update statobs reader for scientific notation

diyabc · Oct 7, 2024 · a20e3ea · a20e3ea
1 parent 39c3a35
commit a20e3ea
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Showing 6 changed files with 256 additions and 1 deletion.
diff --git a/src/readstatobs.hpp b/src/readstatobs.hpp
@@ -13,7 +13,8 @@ vector<double> readStatObs(const std::string &path) {
     ifstream statobsStream(path,ios::in);
     statobsStream >> noskipws;
     const std::string sS(istream_iterator<char>{statobsStream}, {});
-    const regex stat_re(R"#(\s(-?\d+\.\d+)\s)#");    
+    // const regex stat_re(R"#(\s(-?\d+\.\d+)\s)#"); working for old format   
+    const regex stat_re(R"#(\s([+\-]?(\d+\.\d*|\d*\.\d+|\d+)([eE][+\-]?\d+)?)\s)#");    
     sregex_token_iterator itstat(begin(sS), end(sS), stat_re, {1});
     vector<double> statobs;
     auto it = itstat;

diff --git a/test/data/newformat/headerRF.txt b/test/data/newformat/headerRF.txt
@@ -0,0 +1,111 @@
+SNP_sim_dataset_4POP_S6_car_ra_zero_001.snp
+13 parameters and 130 summary statistics
+
+6 scenarios: 8 8 8 8 8 8 
+scenario 1 [0.16667] (8)
+N1 N2 N3 N4
+0 sample 1
+0 sample 2
+0 sample 3
+0 sample 4
+t423 split 4 2 3 ra
+t32 merge 2 3
+t21 merge 1 2
+scenario 2 [0.16667] (8)
+N1 N2 N3 N4
+0 sample 1
+0 sample 2
+0 sample 3
+0 sample 4
+t421 split 4 2 1 ra
+t32 merge 2 3
+t21 merge 1 2
+scenario 3 [0.16667] (8)
+N1 N2 N3 N4
+0 sample 1
+0 sample 2
+0 sample 3
+0 sample 4
+t431 split 4 1 3 ra
+t32 merge 2 3
+t21 merge 1 2
+scenario 4 [0.16667] (7)
+N1 N2 N3 N4
+0 sample 1
+0 sample 2
+0 sample 3
+0 sample 4
+t41 merge 1 4
+t32 merge 2 3
+t21 merge 1 2
+scenario 5 [0.16667] (7)
+N1 N2 N3 N4
+0 sample 1
+0 sample 2
+0 sample 3
+0 sample 4
+t42 merge 2 4
+t32 merge 2 3
+t21 merge 1 2
+scenario 6 [0.16667] (7)
+N1 N2 N3 N4
+0 sample 1
+0 sample 2
+0 sample 3
+0 sample 4
+t43 merge 3 4
+t32 merge 2 3
+t21 merge 1 2
+
+historical parameters priors (13,6)
+N1 N UN[100,10000,0.0,0.0]
+N2 N UN[100,10000,0.0,0.0]
+N3 N UN[100,10000,0.0,0.0]
+N4 N UN[100,10000,0.0,0.0]
+t423 T UN[10,1000,0.0,0.0]
+ra A UN[0.05,0.95,0.0,0.0]
+t32 T UN[10,1000,0.0,0.0]
+t21 T UN[10,1000,0.0,0.0]
+t421 T UN[10,1000,0.0,0.0]
+t431 T UN[10,1000,0.0,0.0]
+t41 T UN[10,1000,0.0,0.0]
+t42 T UN[10,1000,0.0,0.0]
+t43 T UN[10,1000,0.0,0.0]
+t21>t32
+t42<t21
+t43<t32
+t32>t423
+t431<t32
+t421<t21
+DRAW UNTIL
+
+loci description (1)
+5000 <A> G1 from 1
+
+group summary statistics (130)
+group G1 (130)
+ML1p 1 2 3 4
+ML2p 1.2 1.3 1.4 2.3 2.4 3.4
+ML3p 1.2.3 1.2.4 1.3.4 2.3.4
+HWm 1 2 3 4
+HWv 1 2 3 4
+HBm 1.2 1.3 1.4 2.3 2.4 3.4
+HBv 1.2 1.3 1.4 2.3 2.4 3.4
+FST1m 1 2 3 4
+FST1v 1 2 3 4
+FST2m 1.2 1.3 1.4 2.3 2.4 3.4
+FST2v 1.2 1.3 1.4 2.3 2.4 3.4
+NEIm 1.2 1.3 1.4 2.3 2.4 3.4
+NEIv 1.2 1.3 1.4 2.3 2.4 3.4
+AMLm 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.3.4 3.1.4 4.1.3 2.3.4 3.2.4 4.2.3
+AMLv 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.3.4 3.1.4 4.1.3 2.3.4 3.2.4 4.2.3
+FST3m 1.2.3 1.2.4 1.3.4 2.3.4
+FST3v 1.2.3 1.2.4 1.3.4 2.3.4
+FST4m 1.2.3.4
+FST4v 1.2.3.4
+F3m 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.3.4 3.1.4 4.1.3 2.3.4 3.2.4 4.2.3
+F3v 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.3.4 3.1.4 4.1.3 2.3.4 3.2.4 4.2.3
+F4m 1.2.3.4 1.3.2.4 1.4.2.3
+F4v 1.2.3.4 1.3.2.4 1.4.2.3
+
+scenario N1 N2 N3 N4 t423 ra t32 t21 t421 t431 t41 t42 t43    ML1p_1        ML1p_2        ML1p_3        ML1p_4       ML2p_1.2      ML2p_1.3      ML2p_1.4      ML2p_2.3      ML2p_2.4      ML2p_3.4     ML3p_1.2.3    ML3p_1.2.4    ML3p_1.3.4    ML3p_2.3.4      HWm_1         HWm_2         HWm_3         HWm_4         HWv_1         HWv_2         HWv_3         HWv_4        HBm_1.2       HBm_1.3       HBm_1.4       HBm_2.3       HBm_2.4       HBm_3.4       HBv_1.2       HBv_1.3       HBv_1.4       HBv_2.3       HBv_2.4       HBv_3.4       FST1m_1       FST1m_2       FST1m_3       FST1m_4       FST1v_1       FST1v_2       FST1v_3       FST1v_4      FST2m_1.2     FST2m_1.3     FST2m_1.4     FST2m_2.3     FST2m_2.4     FST2m_3.4     FST2v_1.2     FST2v_1.3     FST2v_1.4     FST2v_2.3     FST2v_2.4     FST2v_3.4      NEIm_1.2      NEIm_1.3      NEIm_1.4      NEIm_2.3      NEIm_2.4      NEIm_3.4      NEIv_1.2      NEIv_1.3      NEIv_1.4      NEIv_2.3      NEIv_2.4      NEIv_3.4     AMLm_1.2.3    AMLm_2.1.3    AMLm_3.1.2    AMLm_1.2.4    AMLm_2.1.4    AMLm_4.1.2    AMLm_1.3.4    AMLm_3.1.4    AMLm_4.1.3    AMLm_2.3.4    AMLm_3.2.4    AMLm_4.2.3    AMLv_1.2.3    AMLv_2.1.3    AMLv_3.1.2    AMLv_1.2.4    AMLv_2.1.4    AMLv_4.1.2    AMLv_1.3.4    AMLv_3.1.4    AMLv_4.1.3    AMLv_2.3.4    AMLv_3.2.4    AMLv_4.2.3   FST3m_1.2.3   FST3m_1.2.4   FST3m_1.3.4   FST3m_2.3.4   FST3v_1.2.3   FST3v_1.2.4   FST3v_1.3.4   FST3v_2.3.4   FST4m_1.2.3.4  FST4v_1.2.3.4   F3m_1.2.3     F3m_2.1.3     F3m_3.1.2     F3m_1.2.4     F3m_2.1.4     F3m_4.1.2     F3m_1.3.4     F3m_3.1.4     F3m_4.1.3     F3m_2.3.4     F3m_3.2.4     F3m_4.2.3     F3v_1.2.3     F3v_2.1.3     F3v_3.1.2     F3v_1.2.4     F3v_2.1.4     F3v_4.1.2     F3v_1.3.4     F3v_3.1.4     F3v_4.1.3     F3v_2.3.4     F3v_3.2.4     F3v_4.2.3    F4m_1.2.3.4   F4m_1.3.2.4   F4m_1.4.2.3   F4v_1.2.3.4   F4v_1.3.2.4   F4v_1.4.2.3  
diff --git a/test/data/newformat/reftableRF.bin b/test/data/newformat/reftableRF.bin
diff --git a/test/data/newformat/statobsRF.txt b/test/data/newformat/statobsRF.txt
@@ -0,0 +1,3 @@
+    ML1p_1        ML1p_2        ML1p_3        ML1p_4       ML2p_1.2      ML2p_1.3      ML2p_1.4      ML2p_2.3      ML2p_2.4      ML2p_3.4     ML3p_1.2.3    ML3p_1.2.4    ML3p_1.3.4    ML3p_2.3.4      HWm_1         HWm_2         HWm_3         HWm_4         HWv_1         HWv_2         HWv_3         HWv_4        HBm_1.2       HBm_1.3       HBm_1.4       HBm_2.3       HBm_2.4       HBm_3.4       HBv_1.2       HBv_1.3       HBv_1.4       HBv_2.3       HBv_2.4       HBv_3.4       FST1m_1       FST1m_2       FST1m_3       FST1m_4       FST1v_1       FST1v_2       FST1v_3       FST1v_4      FST2m_1.2     FST2m_1.3     FST2m_1.4     FST2m_2.3     FST2m_2.4     FST2m_3.4     FST2v_1.2     FST2v_1.3     FST2v_1.4     FST2v_2.3     FST2v_2.4     FST2v_3.4      NEIm_1.2      NEIm_1.3      NEIm_1.4      NEIm_2.3      NEIm_2.4      NEIm_3.4      NEIv_1.2      NEIv_1.3      NEIv_1.4      NEIv_2.3      NEIv_2.4      NEIv_3.4     AMLm_1.2.3    AMLm_2.1.3    AMLm_3.1.2    AMLm_1.2.4    AMLm_2.1.4    AMLm_4.1.2    AMLm_1.3.4    AMLm_3.1.4    AMLm_4.1.3    AMLm_2.3.4    AMLm_3.2.4    AMLm_4.2.3    AMLv_1.2.3    AMLv_2.1.3    AMLv_3.1.2    AMLv_1.2.4    AMLv_2.1.4    AMLv_4.1.2    AMLv_1.3.4    AMLv_3.1.4    AMLv_4.1.3    AMLv_2.3.4    AMLv_3.2.4    AMLv_4.2.3   FST3m_1.2.3   FST3m_1.2.4   FST3m_1.3.4   FST3m_2.3.4   FST3v_1.2.3   FST3v_1.2.4   FST3v_1.3.4   FST3v_2.3.4   FST4m_1.2.3.4  FST4v_1.2.3.4   F3m_1.2.3     F3m_2.1.3     F3m_3.1.2     F3m_1.2.4     F3m_2.1.4     F3m_4.1.2     F3m_1.3.4     F3m_3.1.4     F3m_4.1.3     F3m_2.3.4     F3m_3.2.4     F3m_4.2.3     F3v_1.2.3     F3v_2.1.3     F3v_3.1.2     F3v_1.2.4     F3v_2.1.4     F3v_4.1.2     F3v_1.3.4     F3v_3.1.4     F3v_4.1.3     F3v_2.3.4     F3v_3.2.4     F3v_4.2.3    F4m_1.2.3.4   F4m_1.3.2.4   F4m_1.4.2.3   F4v_1.2.3.4   F4v_1.3.2.4   F4v_1.4.2.3  
+
+  1.568000000000000e-01    1.678000000000000e-01    1.326000000000000e-01    1.352000000000000e-01    3.440000000000000e-02    2.900000000000000e-02    2.780000000000000e-02    4.200000000000000e-02    4.380000000000000e-02    4.900000000000000e-02    4.000000000000000e-03    2.800000000000000e-03    7.800000000000000e-03    1.880000000000000e-02    2.846968421052632e-01    2.790715789473684e-01    2.868642105263158e-01    2.870389473684211e-01    3.223984027387196e-02    3.295100690609037e-02    3.107921258379100e-02    3.105523601229942e-02    3.070560000000000e-01    3.049800000000000e-01    3.062590000000000e-01    3.011170000000000e-01    3.015100000000000e-01    2.954530000000000e-01    2.664342154830966e-02    2.573648689737948e-02    2.566292250350070e-02    2.709084548009602e-02    2.684200830166033e-02    2.590368052710542e-02    5.956586463060817e-02    7.814769874931629e-02    5.240643415710141e-02    5.182922898050992e-02    3.517906971860676e-01    3.595507171873558e-01    3.391263036655473e-01    3.388646790815076e-01    8.197784597494988e-02    6.295322212673135e-02    6.658124418599255e-02    6.027260255368477e-02    6.120771066334537e-02    2.877419099698287e-02    1.466438427950965e-02    1.182408658374722e-02    1.248787863125582e-02    1.154724195873864e-02    1.186788804287042e-02    7.416059059191221e-03    5.014892847050694e-02    4.314128447341042e-02    4.453979690855386e-02    4.206224351259095e-02    4.222062285822909e-02    2.975466744207970e-02    7.297426651402327e-03    5.385952529871507e-03    5.983948559867485e-03    5.619270245055672e-03    5.719695522559435e-03    2.917812081342846e-03    4.652855467510640e-01    4.549712017078646e-01    4.866101224778395e-01    4.721121897616337e-01    4.564741239130648e-01    4.822697120758785e-01    5.032114876143826e-01    4.233300963157161e-01    4.243215896223842e-01    5.047798770054500e-01    4.359136821370371e-01    4.283899749416991e-01    2.000261014216488e-01    2.006885644645834e-01    1.902469960900266e-01    2.027329869557309e-01    1.983119335425060e-01    1.916273139734523e-01    2.084522858920826e-01    1.882430038657947e-01    1.901762833425623e-01    2.101916725859375e-01    1.896867894602543e-01    1.889118529832192e-01    6.846647650618530e-02    6.997800844855286e-02    5.304116502627133e-02    5.022410381914166e-02    8.746173289655702e-03    9.074458173706331e-03    7.294536070063879e-03    7.047118530593053e-03    6.048730662938400e-02    6.428613164721039e-03    1.311107894736842e-02    1.206071052631579e-02    6.088394736842105e-03    1.355407894736842e-02    1.161771052631579e-02    6.837026315789474e-03    1.554457894736842e-02    3.654894736842105e-03    4.846526315789474e-03    1.405121052631579e-02    4.097894736842105e-03    4.403526315789474e-03    1.924490493776733e-03    1.938259936440889e-03    1.481296964461452e-03    1.967414045118581e-03    2.023265162222888e-03    1.578696838918338e-03    1.926895655006347e-03    1.015786065110529e-03    1.089569401259753e-03    1.865684708329478e-03    1.032712333048327e-03    1.089472418336853e-03    4.430000000000000e-04    2.433500000000000e-03    1.990500000000000e-03    1.006890129025805e-03    1.287489325615123e-03    1.254577575265053e-03  
diff --git a/test/readreftable-test.cpp b/test/readreftable-test.cpp
@@ -134,3 +134,9 @@ TEST_CASE("Read statobs from txt") {
     const auto expected = Catch::Matchers::Approx(readstatobs).epsilon(0.001);
     CHECK_THAT( statobs, expected );
 }
+
+TEST_CASE("Read statobs from txt new format") {
+    const auto readstatobs = readStatObs("newformat/statobsRF.txt");
+    const auto expected = Catch::Matchers::Approx(readstatobs).epsilon(0.001);
+    CHECK_THAT( statobs2, expected );
+}
diff --git a/test/statobsTest.hpp b/test/statobsTest.hpp
@@ -131,4 +131,138 @@ std::vector<double> statobs {
     0.00057110,
     0.00065931,
     0.00050151
+};
+
+std::vector<double> statobs2 {
+    1.568000000000000e-01,
+    1.678000000000000e-01,
+    1.326000000000000e-01,
+    1.352000000000000e-01,
+    3.440000000000000e-02,
+    2.900000000000000e-02,
+    2.780000000000000e-02,
+    4.200000000000000e-02,
+    4.380000000000000e-02,
+    4.900000000000000e-02,
+    4.000000000000000e-03,
+    2.800000000000000e-03,
+    7.800000000000000e-03,
+    1.880000000000000e-02,
+    2.846968421052632e-01,
+    2.790715789473684e-01,
+    2.868642105263158e-01,
+    2.870389473684211e-01,
+    3.223984027387196e-02,
+    3.295100690609037e-02,
+    3.107921258379100e-02,
+    3.105523601229942e-02,
+    3.070560000000000e-01,
+    3.049800000000000e-01,
+    3.062590000000000e-01,
+    3.011170000000000e-01,
+    3.015100000000000e-01,
+    2.954530000000000e-01,
+    2.664342154830966e-02,
+    2.573648689737948e-02,
+    2.566292250350070e-02,
+    2.709084548009602e-02,
+    2.684200830166033e-02,
+    2.590368052710542e-02,
+    5.956586463060817e-02,
+    7.814769874931629e-02,
+    5.240643415710141e-02,
+    5.182922898050992e-02,
+    3.517906971860676e-01,
+    3.595507171873558e-01,
+    3.391263036655473e-01,
+    3.388646790815076e-01,
+    8.197784597494988e-02,
+    6.295322212673135e-02,
+    6.658124418599255e-02,
+    6.027260255368477e-02,
+    6.120771066334537e-02,
+    2.877419099698287e-02,
+    1.466438427950965e-02,
+    1.182408658374722e-02,
+    1.248787863125582e-02,
+    1.154724195873864e-02,
+    1.186788804287042e-02,
+    7.416059059191221e-03,
+    5.014892847050694e-02,
+    4.314128447341042e-02,
+    4.453979690855386e-02,
+    4.206224351259095e-02,
+    4.222062285822909e-02,
+    2.975466744207970e-02,
+    7.297426651402327e-03,
+    5.385952529871507e-03,
+    5.983948559867485e-03,
+    5.619270245055672e-03,
+    5.719695522559435e-03,
+    2.917812081342846e-03,
+    4.652855467510640e-01,
+    4.549712017078646e-01,
+    4.866101224778395e-01,
+    4.721121897616337e-01,
+    4.564741239130648e-01,
+    4.822697120758785e-01,
+    5.032114876143826e-01,
+    4.233300963157161e-01,
+    4.243215896223842e-01,
+    5.047798770054500e-01,
+    4.359136821370371e-01,
+    4.283899749416991e-01,
+    2.000261014216488e-01,
+    2.006885644645834e-01,
+    1.902469960900266e-01,
+    2.027329869557309e-01,
+    1.983119335425060e-01,
+    1.916273139734523e-01,
+    2.084522858920826e-01,
+    1.882430038657947e-01,
+    1.901762833425623e-01,
+    2.101916725859375e-01,
+    1.896867894602543e-01,
+    1.889118529832192e-01,
+    6.846647650618530e-02,
+    6.997800844855286e-02,
+    5.304116502627133e-02,
+    5.022410381914166e-02,
+    8.746173289655702e-03,
+    9.074458173706331e-03,
+    7.294536070063879e-03,
+    7.047118530593053e-03,
+    6.048730662938400e-02,
+    6.428613164721039e-03,
+    1.311107894736842e-02,
+    1.206071052631579e-02,
+    6.088394736842105e-03,
+    1.355407894736842e-02,
+    1.161771052631579e-02,
+    6.837026315789474e-03,
+    1.554457894736842e-02,
+    3.654894736842105e-03,
+    4.846526315789474e-03,
+    1.405121052631579e-02,
+    4.097894736842105e-03,
+    4.403526315789474e-03,
+    1.924490493776733e-03,
+    1.938259936440889e-03,
+    1.481296964461452e-03,
+    1.967414045118581e-03,
+    2.023265162222888e-03,
+    1.578696838918338e-03,
+    1.926895655006347e-03,
+    1.015786065110529e-03,
+    1.089569401259753e-03,
+    1.865684708329478e-03,
+    1.032712333048327e-03,
+    1.089472418336853e-03,
+    4.430000000000000e-04,
+    2.433500000000000e-03,
+    1.990500000000000e-03,
+    1.006890129025805e-03,
+    1.287489325615123e-03,
+    1.254577575265053e-03  
+
 };
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		ML1p_1 ML1p_2 ML1p_3 ML1p_4 ML2p_1.2 ML2p_1.3 ML2p_1.4 ML2p_2.3 ML2p_2.4 ML2p_3.4 ML3p_1.2.3 ML3p_1.2.4 ML3p_1.3.4 ML3p_2.3.4 HWm_1 HWm_2 HWm_3 HWm_4 HWv_1 HWv_2 HWv_3 HWv_4 HBm_1.2 HBm_1.3 HBm_1.4 HBm_2.3 HBm_2.4 HBm_3.4 HBv_1.2 HBv_1.3 HBv_1.4 HBv_2.3 HBv_2.4 HBv_3.4 FST1m_1 FST1m_2 FST1m_3 FST1m_4 FST1v_1 FST1v_2 FST1v_3 FST1v_4 FST2m_1.2 FST2m_1.3 FST2m_1.4 FST2m_2.3 FST2m_2.4 FST2m_3.4 FST2v_1.2 FST2v_1.3 FST2v_1.4 FST2v_2.3 FST2v_2.4 FST2v_3.4 NEIm_1.2 NEIm_1.3 NEIm_1.4 NEIm_2.3 NEIm_2.4 NEIm_3.4 NEIv_1.2 NEIv_1.3 NEIv_1.4 NEIv_2.3 NEIv_2.4 NEIv_3.4 AMLm_1.2.3 AMLm_2.1.3 AMLm_3.1.2 AMLm_1.2.4 AMLm_2.1.4 AMLm_4.1.2 AMLm_1.3.4 AMLm_3.1.4 AMLm_4.1.3 AMLm_2.3.4 AMLm_3.2.4 AMLm_4.2.3 AMLv_1.2.3 AMLv_2.1.3 AMLv_3.1.2 AMLv_1.2.4 AMLv_2.1.4 AMLv_4.1.2 AMLv_1.3.4 AMLv_3.1.4 AMLv_4.1.3 AMLv_2.3.4 AMLv_3.2.4 AMLv_4.2.3 FST3m_1.2.3 FST3m_1.2.4 FST3m_1.3.4 FST3m_2.3.4 FST3v_1.2.3 FST3v_1.2.4 FST3v_1.3.4 FST3v_2.3.4 FST4m_1.2.3.4 FST4v_1.2.3.4 F3m_1.2.3 F3m_2.1.3 F3m_3.1.2 F3m_1.2.4 F3m_2.1.4 F3m_4.1.2 F3m_1.3.4 F3m_3.1.4 F3m_4.1.3 F3m_2.3.4 F3m_3.2.4 F3m_4.2.3 F3v_1.2.3 F3v_2.1.3 F3v_3.1.2 F3v_1.2.4 F3v_2.1.4 F3v_4.1.2 F3v_1.3.4 F3v_3.1.4 F3v_4.1.3 F3v_2.3.4 F3v_3.2.4 F3v_4.2.3 F4m_1.2.3.4 F4m_1.3.2.4 F4m_1.4.2.3 F4v_1.2.3.4 F4v_1.3.2.4 F4v_1.4.2.3

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