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authorzsloan2018-04-09 16:32:25 +0000
committerzsloan2018-04-09 16:32:25 +0000
commitab914075b0a83428e471ce7ffbe5700c5c0a9625 (patch)
tree08ffbc304ead5add9a32692f78e5687a5626d5f1 /wqflask
parent275cf9b5512df676d23f6f26ba85b5cb2d772b68 (diff)
downloadgenenetwork2-ab914075b0a83428e471ce7ffbe5700c5c0a9625.tar.gz
Removed some unused code in webqtlConfig; some might need to be added back in later when other third party links are implemented on the trait/collection pages
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/webqtlConfig.py28
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py40
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: