diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 28 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 40 |
2 files changed, 1 insertions, 67 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 1e66e957..4708bf0a 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -20,46 +20,20 @@ USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4} #minimum number of informative strains KMININFORMATIVE = 5 -#maximum number of traits for interval mapping -MULTIPLEMAPPINGLIMIT = 11 - -#maximum number of traits for correlation -MAXCORR = 100 - #Daily download limit from one IP DAILYMAXIMUM = 1000 #maximum LRS value MAXLRS = 460.0 -#temporary data life span -MAXLIFE = 86400 - #MINIMUM Database public value PUBLICTHRESH = 0 -#NBCI address -NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" -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"; -HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s" +#EXTERNAL LINK ADDRESSES 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" UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' -UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s" -ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s' -DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s' -UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s" -GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit" -ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s" - -# The following paths are no longer in use! -# HTMLPATH is replaced by GENODIR -# IMGDIR is replaced by GENERATED_IMAGE_DIR # Temporary storage (note that this TMPDIR can be set as an # environment variable - use utility.tools.TEMPDIR when you diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index a55b6c10..c196b58b 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -406,51 +406,11 @@ class MarkerRegression(object): else: self.GraphInterval = self.cMGraphInterval #cM - ################################################################ - # Get Trait Values and Infomation - ################################################################ - ##input from search page or selection page - #self.searchResult = fd.formdata.getvalue('searchResult') - ##convert single selection into a list - #if type("1") == type(self.searchResult): - # self.searchResult = string.split(self.searchResult,'\t') - # - #self.traitList = [] - #if self.searchResult and len(self.searchResult) > webqtlConfig.MULTIPLEMAPPINGLIMIT: - # heading = 'Multiple Interval Mapping' - # detail = ['In order to get clear result, do not select more than %d traits for \ - # Multiple Interval Mapping analysis.' % webqtlConfig.MULTIPLEMAPPINGLIMIT] - # self.error(heading=heading,detail=detail) - # return - #elif self.searchResult: - # self.dataSource = 'selectionPage' - # for item in self.searchResult: - # thisTrait = webqtlTrait(fullname=item, cursor=self.cursor) - # thisTrait.retrieveInfo() - # thisTrait.retrieveData(fd.strainlist) - # self.traitList.append(thisTrait) - #else: - - #input from data editing page - #fd.readData() - #if not fd.allTraitData: - # heading = "Mapping" - # detail = ['No trait data was selected for %s data set. No mapping attempted.' % fd.RISet] - # self.error(heading=heading,detail=detail) - # return - self.dataSource = 'editingPage' self.traitList = [] thisTrait = start_vars['this_trait'] - #fullname = fd.formdata.getvalue('fullname', '') - #if fullname: - # thisTrait = webqtlTrait(fullname=fullname, data=fd.allTraitData, cursor=self.cursor) - # thisTrait.retrieveInfo() - #else: - # thisTrait = webqtlTrait(data=fd.allTraitData) self.traitList.append(thisTrait) - ## BEGIN HaplotypeAnalyst ## count the amount of individuals to be plotted, and increase self.graphHeight if self.haplotypeAnalystChecked and self.selectedChr > -1: |