893916;33893934;33893977,33861670;33861679;33861693;33861711;33861754,rs3800333;rs2031377;rs3800335;rs2031378;rs3800337,Yu2022G1
mh06WL-075,5,134,chr6,36734497,36734630,36734497;36734507;36734602;36734610;36734630,36702274;36702284;36702379;36702387;36702407,rs236453;rs236452;rs236451;rs77394127;rs236450,Yu2022G1
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