From 6fbbfe5e8bcc3b57c4177687bbf67bf041da3cba Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Wed, 26 Jun 2013 21:35:07 +0000 Subject: Got code that creates DataSets object running Fixed one genofile that had extra quotation marks in the comments that caused an error Defaults mb_graph_interval to 1 for species without chromosome lengths in megabases --- web/genotypes/B6D2F2-PSU.geno | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'web/genotypes') diff --git a/web/genotypes/B6D2F2-PSU.geno b/web/genotypes/B6D2F2-PSU.geno index 2c8876a0..a0c1728f 100755 --- a/web/genotypes/B6D2F2-PSU.geno +++ b/web/genotypes/B6D2F2-PSU.geno @@ -1,5 +1,5 @@ -"#This is B6D2F2-PSU genotype file, it should be tab-delimited" -"#the first three/four columns should be ""Chr, Locus, cM, [Mb]"" (case sensitive)" +#This is B6D2F2-PSU genotype file, it should be tab-delimited +#the first three/four columns should be ""Chr, Locus, cM, [Mb]"" (case sensitive) #please save as Unix format text file. #comment line always start with a '#' #type riset or intercross @@ -8,9 +8,9 @@ #abbreviation of maternal or paternal parents @mat:B @pat:D -"#heterozygous , optional, default is ""H""" +#heterozygous , optional, default is ""H"" @het:H -"#Unknown , optional, default is ""U""" +#Unknown , optional, default is ""U"" @unk:U Chr Locus cM Mb PSU0001 PSU0004 PSU0007 PSU0022 PSU0024 PSU0042 PSU0044 PSU0045 PSU0046 PSU0048 PSU0049 PSU0050 PSU0052 PSU0053 PSU0054 PSU0055 PSU0056 PSU0057 PSU0058 PSU0059 PSU0060 PSU0061 PSU0062 PSU0063 PSU0066 PSU0067 PSU0068 PSU0069 PSU0070 PSU0071 PSU0072 PSU0074 PSU0077 PSU0079 PSU0080 PSU0082 PSU0083 PSU0084 PSU0085 PSU0086 PSU0087 PSU0089 PSU0090 PSU0091 PSU0092 PSU0093 PSU0094 PSU0095 PSU0096 PSU0097 PSU0098 PSU0099 PSU0100 PSU0102 PSU0103 PSU0104 PSU0107 PSU0108 PSU0109 PSU0110 PSU0112 PSU0113 PSU0114 PSU0116 PSU0117 PSU0118 PSU0119 PSU0122 PSU0124 PSU0126 PSU0128 PSU0130 PSU0131 PSU0132 PSU0133 PSU0134 PSU0135 PSU0136 PSU0137 PSU0138 PSU0139 PSU0140 PSU0141 PSU0142 PSU0143 PSU0146 PSU0147 PSU0148 PSU0152 PSU0153 PSU0155 PSU0158 PSU0159 PSU0163 PSU0164 PSU0165 PSU0166 PSU0167 PSU0168 PSU0169 PSU0170 PSU0172 PSU0173 PSU0174 PSU0175 PSU0177 PSU0178 PSU0179 PSU0180 PSU0182 PSU0183 PSU0187 PSU0188 PSU0190 PSU0191 PSU0193 PSU0194 PSU0196 PSU0197 PSU0198 PSU0199 PSU0205 PSU0206 PSU0207 PSU0208 PSU0209 PSU0210 PSU0211 PSU0212 PSU0213 PSU0214 PSU0216 PSU0218 PSU0219 PSU0220 PSU0222 PSU0223 PSU0225 PSU0226 PSU0227 PSU0229 PSU0230 PSU0231 PSU0234 PSU0235 PSU0236 PSU0238 PSU0239 PSU0241 PSU0242 PSU0243 PSU0244 PSU0246 PSU0247 PSU0248 PSU0250 PSU0251 PSU0255 PSU0257 PSU0258 PSU0260 PSU0261 PSU0262 PSU0263 PSU0264 PSU0271 PSU0272 PSU0273 PSU0274 PSU0275 PSU0276 PSU0278 PSU0280 PSU0282 PSU0283 PSU0285 PSU0286 PSU0287 PSU0288 PSU0289 PSU0291 PSU0292 PSU0293 PSU0295 PSU0296 PSU0299 PSU0300 PSU0301 PSU0302 PSU0304 PSU0305 PSU0306 PSU0308 PSU0309 PSU0310 PSU0311 PSU0312 PSU0313 PSU0314 PSU0315 PSU0316 PSU0317 PSU0318 PSU0319 PSU0320 PSU0321 PSU0323 PSU0325 PSU0326 PSU0327 PSU0328 PSU0329 PSU0330 PSU0331 PSU0334 PSU0336 PSU0337 PSU0338 PSU0339 PSU0340 PSU0341 PSU0342 PSU0343 PSU0344 PSU0346 PSU0349 PSU0351 PSU0352 PSU0353 PSU0355 PSU0356 PSU0357 PSU0358 PSU0359 PSU0360 PSU0361 PSU0362 PSU0363 PSU0366 PSU0367 PSU0369 PSU0370 PSU0371 PSU0372 PSU0373 PSU0374 PSU0375 PSU0376 PSU0378 PSU0379 PSU0381 PSU0382 PSU0383 PSU0384 PSU0385 PSU0388 PSU0390 PSU0391 PSU0392 PSU0393 PSU0395 PSU0397 PSU0399 PSU0400 PSU0401 PSU0403 PSU0405 PSU0406 PSU0408 PSU0410 PSU0412 PSU0413 PSU0414 PSU0416 PSU0417 PSU0418 PSU0420 PSU0421 PSU0423 PSU0425 PSU0426 PSU0430 PSU0431 PSU0434 PSU0435 PSU0437 PSU0438 PSU0441 PSU0445 PSU0449 PSU0450 PSU0451 PSU0452 PSU0454 PSU0455 PSU0458 PSU0461 PSU0462 PSU0464 PSU0466 PSU0468 PSU0470 PSU0472 PSU0478 PSU0479 PSU0480 PSU0482 PSU0483 PSU0487 PSU0488 PSU0490 PSU0492 PSU0493 PSU0494 PSU0495 PSU0499 PSU0501 PSU0502 PSU0503 PSU0504 PSU0505 PSU0506 PSU0508 PSU0511 PSU0513 PSU0514 PSU0517 PSU0519 PSU0521 PSU0522 PSU0523 PSU0524 PSU0527 PSU0529 PSU0531 PSU0533 PSU0535 PSU0536 PSU0537 PSU0540 PSU0542 PSU0543 PSU0545 PSU0546 PSU0549 PSU0551 PSU0553 PSU0554 PSU0557 PSU0561 PSU0562 PSU0565 PSU0566 PSU0568 PSU0569 PSU0570 PSU0571 PSU0575 PSU0576 PSU0586 PSU0593 PSU0597 PSU0598 PSU0603 PSU0604 PSU0606 PSU0609 PSU0610 PSU0612 PSU0616 PSU0617 PSU0620 PSU0621 PSU0623 PSU0624 PSU0626 PSU0629 PSU0630 PSU0631 PSU0632 PSU0634 PSU0637 PSU0639 PSU0641 PSU0642 PSU0643 PSU0645 PSU0646 PSU0647 PSU0648 PSU0649 PSU0650 PSU0651 PSU0652 PSU0654 PSU0655 PSU0659 PSU0661 PSU0662 PSU0663 PSU0665 PSU0667 PSU0668 PSU0669 PSU0671 PSU0672 PSU0673 PSU0674 PSU0675 PSU0677 PSU0680 PSU0682 PSU0683 PSU0684 PSU0686 PSU0687 PSU0689 PSU0690 PSU0691 PSU0696 PSU0697 PSU0699 PSU0701 PSU0702 PSU0704 PSU0705 PSU0706 PSU0709 PSU0710 PSU0712 PSU0714 PSU0716 PSU0717 PSU0718 PSU0719 PSU0720 PSU0721 PSU0724 PSU0725 PSU0727 PSU0728 PSU0729 PSU0730 PSU0731 PSU0733 PSU0734 PSU0736 PSU0737 PSU0738 PSU0741 PSU0742 PSU0743 PSU0744 PSU0745 PSU0749 PSU0750 PSU0751 PSU0753 PSU0756 PSU0757 PSU0758 PSU0759 PSU0760 PSU0763 PSU0764 PSU0765 PSU0766 PSU0767 PSU0769 PSU0770 PSU0771 PSU0772 PSU0773 PSU0776 PSU0780 PSU0781 PSU0782 PSU0783 PSU0784 PSU0787 PSU0788 PSU0789 PSU0790 PSU0791 PSU0792 PSU0794 PSU0798 PSU0799 PSU0804 PSU0806 PSU0807 PSU0808 PSU0810 PSU0811 PSU0813 PSU0814 PSU0815 PSU0816 PSU0818 PSU0821 PSU0822 PSU0824 PSU0825 PSU0828 PSU0830 PSU0831 PSU0833 PSU0834 PSU0837 PSU0840 PSU0843 PSU0844 PSU0847 PSU0849 PSU0851 PSU0853 PSU0855 PSU0856 PSU0858 PSU0860 PSU0862 PSU0863 PSU0864 PSU1060 PSU1095 PSU1372 PSU1373 PSU1374 PSU1381 PSU1392 PSU1399 PSU1414 PSU1421 PSU1422 PSU1430 PSU1432 PSU1470 PSU1473 PSU1490 PSU1526 PSU1540 PSU1549 PSU1553 PSU1556 PSU1561 PSU1564 PSU1576 PSU1591 PSU1609 PSU1613 PSU1625 PSU1626 PSU1630 PSU1638 PSU1639 1 rs13475697 0.01 3.385827 U H H H H B D B H B H H D H H H H H H H H B H H H H D H D B B D H H B H D H B H H H B B B D B H H D H D B H H H B H B B B B B B H H B D D H H D D H D D H H B D D B B D B B D B B H B B H D B H H H D H D B D B D H H D B D D H H H D B H B H D H D H D B D D D H H D H B B H H B H B H B D H D D D D H D H H H D B D H D H H D B D B B B D H H B D H H H H D H D H D H D H D D B H D B H D H D D H H H H H D D B H H D B H H H H D H H H D H B D D D H H H H B D H H H D H B B B D B H H H H B H H B H B D D D D H D H D H D B H H H B B B B B H U B H H B D H D H D H H B B B H H H H H D B H H H B H D H D B B D B H H B D H H H B B H H H D H B H B D H B H D B H B H H H B H B H D D B H D B H H D H H D D H H H H B B H D H D H H D D B D D H H D D H H B H H H H B H H D H D H B H D D H H D D B H H H H H H D B D H H B H B H H H H H D H B B D H H D D D B B H H B H H B H B B H B D H H H B B H D B B B D D B D H H B H D D H H H B H H D B D H B H D D B H H D H D H B H H H H H D H B D B H H H D H H B H H B D H D D B H D H D B H H H D H D H D D H B B D B H D B H D H H B B H H H H B H D H H B D B D H D D H B D H B H H H D D H D H -- cgit v1.2.3 From 0fcadee805a6d4a2007e57a69ab130eb9b1c1a3c Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Thu, 18 Jul 2013 17:39:10 -0500 Subject: Added Amelie's rat data genotypes Got human mapping mostly working Fixed dataset dropdown menus --- misc/notes.txt | 5 + web/genotypes/HSNIH.geno.gz | Bin 0 -> 63400027 bytes wqflask/base/trait.py | 3 +- wqflask/base/webqtlConfig.py | 4 +- wqflask/maintenance/gen_select_dataset.py | 15 +- wqflask/wqflask/correlation/show_corr_results.py | 2 - wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 4 +- .../new/javascript/dataset_menu_structure.json | 248 ++++++++++----------- 8 files changed, 136 insertions(+), 145 deletions(-) create mode 100755 web/genotypes/HSNIH.geno.gz (limited to 'web/genotypes') diff --git a/misc/notes.txt b/misc/notes.txt index 9da6c4ea..d9bd6e41 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -245,6 +245,11 @@ To iterate through dictionary items: for X, Y in MyDictionary.items(): =========================================== +Change import path from command line +export PYTHONPATH=~/gene/wqflask (or whatever) + +=========================================== + Create symbolic link: ln -s dir_to_link_to linking_dir diff --git a/web/genotypes/HSNIH.geno.gz b/web/genotypes/HSNIH.geno.gz new file mode 100755 index 00000000..96584768 Binary files /dev/null and b/web/genotypes/HSNIH.geno.gz differ diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 6648047c..a1e6b0d3 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -319,10 +319,9 @@ class GeneralTrait(object): #XZ: assign SQL query result to trait attributes. for i, field in enumerate(self.dataset.display_fields): - print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i])) + #print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i])) holder = trait_info[i] if isinstance(trait_info[i], basestring): - print("is basestring") holder = unicode(trait_info[i], "utf8") setattr(self, field, holder) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 716986db..d4511212 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -53,8 +53,8 @@ GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'web/' -PYLMM_PATH = '/home/zas1024/' -SNP_PATH = '/mnt/xvdf1/snps/' +PYLMM_PATH = '/home/zas1024/plink/' +SNP_PATH = '/home/zas1024/snps/' IMGDIR = HTMLPATH +'image/' IMAGESPATH = HTMLPATH + 'images/' UPLOADPATH = IMAGESPATH + 'upload/' diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index d653fd2d..8cb94f20 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -47,6 +47,15 @@ import urlparse from pprint import pformat as pf +#Engine = sa.create_engine(our_settings.SQLALCHEMY_DATABASE_URI) + +# build MySql database connection + +#conn = Engine.connect() + + + + def parse_db_uri(db_uri): """Converts a database URI to the db name, host name, user name, and password""" @@ -106,7 +115,7 @@ def build_types(species, group): (all types except phenotype/genotype are tissues) """ - Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') + Cursor.execute("""select distinct Tissue.Name, Tissue.Name from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species where Species.Name = %s and Species.Id = InbredSet.SpeciesId and InbredSet.Name = %s and @@ -161,13 +170,9 @@ def build_datasets(species, group, type_name): def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" -<<<<<<< HEAD parse_db_uri(our_settings.DB_URI) -======= - ->>>>>>> 1a3a456eb7635337a966913f2e2e75c8a89bb92e species = get_species() groups = get_groups(species) types = get_types(groups) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 422fa8af..07d70897 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -140,8 +140,6 @@ class CorrelationResults(object): this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values( this_trait_vals, target_vals) - print("num_overlap:", num_overlap) - if self.corr_method == 'pearson': sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals) else: diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 5bfc3a01..38a49f12 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -138,8 +138,8 @@ def run_human(pheno_vector, #print("***** Added to {} queue *****".format(key)) for snp, this_id in plink_input: #with Bench("part before association"): - if count > 2000: - break + #if count > 2000: + # break count += 1 percent_complete = (float(count) / total_snps) * 100 diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index a4de53bd..49c44fbd 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -793,10 +793,6 @@ ] ], "Striatum mRNA": [ - [ - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" - ], [ "SA_M2_0905_R", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" @@ -1051,10 +1047,6 @@ ] ], "Cerebellum mRNA": [ - [ - "CB_M_1004_M", - "SJUT Cerebellum mRNA M430 (Oct04) MAS5" - ], [ "CB_M_1004_R", "SJUT Cerebellum mRNA M430 (Oct04) RMA" @@ -1063,6 +1055,10 @@ "CB_M_1004_P", "SJUT Cerebellum mRNA M430 (Oct04) PDNN" ], + [ + "CB_M_1004_M", + "SJUT Cerebellum mRNA M430 (Oct04) MAS5" + ], [ "CB_M_1003_M", "SJUT Cerebellum mRNA M430 (Oct03) MAS5" @@ -1551,10 +1547,6 @@ ] ], "Prefrontal Cortex mRNA": [ - [ - "VCUEtOH_1206_R", - "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" - ], [ "VCUSal_1206_R", "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" @@ -1725,10 +1717,6 @@ ] ], "Ventral Tegmental Area mRNA": [ - [ - "VCUEtOH_0609_R", - "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" - ], [ "VCUEtOH_0609_R", "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" @@ -2013,10 +2001,6 @@ ] ], "Prefrontal Cortex mRNA": [ - [ - "VCUEtOH_0806_R", - "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" - ], [ "VCUEtOH_0806_R", "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" @@ -2572,7 +2556,7 @@ ], [ "Leaf mRNA", - "Leaf mRNA mRNA" + "Leaf mRNA" ] ], "SXM": [ @@ -2586,11 +2570,11 @@ ], [ "Embryo mRNA", - "Embryo mRNA mRNA" + "Embryo mRNA" ], [ "Leaf mRNA", - "Leaf mRNA mRNA" + "Leaf mRNA" ] ] }, @@ -2606,7 +2590,7 @@ ], [ "Whole Body mRNA", - "Whole Body mRNA mRNA" + "Whole Body mRNA" ] ], "Oregon-R_x_2b3": [ @@ -2620,7 +2604,7 @@ ], [ "Whole Body mRNA", - "Whole Body mRNA mRNA" + "Whole Body mRNA" ] ] }, @@ -2636,7 +2620,7 @@ ], [ "Brain mRNA", - "Brain mRNA mRNA" + "Brain mRNA" ] ], "AD-cases-controls-Myers": [ @@ -2650,7 +2634,7 @@ ], [ "Brain mRNA", - "Brain mRNA mRNA" + "Brain mRNA" ] ], "CANDLE": [ @@ -2664,11 +2648,11 @@ ], [ "Methylation", - "Methylation mRNA" + "Methylation" ], [ "Newborn Cord Blood mRNA", - "Newborn Cord Blood mRNA mRNA" + "Newborn Cord Blood mRNA" ] ], "CEPH-2004": [ @@ -2682,7 +2666,7 @@ ], [ "Lymphoblast B-cell mRNA", - "Lymphoblast B-cell mRNA mRNA" + "Lymphoblast B-cell mRNA" ] ], "HB": [ @@ -2696,15 +2680,15 @@ ], [ "Cerebellum mRNA", - "Cerebellum mRNA mRNA" + "Cerebellum mRNA" ], [ "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA mRNA" + "Prefrontal Cortex mRNA" ], [ "Primary Visual Cortex mRNA", - "Primary Visual Cortex mRNA mRNA" + "Primary Visual Cortex mRNA" ] ], "HLC": [ @@ -2718,7 +2702,7 @@ ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ] ], "HLT": [ @@ -2732,7 +2716,7 @@ ], [ "Lung mRNA", - "Lung mRNA mRNA" + "Lung mRNA" ] ], "HSB": [ @@ -2746,67 +2730,67 @@ ], [ "Amygdala mRNA", - "Amygdala mRNA mRNA" + "Amygdala mRNA" ], [ "Cerebellar Cortex mRNA", - "Cerebellar Cortex mRNA mRNA" + "Cerebellar Cortex mRNA" ], [ "Dorsolateral Prefrontal Cortex mRNA", - "Dorsolateral Prefrontal Cortex mRNA mRNA" + "Dorsolateral Prefrontal Cortex mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA mRNA" + "Hippocampus mRNA" ], [ "Inferior Temporal Cortex mRNA", - "Inferior Temporal Cortex mRNA mRNA" + "Inferior Temporal Cortex mRNA" ], [ "Medial Prefrontal Cortex mRNA", - "Medial Prefrontal Cortex mRNA mRNA" + "Medial Prefrontal Cortex mRNA" ], [ "Mediodorsal Nucleus of Thalamus mRNA", - "Mediodorsal Nucleus of Thalamus mRNA mRNA" + "Mediodorsal Nucleus of Thalamus mRNA" ], [ "Orbital Prefrontal Cortex mRNA", - "Orbital Prefrontal Cortex mRNA mRNA" + "Orbital Prefrontal Cortex mRNA" ], [ "Posterior Inferior Parietal Cortex mRNA", - "Posterior Inferior Parietal Cortex mRNA mRNA" + "Posterior Inferior Parietal Cortex mRNA" ], [ "Posterior Superior Temporal Cortex mRNA", - "Posterior Superior Temporal Cortex mRNA mRNA" + "Posterior Superior Temporal Cortex mRNA" ], [ "Primary Auditory (A1) Cortex mRNA", - "Primary Auditory (A1) Cortex mRNA mRNA" + "Primary Auditory (A1) Cortex mRNA" ], [ "Primary Motor (M1) Cortex mRNA", - "Primary Motor (M1) Cortex mRNA mRNA" + "Primary Motor (M1) Cortex mRNA" ], [ "Primary Somatosensory (S1) Cortex mRNA", - "Primary Somatosensory (S1) Cortex mRNA mRNA" + "Primary Somatosensory (S1) Cortex mRNA" ], [ "Primary Visual Cortex mRNA", - "Primary Visual Cortex mRNA mRNA" + "Primary Visual Cortex mRNA" ], [ "Striatum mRNA", - "Striatum mRNA mRNA" + "Striatum mRNA" ], [ "Ventrolateral Prefrontal Cortex mRNA", - "Ventrolateral Prefrontal Cortex mRNA mRNA" + "Ventrolateral Prefrontal Cortex mRNA" ] ] }, @@ -2822,23 +2806,23 @@ ], [ "Amygdala mRNA", - "Amygdala mRNA mRNA" + "Amygdala mRNA" ], [ "Brain mRNA", - "Brain mRNA mRNA" + "Brain mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA mRNA" + "Hippocampus mRNA" ], [ "Nucleus Accumbens mRNA", - "Nucleus Accumbens mRNA mRNA" + "Nucleus Accumbens mRNA" ], [ "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA mRNA" + "Prefrontal Cortex mRNA" ] ] }, @@ -2854,7 +2838,7 @@ ], [ "Mammary Tumors mRNA", - "Mammary Tumors mRNA mRNA" + "Mammary Tumors mRNA" ] ], "AXBXA": [ @@ -2868,19 +2852,19 @@ ], [ "Bone Femur mRNA", - "Bone Femur mRNA mRNA" + "Bone Femur mRNA" ], [ "Eye mRNA", - "Eye mRNA mRNA" + "Eye mRNA" ], [ "Heart mRNA", - "Heart mRNA mRNA" + "Heart mRNA" ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ] ], "B6BTBRF2": [ @@ -2894,7 +2878,7 @@ ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ] ], "B6D2F2": [ @@ -2908,7 +2892,7 @@ ], [ "Brain mRNA", - "Brain mRNA mRNA" + "Brain mRNA" ] ], "B6D2F2-PSU": [ @@ -2922,7 +2906,7 @@ ], [ "Muscle mRNA", - "Muscle mRNA mRNA" + "Muscle mRNA" ] ], "B6D2RI": [ @@ -2936,7 +2920,7 @@ ], [ "Hippocampus mRNA", - "Hippocampus mRNA mRNA" + "Hippocampus mRNA" ] ], "BDF2-1999": [ @@ -2950,7 +2934,7 @@ ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ] ], "BDF2-2005": [ @@ -2964,7 +2948,7 @@ ], [ "Striatum mRNA", - "Striatum mRNA mRNA" + "Striatum mRNA" ] ], "BHF2": [ @@ -2978,19 +2962,19 @@ ], [ "Adipose mRNA", - "Adipose mRNA mRNA" + "Adipose mRNA" ], [ "Brain mRNA", - "Brain mRNA mRNA" + "Brain mRNA" ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ], [ "Muscle mRNA", - "Muscle mRNA mRNA" + "Muscle mRNA" ] ], "BHHBF2": [ @@ -3004,19 +2988,19 @@ ], [ "Adipose mRNA", - "Adipose mRNA mRNA" + "Adipose mRNA" ], [ "Brain mRNA", - "Brain mRNA mRNA" + "Brain mRNA" ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ], [ "Muscle mRNA", - "Muscle mRNA mRNA" + "Muscle mRNA" ] ], "BXD": [ @@ -3030,119 +3014,119 @@ ], [ "Adrenal Gland mRNA", - "Adrenal Gland mRNA mRNA" + "Adrenal Gland mRNA" ], [ "Amygdala mRNA", - "Amygdala mRNA mRNA" + "Amygdala mRNA" ], [ "Bone Femur mRNA", - "Bone Femur mRNA mRNA" + "Bone Femur mRNA" ], [ "Brain mRNA", - "Brain mRNA mRNA" + "Brain mRNA" ], [ "Cartilage mRNA", - "Cartilage mRNA mRNA" + "Cartilage mRNA" ], [ "Cerebellum mRNA", - "Cerebellum mRNA mRNA" + "Cerebellum mRNA" ], [ "Eye mRNA", - "Eye mRNA mRNA" + "Eye mRNA" ], [ "Hematopoietic Cells mRNA", - "Hematopoietic Cells mRNA mRNA" + "Hematopoietic Cells mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA mRNA" + "Hippocampus mRNA" ], [ "Hypothalamus mRNA", - "Hypothalamus mRNA mRNA" + "Hypothalamus mRNA" ], [ "Kidney mRNA", - "Kidney mRNA mRNA" + "Kidney mRNA" ], [ "Leucocytes mRNA", - "Leucocytes mRNA mRNA" + "Leucocytes mRNA" ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ], [ "Liver Proteome", - "Liver Proteome mRNA" + "Liver Proteome" ], [ "Lung mRNA", - "Lung mRNA mRNA" + "Lung mRNA" ], [ "Midbrain mRNA", - "Midbrain mRNA mRNA" + "Midbrain mRNA" ], [ "Muscle mRNA", - "Muscle mRNA mRNA" + "Muscle mRNA" ], [ "Neocortex mRNA", - "Neocortex mRNA mRNA" + "Neocortex mRNA" ], [ "Nucleus Accumbens mRNA", - "Nucleus Accumbens mRNA mRNA" + "Nucleus Accumbens mRNA" ], [ "Pituitary Gland mRNA", - "Pituitary Gland mRNA mRNA" + "Pituitary Gland mRNA" ], [ "Popliteal Lymph Node mRNA", - "Popliteal Lymph Node mRNA mRNA" + "Popliteal Lymph Node mRNA" ], [ "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA mRNA" + "Prefrontal Cortex mRNA" ], [ "Retina mRNA", - "Retina mRNA mRNA" + "Retina mRNA" ], [ "Spleen mRNA", - "Spleen mRNA mRNA" + "Spleen mRNA" ], [ "Striatum mRNA", - "Striatum mRNA mRNA" + "Striatum mRNA" ], [ "T Cell (helper) mRNA", - "T Cell (helper) mRNA mRNA" + "T Cell (helper) mRNA" ], [ "T Cell (regulatory) mRNA", - "T Cell (regulatory) mRNA mRNA" + "T Cell (regulatory) mRNA" ], [ "Thymus mRNA", - "Thymus mRNA mRNA" + "Thymus mRNA" ], [ "Ventral Tegmental Area mRNA", - "Ventral Tegmental Area mRNA mRNA" + "Ventral Tegmental Area mRNA" ] ], "BXH": [ @@ -3156,15 +3140,15 @@ ], [ "Bone Femur mRNA", - "Bone Femur mRNA mRNA" + "Bone Femur mRNA" ], [ "Cartilage mRNA", - "Cartilage mRNA mRNA" + "Cartilage mRNA" ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ] ], "C57BL-6JxC57BL-6NJF2": [ @@ -3188,19 +3172,19 @@ ], [ "Adipose mRNA", - "Adipose mRNA mRNA" + "Adipose mRNA" ], [ "Brain mRNA", - "Brain mRNA mRNA" + "Brain mRNA" ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ], [ "Muscle mRNA", - "Muscle mRNA mRNA" + "Muscle mRNA" ] ], "CXB": [ @@ -3214,11 +3198,11 @@ ], [ "Hippocampus mRNA", - "Hippocampus mRNA mRNA" + "Hippocampus mRNA" ], [ "Spleen mRNA", - "Spleen mRNA mRNA" + "Spleen mRNA" ] ], "HS": [ @@ -3232,15 +3216,15 @@ ], [ "Hippocampus mRNA", - "Hippocampus mRNA mRNA" + "Hippocampus mRNA" ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ], [ "Lung mRNA", - "Lung mRNA mRNA" + "Lung mRNA" ] ], "HS-CC": [ @@ -3254,7 +3238,7 @@ ], [ "Striatum mRNA", - "Striatum mRNA mRNA" + "Striatum mRNA" ] ], "LXS": [ @@ -3268,11 +3252,11 @@ ], [ "Hippocampus mRNA", - "Hippocampus mRNA mRNA" + "Hippocampus mRNA" ], [ "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA mRNA" + "Prefrontal Cortex mRNA" ] ], "MDP": [ @@ -3286,19 +3270,19 @@ ], [ "Bone Femur mRNA", - "Bone Femur mRNA mRNA" + "Bone Femur mRNA" ], [ "Dorsal Root Ganglia mRNA", - "Dorsal Root Ganglia mRNA mRNA" + "Dorsal Root Ganglia mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA mRNA" + "Hippocampus mRNA" ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ] ], "NZBXFVB-N2": [ @@ -3312,7 +3296,7 @@ ], [ "Mammary Tumors mRNA", - "Mammary Tumors mRNA mRNA" + "Mammary Tumors mRNA" ] ], "SOTNOT-OHSU": [ @@ -3336,7 +3320,7 @@ ], [ "Anterior Cingulate Cortex mRNA", - "Anterior Cingulate Cortex mRNA mRNA" + "Anterior Cingulate Cortex mRNA" ] ] }, @@ -3362,27 +3346,27 @@ ], [ "Adrenal Gland mRNA", - "Adrenal Gland mRNA mRNA" + "Adrenal Gland mRNA" ], [ "Heart mRNA", - "Heart mRNA mRNA" + "Heart mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA mRNA" + "Hippocampus mRNA" ], [ "Kidney mRNA", - "Kidney mRNA mRNA" + "Kidney mRNA" ], [ "Liver mRNA", - "Liver mRNA mRNA" + "Liver mRNA" ], [ "Peritoneal Fat mRNA", - "Peritoneal Fat mRNA mRNA" + "Peritoneal Fat mRNA" ] ], "SRxSHRSPF2": [ @@ -3396,7 +3380,7 @@ ], [ "Eye mRNA", - "Eye mRNA mRNA" + "Eye mRNA" ] ] }, -- cgit v1.2.3 From 6aaefdaae3a9fb068278d9b94d8cdf25d4f8d852 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Fri, 19 Jul 2013 16:13:47 -0500 Subject: Created file gen_group_samplelists that iterates through all genofiles and builds each groups' samplelist --- web/genotypes/HSNIH.geno.gz | Bin wqflask/base/data_set.py | 50 ++++- wqflask/base/webqtlConfig.py | 8 +- wqflask/maintenance/gen_select_dataset.py | 4 +- wqflask/maintenance/get_group_samplelists.py | 43 ++++ .../new/javascript/dataset_menu_structure.json | 224 ++++++++++----------- 6 files changed, 206 insertions(+), 123 deletions(-) mode change 100755 => 100644 web/genotypes/HSNIH.geno.gz create mode 100644 wqflask/maintenance/get_group_samplelists.py (limited to 'web/genotypes') diff --git a/web/genotypes/HSNIH.geno.gz b/web/genotypes/HSNIH.geno.gz old mode 100755 new mode 100644 diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 30221503..cf219fda 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -16,8 +16,6 @@ # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # -#we -# # This module is used by GeneNetwork project (www.genenetwork.org) from __future__ import absolute_import, print_function, division @@ -27,6 +25,7 @@ import string import collections import json +import gzip import cPickle as pickle import itertools @@ -52,8 +51,6 @@ from pprint import pformat as pf DS_NAME_MAP = {} def create_dataset(dataset_name, dataset_type = None): - - print("dataset_type:", dataset_type) if not dataset_type: dataset_type = Dataset_Getter(dataset_name) #dataset_type = get_dataset_type_from_json(dataset_name) @@ -129,7 +126,7 @@ def create_datasets_list(): for result in g.db.execute(query).fetchall(): #The query at the beginning of this function isn't necessary here, but still would #rather just reuse it - print("type: {}\tname: {}".format(dataset_type, result.Name)) + #print("type: {}\tname: {}".format(dataset_type, result.Name)) dataset = create_dataset(result.Name, dataset_type) datasets.append(dataset) @@ -261,6 +258,36 @@ class DatasetGroup(object): if maternal and paternal: self.parlist = [maternal, paternal] + def get_sample_list(self): + genofilename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno')) + genofile = open(genofilename, "r") + for line in genofile: + line = line.strip() + if line.startswith(("#", "@")): + continue + headline = line + break + headers = headline.split("\t") + if headers[3] == "Mb": + self.samplelist = headers[4:] + else: + self.samplelist = headers[3:] + + #if genotype_1.type == "group" and self.parlist: + # genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) + #else: + # genotype_2 = genotype_1 + + #determine default genotype object + #if self.incparentsf1 and genotype_1.type != "intercross": + # genotype = genotype_2 + #else: + # self.incparentsf1 = 0 + # genotype = genotype_1 + + #self.samplelist = list(genotype.prgy) + + def read_genotype_file(self): '''Read genotype from .geno file instead of database''' #if self.group == 'BXD300': @@ -275,7 +302,18 @@ class DatasetGroup(object): # reaper barfs on unicode filenames, so here we ensure it's a string full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno')) - genotype_1.read(full_filename) + if os.path.isfile(full_filename): + print("Reading file: ", full_filename) + genotype_1.read(full_filename) + print("File read") + else: + try: + full_filename = str(os.path.join(webqtlConfig.TMPDIR, self.name + '.geno')) + #print("Reading file") + genotype_1.read(full_filename) + #print("File read") + except IOError: + print("File doesn't exist!") if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index d4511212..67a9c63f 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -35,7 +35,7 @@ NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrie UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s" GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s" OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s" -UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s" +UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s"; HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s" PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit" @@ -53,12 +53,12 @@ GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'web/' -PYLMM_PATH = '/home/zas1024/plink/' -SNP_PATH = '/home/zas1024/snps/' +PYLMM_PATH = '/home/zas1024/' +SNP_PATH = '/mnt/xvdf1/snps/' IMGDIR = HTMLPATH +'image/' IMAGESPATH = HTMLPATH + 'images/' UPLOADPATH = IMAGESPATH + 'upload/' -TMPDIR = HTMLPATH + 'tmp/' +TMPDIR = '/tmp/' GENODIR = HTMLPATH + 'genotypes/' NEWGENODIR = HTMLPATH + 'new_genotypes/' GENO_ARCHIVE_DIR = GENODIR + 'archive/' diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 8cb94f20..d4e47327 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -115,7 +115,7 @@ def build_types(species, group): (all types except phenotype/genotype are tissues) """ - Cursor.execute("""select distinct Tissue.Name, Tissue.Name + Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species where Species.Name = %s and Species.Id = InbredSet.SpeciesId and InbredSet.Name = %s and @@ -192,6 +192,8 @@ def main(): datasets=datasets, ) + print("data:", data) + output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json""" with open(output_file, 'w') as fh: diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py new file mode 100644 index 00000000..2434038e --- /dev/null +++ b/wqflask/maintenance/get_group_samplelists.py @@ -0,0 +1,43 @@ +from __future__ import absolute_import, print_function, division + +import os +import glob +import gzip + +from base import webqtlConfig + + +def get_sample_list_dir(geno_dir="/home/zas1024/gene/web/genotypes/"): + os.chdir(geno_dir) + + for group_file in glob.glob("*"): + if group_file.lower().endswith(('.geno', '.geno.gz')): + #group_name = genofilename.split('.')[0] + sample_list = get_sample_list(group_file) + print("\n\n{}\n\n".format(sample_list)) + + +def get_sample_list(group_file): + print(group_file) + genofilename = str(os.path.join(webqtlConfig.GENODIR, group_file)) + if genofilename.lower().endswith('.geno.gz'): + genofile = gzip.open(genofilename) + else: + genofile = open(genofilename) + for line in genofile: + line = line.strip() + if not line: + continue + if line.startswith(("#", "@")): + continue + headline = line + break + headers = headline.split("\t") + if headers[3] == "Mb": + samplelist = headers[4:] + else: + samplelist = headers[3:] + return samplelist + +if __name__ == '__main__': + get_sample_list_dir() diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 49c44fbd..4aae20ba 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -2556,7 +2556,7 @@ ], [ "Leaf mRNA", - "Leaf mRNA" + "Leaf mRNA mRNA" ] ], "SXM": [ @@ -2570,11 +2570,11 @@ ], [ "Embryo mRNA", - "Embryo mRNA" + "Embryo mRNA mRNA" ], [ "Leaf mRNA", - "Leaf mRNA" + "Leaf mRNA mRNA" ] ] }, @@ -2590,7 +2590,7 @@ ], [ "Whole Body mRNA", - "Whole Body mRNA" + "Whole Body mRNA mRNA" ] ], "Oregon-R_x_2b3": [ @@ -2604,7 +2604,7 @@ ], [ "Whole Body mRNA", - "Whole Body mRNA" + "Whole Body mRNA mRNA" ] ] }, @@ -2620,7 +2620,7 @@ ], [ "Brain mRNA", - "Brain mRNA" + "Brain mRNA mRNA" ] ], "AD-cases-controls-Myers": [ @@ -2634,7 +2634,7 @@ ], [ "Brain mRNA", - "Brain mRNA" + "Brain mRNA mRNA" ] ], "CANDLE": [ @@ -2648,11 +2648,11 @@ ], [ "Methylation", - "Methylation" + "Methylation mRNA" ], [ "Newborn Cord Blood mRNA", - "Newborn Cord Blood mRNA" + "Newborn Cord Blood mRNA mRNA" ] ], "CEPH-2004": [ @@ -2666,7 +2666,7 @@ ], [ "Lymphoblast B-cell mRNA", - "Lymphoblast B-cell mRNA" + "Lymphoblast B-cell mRNA mRNA" ] ], "HB": [ @@ -2680,15 +2680,15 @@ ], [ "Cerebellum mRNA", - "Cerebellum mRNA" + "Cerebellum mRNA mRNA" ], [ "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA" + "Prefrontal Cortex mRNA mRNA" ], [ "Primary Visual Cortex mRNA", - "Primary Visual Cortex mRNA" + "Primary Visual Cortex mRNA mRNA" ] ], "HLC": [ @@ -2702,7 +2702,7 @@ ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ] ], "HLT": [ @@ -2716,7 +2716,7 @@ ], [ "Lung mRNA", - "Lung mRNA" + "Lung mRNA mRNA" ] ], "HSB": [ @@ -2730,67 +2730,67 @@ ], [ "Amygdala mRNA", - "Amygdala mRNA" + "Amygdala mRNA mRNA" ], [ "Cerebellar Cortex mRNA", - "Cerebellar Cortex mRNA" + "Cerebellar Cortex mRNA mRNA" ], [ "Dorsolateral Prefrontal Cortex mRNA", - "Dorsolateral Prefrontal Cortex mRNA" + "Dorsolateral Prefrontal Cortex mRNA mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus mRNA mRNA" ], [ "Inferior Temporal Cortex mRNA", - "Inferior Temporal Cortex mRNA" + "Inferior Temporal Cortex mRNA mRNA" ], [ "Medial Prefrontal Cortex mRNA", - "Medial Prefrontal Cortex mRNA" + "Medial Prefrontal Cortex mRNA mRNA" ], [ "Mediodorsal Nucleus of Thalamus mRNA", - "Mediodorsal Nucleus of Thalamus mRNA" + "Mediodorsal Nucleus of Thalamus mRNA mRNA" ], [ "Orbital Prefrontal Cortex mRNA", - "Orbital Prefrontal Cortex mRNA" + "Orbital Prefrontal Cortex mRNA mRNA" ], [ "Posterior Inferior Parietal Cortex mRNA", - "Posterior Inferior Parietal Cortex mRNA" + "Posterior Inferior Parietal Cortex mRNA mRNA" ], [ "Posterior Superior Temporal Cortex mRNA", - "Posterior Superior Temporal Cortex mRNA" + "Posterior Superior Temporal Cortex mRNA mRNA" ], [ "Primary Auditory (A1) Cortex mRNA", - "Primary Auditory (A1) Cortex mRNA" + "Primary Auditory (A1) Cortex mRNA mRNA" ], [ "Primary Motor (M1) Cortex mRNA", - "Primary Motor (M1) Cortex mRNA" + "Primary Motor (M1) Cortex mRNA mRNA" ], [ "Primary Somatosensory (S1) Cortex mRNA", - "Primary Somatosensory (S1) Cortex mRNA" + "Primary Somatosensory (S1) Cortex mRNA mRNA" ], [ "Primary Visual Cortex mRNA", - "Primary Visual Cortex mRNA" + "Primary Visual Cortex mRNA mRNA" ], [ "Striatum mRNA", - "Striatum mRNA" + "Striatum mRNA mRNA" ], [ "Ventrolateral Prefrontal Cortex mRNA", - "Ventrolateral Prefrontal Cortex mRNA" + "Ventrolateral Prefrontal Cortex mRNA mRNA" ] ] }, @@ -2806,23 +2806,23 @@ ], [ "Amygdala mRNA", - "Amygdala mRNA" + "Amygdala mRNA mRNA" ], [ "Brain mRNA", - "Brain mRNA" + "Brain mRNA mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus mRNA mRNA" ], [ "Nucleus Accumbens mRNA", - "Nucleus Accumbens mRNA" + "Nucleus Accumbens mRNA mRNA" ], [ "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA" + "Prefrontal Cortex mRNA mRNA" ] ] }, @@ -2838,7 +2838,7 @@ ], [ "Mammary Tumors mRNA", - "Mammary Tumors mRNA" + "Mammary Tumors mRNA mRNA" ] ], "AXBXA": [ @@ -2852,19 +2852,19 @@ ], [ "Bone Femur mRNA", - "Bone Femur mRNA" + "Bone Femur mRNA mRNA" ], [ "Eye mRNA", - "Eye mRNA" + "Eye mRNA mRNA" ], [ "Heart mRNA", - "Heart mRNA" + "Heart mRNA mRNA" ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ] ], "B6BTBRF2": [ @@ -2878,7 +2878,7 @@ ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ] ], "B6D2F2": [ @@ -2892,7 +2892,7 @@ ], [ "Brain mRNA", - "Brain mRNA" + "Brain mRNA mRNA" ] ], "B6D2F2-PSU": [ @@ -2906,7 +2906,7 @@ ], [ "Muscle mRNA", - "Muscle mRNA" + "Muscle mRNA mRNA" ] ], "B6D2RI": [ @@ -2920,7 +2920,7 @@ ], [ "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus mRNA mRNA" ] ], "BDF2-1999": [ @@ -2934,7 +2934,7 @@ ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ] ], "BDF2-2005": [ @@ -2948,7 +2948,7 @@ ], [ "Striatum mRNA", - "Striatum mRNA" + "Striatum mRNA mRNA" ] ], "BHF2": [ @@ -2962,19 +2962,19 @@ ], [ "Adipose mRNA", - "Adipose mRNA" + "Adipose mRNA mRNA" ], [ "Brain mRNA", - "Brain mRNA" + "Brain mRNA mRNA" ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ], [ "Muscle mRNA", - "Muscle mRNA" + "Muscle mRNA mRNA" ] ], "BHHBF2": [ @@ -2988,19 +2988,19 @@ ], [ "Adipose mRNA", - "Adipose mRNA" + "Adipose mRNA mRNA" ], [ "Brain mRNA", - "Brain mRNA" + "Brain mRNA mRNA" ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ], [ "Muscle mRNA", - "Muscle mRNA" + "Muscle mRNA mRNA" ] ], "BXD": [ @@ -3014,119 +3014,119 @@ ], [ "Adrenal Gland mRNA", - "Adrenal Gland mRNA" + "Adrenal Gland mRNA mRNA" ], [ "Amygdala mRNA", - "Amygdala mRNA" + "Amygdala mRNA mRNA" ], [ "Bone Femur mRNA", - "Bone Femur mRNA" + "Bone Femur mRNA mRNA" ], [ "Brain mRNA", - "Brain mRNA" + "Brain mRNA mRNA" ], [ "Cartilage mRNA", - "Cartilage mRNA" + "Cartilage mRNA mRNA" ], [ "Cerebellum mRNA", - "Cerebellum mRNA" + "Cerebellum mRNA mRNA" ], [ "Eye mRNA", - "Eye mRNA" + "Eye mRNA mRNA" ], [ "Hematopoietic Cells mRNA", - "Hematopoietic Cells mRNA" + "Hematopoietic Cells mRNA mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus mRNA mRNA" ], [ "Hypothalamus mRNA", - "Hypothalamus mRNA" + "Hypothalamus mRNA mRNA" ], [ "Kidney mRNA", - "Kidney mRNA" + "Kidney mRNA mRNA" ], [ "Leucocytes mRNA", - "Leucocytes mRNA" + "Leucocytes mRNA mRNA" ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ], [ "Liver Proteome", - "Liver Proteome" + "Liver Proteome mRNA" ], [ "Lung mRNA", - "Lung mRNA" + "Lung mRNA mRNA" ], [ "Midbrain mRNA", - "Midbrain mRNA" + "Midbrain mRNA mRNA" ], [ "Muscle mRNA", - "Muscle mRNA" + "Muscle mRNA mRNA" ], [ "Neocortex mRNA", - "Neocortex mRNA" + "Neocortex mRNA mRNA" ], [ "Nucleus Accumbens mRNA", - "Nucleus Accumbens mRNA" + "Nucleus Accumbens mRNA mRNA" ], [ "Pituitary Gland mRNA", - "Pituitary Gland mRNA" + "Pituitary Gland mRNA mRNA" ], [ "Popliteal Lymph Node mRNA", - "Popliteal Lymph Node mRNA" + "Popliteal Lymph Node mRNA mRNA" ], [ "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA" + "Prefrontal Cortex mRNA mRNA" ], [ "Retina mRNA", - "Retina mRNA" + "Retina mRNA mRNA" ], [ "Spleen mRNA", - "Spleen mRNA" + "Spleen mRNA mRNA" ], [ "Striatum mRNA", - "Striatum mRNA" + "Striatum mRNA mRNA" ], [ "T Cell (helper) mRNA", - "T Cell (helper) mRNA" + "T Cell (helper) mRNA mRNA" ], [ "T Cell (regulatory) mRNA", - "T Cell (regulatory) mRNA" + "T Cell (regulatory) mRNA mRNA" ], [ "Thymus mRNA", - "Thymus mRNA" + "Thymus mRNA mRNA" ], [ "Ventral Tegmental Area mRNA", - "Ventral Tegmental Area mRNA" + "Ventral Tegmental Area mRNA mRNA" ] ], "BXH": [ @@ -3140,15 +3140,15 @@ ], [ "Bone Femur mRNA", - "Bone Femur mRNA" + "Bone Femur mRNA mRNA" ], [ "Cartilage mRNA", - "Cartilage mRNA" + "Cartilage mRNA mRNA" ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ] ], "C57BL-6JxC57BL-6NJF2": [ @@ -3172,19 +3172,19 @@ ], [ "Adipose mRNA", - "Adipose mRNA" + "Adipose mRNA mRNA" ], [ "Brain mRNA", - "Brain mRNA" + "Brain mRNA mRNA" ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ], [ "Muscle mRNA", - "Muscle mRNA" + "Muscle mRNA mRNA" ] ], "CXB": [ @@ -3198,11 +3198,11 @@ ], [ "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus mRNA mRNA" ], [ "Spleen mRNA", - "Spleen mRNA" + "Spleen mRNA mRNA" ] ], "HS": [ @@ -3216,15 +3216,15 @@ ], [ "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus mRNA mRNA" ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ], [ "Lung mRNA", - "Lung mRNA" + "Lung mRNA mRNA" ] ], "HS-CC": [ @@ -3238,7 +3238,7 @@ ], [ "Striatum mRNA", - "Striatum mRNA" + "Striatum mRNA mRNA" ] ], "LXS": [ @@ -3252,11 +3252,11 @@ ], [ "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus mRNA mRNA" ], [ "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA" + "Prefrontal Cortex mRNA mRNA" ] ], "MDP": [ @@ -3270,19 +3270,19 @@ ], [ "Bone Femur mRNA", - "Bone Femur mRNA" + "Bone Femur mRNA mRNA" ], [ "Dorsal Root Ganglia mRNA", - "Dorsal Root Ganglia mRNA" + "Dorsal Root Ganglia mRNA mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus mRNA mRNA" ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ] ], "NZBXFVB-N2": [ @@ -3296,7 +3296,7 @@ ], [ "Mammary Tumors mRNA", - "Mammary Tumors mRNA" + "Mammary Tumors mRNA mRNA" ] ], "SOTNOT-OHSU": [ @@ -3320,7 +3320,7 @@ ], [ "Anterior Cingulate Cortex mRNA", - "Anterior Cingulate Cortex mRNA" + "Anterior Cingulate Cortex mRNA mRNA" ] ] }, @@ -3346,27 +3346,27 @@ ], [ "Adrenal Gland mRNA", - "Adrenal Gland mRNA" + "Adrenal Gland mRNA mRNA" ], [ "Heart mRNA", - "Heart mRNA" + "Heart mRNA mRNA" ], [ "Hippocampus mRNA", - "Hippocampus mRNA" + "Hippocampus mRNA mRNA" ], [ "Kidney mRNA", - "Kidney mRNA" + "Kidney mRNA mRNA" ], [ "Liver mRNA", - "Liver mRNA" + "Liver mRNA mRNA" ], [ "Peritoneal Fat mRNA", - "Peritoneal Fat mRNA" + "Peritoneal Fat mRNA mRNA" ] ], "SRxSHRSPF2": [ @@ -3380,7 +3380,7 @@ ], [ "Eye mRNA", - "Eye mRNA" + "Eye mRNA mRNA" ] ] }, -- cgit v1.2.3