diff options
| -rw-r--r-- | wqflask/base/data_set.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 73 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 42 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/mapping_results.html | 8 |
6 files changed, 74 insertions, 63 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4fee5c7a..d766e284 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -433,7 +433,7 @@ def datasets(group_name, this_group = None): and InbredSet.Name like %s and ProbeSetFreeze.public > %s and ProbeSetFreeze.confidentiality < 1 - ORDER BY Tissue.Name) + ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC) ''' % (group_name, webqtlConfig.PUBLICTHRESH, group_name, webqtlConfig.PUBLICTHRESH, "'" + group_name + "'", webqtlConfig.PUBLICTHRESH)) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index cafbf38c..41cdf819 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2127,7 +2127,7 @@ class DisplayMappingResults(object): tableIterationsCnt = tableIterationsCnt + 1 this_row = [] #container for the cells of each row - selectCheck = HT.Input(type="checkbox", name="searchResult", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row + selectCheck = HT.Input(type="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0 tenPercentLength = geneLength*0.0001 @@ -2213,7 +2213,7 @@ class DisplayMappingResults(object): elif self.dataset.group.species == 'rat': for gIndex, theGO in enumerate(geneCol): this_row = [] #container for the cells of each row - selectCheck = HT.Input(type="checkbox", name="searchResult", Class="checkbox", onClick="highlight(this)").__str__() #checkbox for each row + selectCheck = HT.Input(type="checkbox", name="selectCheck", Class="checkbox trait_checkbox").__str__() #checkbox for each row #ZS: May want to get this working again later #webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__() @@ -2240,14 +2240,14 @@ class DisplayMappingResults(object): #Mouse Gene if theGO['mouseGene']: mouseChr = theGO['mouseGene']["Chromosome"] - mouseTxStart = theGO['mouseGene']["TxStart"] + mouseTxStart = "%0.6f" % theGO['mouseGene']["TxStart"] else: mouseChr = mouseTxStart = "" #the chromosomes for human 1 are 1qXX.XX if theGO['humanGene']: humanChr = theGO['humanGene']["Chromosome"] - humanTxStart = theGO['humanGene']["TxStart"] + humanTxStart = "%0.6f" % theGO['humanGene']["TxStart"] else: humanChr = humanTxStart = "" @@ -2258,7 +2258,7 @@ class DisplayMappingResults(object): this_row = [selectCheck.__str__(), str(gIndex+1), geneSymbolNCBI, - theGO["TxStart"], + "%0.6f" % theGO["TxStart"], HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)).__str__(), avgExprVal, mouseChr, diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 0f37e711..4e3c203d 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -73,50 +73,51 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf gwa_output_filename) else: - generate_k_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk -outdir %s/gn2/ -o %s' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename, - flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - k_output_filename) - #generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), - # genofile_name, - # flat_files('genotype/bimbam'), - # trait_filename, - # flat_files('genotype/bimbam'), - # genofile_name, - # TEMPDIR, - # k_output_filename) + # generate_k_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk -outdir %s/gn2/ -o %s' % (flat_files('genotype/bimbam'), + # genofile_name, + # TEMPDIR, + # trait_filename, + # flat_files('genotype/bimbam'), + # genofile_name, + # TEMPDIR, + # k_output_filename) + generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename, + flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + k_output_filename) logger.debug("k_command:" + generate_k_command) os.system(generate_k_command) - gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -k %s/gn2/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename, - flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - k_output_filename, - maf) + # gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -k %s/gn2/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'), + # genofile_name, + # TEMPDIR, + # trait_filename, + # flat_files('genotype/bimbam'), + # genofile_name, + # TEMPDIR, + # k_output_filename, + # maf) - #gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (flat_files('genotype/bimbam'), - # genofile_name, - # flat_files('genotype/bimbam'), - # genofile_name) + gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename) if covariates != "": - gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'), - this_dataset.group.name, - webqtlConfig.GENERATED_IMAGE_DIR, - genofile_name) - else: - gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR, - genofile_name) + gemma_command += ' -c %s/%s_covariates.txt' % (flat_files('mapping'), this_dataset.group.name) + # gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'), + # this_dataset.group.name, + # webqtlConfig.GENERATED_IMAGE_DIR, + # genofile_name) + # else: + # gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR, + # genofile_name) logger.debug("gemma_command:" + gemma_command) diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index e10b31c0..5178ece8 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -168,7 +168,7 @@ class ShowTrait(object): hddn['control_marker'] = self.nearest_marker #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2 hddn['do_control'] = False - hddn['maf'] = 0.01 + hddn['maf'] = 0.05 hddn['compare_traits'] = [] hddn['export_data'] = "" hddn['export_format'] = "excel" diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 21fc99d3..3fd9faf5 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -127,27 +127,35 @@ <a href="http://joss.theoj.org/papers/10.21105/joss.00025"><img src="https://camo.githubusercontent.com/846b750f582ae8f1d0b4f7e8fee78bed705c88ba/687474703a2f2f6a6f73732e7468656f6a2e6f72672f7061706572732f31302e32313130352f6a6f73732e30303032352f7374617475732e737667" alt="JOSS" data-canonical-src="http://joss.theoj.org/papers/10.21105/joss.00025/status.svg" style="max-width:100%;"></a> </p> <br /> - <p>GeneNetwork is supported by:</p> - <UL> - <LI> - <a href="http://citg.uthsc.edu"> + <p>GeneNetwork support from:</p> + <ul> + <li> + <a href="http://citg.uthsc.edu"> The UT Center for Integrative and Translational Genomics - </A> + </a> </li> - <LI><a href="http://www.iniastress.org">NIAAA</A> - Integrative Neuroscience Initiative on Alcoholism - (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425) + <li> + <a href="https://www.nigms.nih.gov/">NIGMS</a> + Systems Genetics and Precision Medicine Project (R01 GM123489, 2017-2021) </li> - <LI> - <a - href="https://www.drugabuse.gov/">NIDA</A>, <a class="smallsize" href="http://www.nimh.nih.gov/">NIMH</A> - , and <a class="smallsize" href="http://www.niaaa.nih.gov/"> - NIAAA</A> (P20-DA 21131) + <li> + <a href="https://www.drugabuse.gov/">NIDA</a> + NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022) </li> - <LI>NCI <a href="http://emice.nci.nih.gov/">MMHCC</A> (U01CA105417) and - <a href="https://en.wikipedia.org/wiki/National_Center_for_Research_Resources">NCRR</a> - <a href="https://en.wikipedia.org/wiki/Biomedical_Informatics_Research_Network">BIRN</a> - (U24 RR021760) + <li> + <a href="http://www.nia.nih.gov/">NIA</a> + Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018) + </li> + <li> + <a href="http://www.iniastress.org/">NIAAA</a> + Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017) + </li> + <li> + <a href="http://www.drugabuse.gov/">NIDA</a>, <a href="http://www.nimh.nih.gov/">NIMH</a>, and <a href="http://www.niaaa.nih.gov/">NIAAA</a> + (P20-DA 21131, 2001-2012) + </li> + <li> + NCI <a href="http://emice.nci.nih.gov/">MMHCC</a> (U01CA105417), NCRR, <a href="http://www.birncommunity.org/">BIRN</a>, (U24 RR021760) </li> </UL> <!--</p>--> diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index ba4d4d7c..00a7b811 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -262,7 +262,7 @@ <div style="width: 100%;"> <h2>Interval Analyst</h2> <div id="table_container"> - <table id="interval_analyst" class="table-hover table-striped cell-border dataTable" style="float: left; width:100%;"> + <table id="trait_table" class="table-hover table-striped cell-border dataTable" style="float: left; width:100%;"> <thead> <tr> {% for header in gene_table_header %} @@ -322,6 +322,7 @@ <script type="text/javascript" charset="utf-8"> $(document).ready( function () { console.time("Creating table"); + {% if selectedChr == -1 %} $('#trait_table').DataTable( { "columns": [ { "type": "natural", "width": "5%" }, @@ -346,8 +347,8 @@ "scrollCollapse": false, "paging": false } ); - - $('#interval_analyst').dataTable( { + {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %} + $('#trait_table').dataTable( { "createdRow": function ( row, data, index ) { $('td', row).eq(1).attr("align", "right"); $('td', row).eq(3).attr("align", "right"); @@ -384,6 +385,7 @@ "scrollCollapse": false, "paging": false } ); + {% endif %} $('#vector_map_tab').click(function(){ $('div#gn1_map_options').hide(); |