diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/data_set.py | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 17 | ||||
| -rwxr-xr-x | wqflask/wqflask/my_pylmm/data/genofile_parser.py | 31 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page.html | 4 |
4 files changed, 27 insertions, 27 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 414cc71a..a572a607 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -163,8 +163,6 @@ class Markers(object): for marker in markers: if (marker['chr'] != "X") and (marker['chr'] != "Y"): marker['chr'] = int(marker['chr']) - #else: - # marker['chr'] = 20 print("Mb:", marker['Mb']) marker['Mb'] = float(marker['Mb']) diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 02e73bb0..617d7942 100755 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -499,7 +499,14 @@ class GoSearch(MrnaAssaySearch): DoSearch.search_types['ProbeSet_GO'] = "GoSearch" - def run(self): + def get_from_clause(self): + from_clause = """, db_GeneOntology.term as GOterm, + db_GeneOntology.association as GOassociation, + db_GeneOntology.gene_product as GOgene_product """ + + return from_clause + + def get_where_clause(self): field = 'GOterm.acc' go_id = 'GO:' + ('0000000'+self.search_term[0])[-7:] @@ -510,9 +517,11 @@ class GoSearch(MrnaAssaySearch): where_clause = " %s = '%s' and %s " % (field, go_id, statements) - from_clause = """ , db_GeneOntology.term as GOterm, - db_GeneOntology.association as GOassociation, - db_GeneOntology.gene_product as GOgene_product """ + return where_clause + + def run(self): + from_clause = self.get_from_clause() + where_clause = self.get_where_clause() query = self.compile_final_query(from_clause, where_clause) diff --git a/wqflask/wqflask/my_pylmm/data/genofile_parser.py b/wqflask/wqflask/my_pylmm/data/genofile_parser.py index 1f4760a9..9191f345 100755 --- a/wqflask/wqflask/my_pylmm/data/genofile_parser.py +++ b/wqflask/wqflask/my_pylmm/data/genofile_parser.py @@ -78,26 +78,19 @@ class ConvertGenoFile(object): # self.process_snps_file() - #def process_row(self, row): - # counter = 0 - # for char in row: - # if char - # counter += 1 - - def process_csv(self): for row_count, row in enumerate(self.process_rows()): - #self.latest_row_pos = row_count - - row_items = row.split() + row_items = row.split("\t") this_marker = Marker() this_marker.name = row_items[1] this_marker.chr = row_items[0] - #this_marker.cM = row_items[2] if self.cm_exists and self.mb_exists: - #print("cm and mb exists") - this_marker.Mb = row_items[2] + this_marker.cM = row_items[2] + this_marker.Mb = row_items[3] + genotypes = row_items[4:] + elif self.cm_exists: + this_marker.cM = row_items[2] genotypes = row_items[3:] elif self.mb_exists: this_marker.Mb = row_items[2] @@ -190,13 +183,13 @@ class ConvertGenoFile(object): if __name__=="__main__": - Old_Geno_Directory = """/home/zas1024/gene/web/genotypes/""" - New_Geno_Directory = """/home/zas1024/gene/web/new_genotypes/""" - #Input_File = """/home/zas1024/gene/web/genotypes/BXD.geno""" + Old_Geno_Directory = """/home/zas1024/gene/genotype_files/genotypes/""" + New_Geno_Directory = """/home/zas1024/gene/genotype_files/new_genotypes/""" + #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno""" #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps""" - convertob = ConvertGenoFile("/home/zas1024/gene/web/genotypes/HSNIH.geno", "/home/zas1024/gene/web/new_genotypes/HSNIH.json") - convertob.convert() - #ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) + #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json") + #convertob.convert() + ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) #ConvertGenoFiles(Geno_Directory) #process_csv(Input_File, Output_File) \ No newline at end of file diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 3d5ddde4..49067e37 100755 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -147,14 +147,14 @@ GeneWiki</a> for genes that you or other users have annotated with the word <i>nicotine</i>.</li> - <!--<li><b>GO:0045202</b> searches for synapse-associated genes listed in the + <li><b>GO:0045202</b> searches for synapse-associated genes listed in the <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank"> Gene Ontology</a>.</li> <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b> finds synapse-associated genes with <a href="http://www.genenetwork.org/glossary.html#E" target="_blank"> cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores - between 9 and 999.</li>--> + between 9 and 999.</li> <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b> finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E" target="_blank"> |