[Genabel-commits] r1125 - in pkg/OmicABEL/src/reshuffle: . data_4test data_4test_check
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 10 18:01:47 CET 2013
Author: sharapovsodbo
Date: 2013-03-10 18:01:46 +0100 (Sun, 10 Mar 2013)
New Revision: 1125
Added:
pkg/OmicABEL/src/reshuffle/data_4test_check/
pkg/OmicABEL/src/reshuffle/data_4test_check/data_chi_trsnp.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/data_chiall.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/data_chiover.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/data_def.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/data_slim.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/data_snpsbynames.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/data_snpsnumbers.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/data_traitnumbers.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/data_traitsbynames.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/data_ts_combo.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/datadims.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/estdef.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/estnames.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/estnum.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/snpnames.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/snpnamesdef.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/traitnames.txt
pkg/OmicABEL/src/reshuffle/data_4test_check/traitnamesdef.txt
Modified:
pkg/OmicABEL/src/reshuffle/DONE.txt
pkg/OmicABEL/src/reshuffle/Parameters.cpp
pkg/OmicABEL/src/reshuffle/Parameters.h
pkg/OmicABEL/src/reshuffle/data_4test/data_annotation.txt
pkg/OmicABEL/src/reshuffle/main.cpp
pkg/OmicABEL/src/reshuffle/reshuffle.cpp
pkg/OmicABEL/src/reshuffle/reshuffle.h
pkg/OmicABEL/src/reshuffle/test.cpp
pkg/OmicABEL/src/reshuffle/test.h
Log:
ver 0.001
test+ some corrections
Modified: pkg/OmicABEL/src/reshuffle/DONE.txt
===================================================================
--- pkg/OmicABEL/src/reshuffle/DONE.txt 2013-03-09 01:14:06 UTC (rev 1124)
+++ pkg/OmicABEL/src/reshuffle/DONE.txt 2013-03-10 17:01:46 UTC (rev 1125)
@@ -2,4 +2,16 @@
improved parsing of command line:
search for parameter's name only after separator
delete parameter's name and value from command line in case of finding it
+ver 0.002
+ tests for all points in specification
+ one bug with traitsbynames test unfixed
+ all datas written ub one file in root folder
+ datadims->datadims.txt
+ trait(snp)names->traits(snp)names.txt
+ traits(snps)->data.txt
+ chi->chi_data.txt
+ traits,snps,chi->chi_data.txt
+ heritabilities->estimates.txt
+ dataslim,chi->slim_data.txt
+
\ No newline at end of file
Modified: pkg/OmicABEL/src/reshuffle/Parameters.cpp
===================================================================
--- pkg/OmicABEL/src/reshuffle/Parameters.cpp 2013-03-09 01:14:06 UTC (rev 1124)
+++ pkg/OmicABEL/src/reshuffle/Parameters.cpp 2013-03-10 17:01:46 UTC (rev 1125)
@@ -18,6 +18,7 @@
cmd_line += argv[i];
}
cmd_line += sep; // Need for cmdline parsing
+ cout<<cmd_line<<endl;
return cmd_line;
}
//Default constructor
@@ -141,4 +142,6 @@
cmdline= chi.delfromcmdline(cmdline);
dataslim= Parameter(cmdline, "dataslim");
cmdline= dataslim.delfromcmdline(cmdline);
+ test= Parameter(cmdline, "test");
+ cmdline=test.delfromcmdline(cmdline);
}
Modified: pkg/OmicABEL/src/reshuffle/Parameters.h
===================================================================
--- pkg/OmicABEL/src/reshuffle/Parameters.h 2013-03-09 01:14:06 UTC (rev 1124)
+++ pkg/OmicABEL/src/reshuffle/Parameters.h 2013-03-10 17:01:46 UTC (rev 1125)
@@ -40,6 +40,7 @@
Parameter heritabilities;
Parameter chi;
Parameter dataslim;
+ Parameter test;
Parameters();
Parameters(int, char*[]); // Constructor from cmdline
static string get_cmd_line(int,char*[]);
Modified: pkg/OmicABEL/src/reshuffle/data_4test/data_annotation.txt
===================================================================
--- pkg/OmicABEL/src/reshuffle/data_4test/data_annotation.txt 2013-03-09 01:14:06 UTC (rev 1124)
+++ pkg/OmicABEL/src/reshuffle/data_4test/data_annotation.txt 2013-03-10 17:01:46 UTC (rev 1125)
@@ -5,9 +5,114 @@
# of snps:100
Traits:
-hgta,tga,tca,ldla,hdla
+TRAIT #1 hgta
+TRAIT #1 tga
+TRAIT #1 tca
+TRAIT #1 ldla
+TRAIT #1 hdla
covariates:
-sex,age
+COV #1 sex
+COV #2 age
-SNPs:
\ No newline at end of file
+SNPs:
+SNP #1 rs3121561
+SNP #2 rs3813193
+SNP #3 rs4075116
+SNP #4 rs3934834
+SNP #5 rs3766193
+SNP #6 rs3766192
+SNP #7 rs3766191
+SNP #8 rs9442371
+SNP #9 rs9442372
+SNP #10 rs10907177
+SNP #11 rs3737728
+SNP #12 rs10907178
+SNP #13 rs9442398
+SNP #14 rs6701114
+SNP #15 rs4074137
+SNP #16 rs6687776
+SNP #17 rs6678318
+SNP #18 rs9651273
+SNP #19 rs11579015
+SNP #20 rs6671356
+SNP #21 rs6666280
+SNP #22 rs4970405
+SNP #23 rs12726255
+SNP #24 rs4970409
+SNP #25 rs7548798
+SNP #26 rs17160824
+SNP #27 rs17160826
+SNP #28 rs12748370
+SNP #29 rs11807848
+SNP #30 rs9442373
+SNP #31 rs6682475
+SNP #32 rs2298217
+SNP #33 rs10907182
+SNP #34 rs10907183
+SNP #35 rs4970357
+SNP #36 rs11260603
+SNP #37 rs9442380
+SNP #38 rs4970358
+SNP #39 rs4970362
+SNP #40 rs9442385
+SNP #41 rs9660710
+SNP #42 rs1891905
+SNP #43 rs4970420
+SNP #44 rs1320565
+SNP #45 rs3813204
+SNP #46 rs11260549
+SNP #47 rs6684820
+SNP #48 rs10907174
+SNP #49 rs11260554
+SNP #50 rs10907175
+SNP #51 rs9729550
+SNP #52 rs1815606
+SNP #53 rs11721
+SNP #54 rs2887286
+SNP #55 rs3813199
+SNP #56 rs3766186
+SNP #57 rs7515488
+SNP #58 rs715643
+SNP #59 rs6675798
+SNP #60 rs6603783
+SNP #61 rs6603785
+SNP #62 rs6603787
+SNP #63 rs3818646
+SNP #64 rs11804831
+SNP #65 rs604618
+SNP #66 rs12142199
+SNP #67 rs17160669
+SNP #68 rs2649588
+SNP #69 rs1781145
+SNP #70 rs819980
+SNP #71 rs6690515
+SNP #72 rs9439458
+SNP #73 rs1571150
+SNP #74 rs7290
+SNP #75 rs3766180
+SNP #76 rs3766178
+SNP #77 rs7533
+SNP #78 rs3766177
+SNP #79 rs7517401
+SNP #80 rs3128342
+SNP #81 rs7531530
+SNP #82 rs7366884
+SNP #83 rs880051
+SNP #84 rs3766169
+SNP #85 rs2296716
+SNP #86 rs9439468
+SNP #87 rs6603791
+SNP #88 rs6656541
+SNP #89 rs6603793
+SNP #90 rs7520996
+SNP #91 rs7519837
+SNP #92 rs7556282
+SNP #93 rs7531583
+SNP #94 rs12044597
+SNP #95 rs2272908
+SNP #96 rs3737628
+SNP #97 rs9660180
+SNP #98 rs10907185
+SNP #99 rs11585349
+SNP #100 rs16825336
Added: pkg/OmicABEL/src/reshuffle/data_4test_check/data_chi_trsnp.txt
===================================================================
--- pkg/OmicABEL/src/reshuffle/data_4test_check/data_chi_trsnp.txt (rev 0)
+++ pkg/OmicABEL/src/reshuffle/data_4test_check/data_chi_trsnp.txt 2013-03-10 17:01:46 UTC (rev 1125)
@@ -0,0 +1,46 @@
+hgta
+beta_intercept beta_sex beta_age beta_SNP se_intercept se_sex se_age se_SNP cov_sex_intercept cov_age_intercept cov_SNP_intercept cov_age_sex cov_SNP_sex cov_SNP_age Chi2
+tga
+beta_intercept beta_sex beta_age beta_SNP se_intercept se_sex se_age se_SNP cov_sex_intercept cov_age_intercept cov_SNP_intercept cov_age_sex cov_SNP_sex cov_SNP_age Chi2
+rs12142199 -0.145846679806709 0.0166560783982277 0.00066832936136052 0.137064591050148 0.0619793385267258 0.0233147107064724 0.000864078814629465 0.053544145077467 -0.000228573000640608 -3.65004380000755e-005 -0.00230495003052056 -4.46790579644585e-007 3.60033191100229e-005 -1.98094923575809e-007 6.55279485392153
+tca
+beta_intercept beta_sex beta_age beta_SNP se_intercept se_sex se_age se_SNP cov_sex_intercept cov_age_intercept cov_SNP_intercept cov_age_sex cov_SNP_sex cov_SNP_age Chi2
+rs3121561 0.11519206315279 0.0138921467587352 -0.00025116978213191 -0.146481543779373 0.0872452557086945 0.0322736985981464 0.00120238901581615 0.0836698412895203 -0.000360472622560337 -7.23058110452257e-005 -0.00511586805805564 -8.21643482140644e-007 -3.46828310284764e-005 1.68063616001746e-006 3.06498198616101
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+ldla
+beta_intercept beta_sex beta_age beta_SNP se_intercept se_sex se_age se_SNP cov_sex_intercept cov_age_intercept cov_SNP_intercept cov_age_sex cov_SNP_sex cov_SNP_age Chi2
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+hdla
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Added: pkg/OmicABEL/src/reshuffle/data_4test_check/data_chiall.txt
===================================================================
--- pkg/OmicABEL/src/reshuffle/data_4test_check/data_chiall.txt (rev 0)
+++ pkg/OmicABEL/src/reshuffle/data_4test_check/data_chiall.txt 2013-03-10 17:01:46 UTC (rev 1125)
@@ -0,0 +1,510 @@
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+rs11260554 0.00779650593176484 0.0465780086815357 0.00398941617459059 -0.274979025125504 0.529947757720947 0.1698137819767 0.0058104544878006 0.508132696151733 -0.00872904807329178 -0.00145929015707225 -0.224032297730446 -3.53137620550115e-005 -0.0012316289357841 -0.000201123708393425 0.292849747765197
+rs10907175 0.43775537610054 0.0452112220227718 0.00397980213165283 -0.721029996871948 0.638484358787537 0.169796481728554 0.00579955149441957 0.611237049102783 -0.00982417911291122 -0.00153550948016346 -0.346418052911758 -3.62812388630118e-005 2.85576552414568e-005 -0.000106005863926839 1.39151318303036
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1125
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