本文整理汇总了Python中reportlib.finish_nonps函数的典型用法代码示例。如果您正苦于以下问题:Python finish_nonps函数的具体用法?Python finish_nonps怎么用?Python finish_nonps使用的例子?那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了finish_nonps函数的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: exit
def exit(
status, # numeric exit status (integer)
message = None # exit message (string)
):
# Purpose:
# Returns: nothing
# Assumes: nothing
# Effects: nothing
# Throws: nothing
if message is not None:
sys.stderr.write('\n' + str(message) + '\n')
try:
diagFile.write('\n\nEnd Date/Time: %s\n' % (mgi_utils.date()))
diagFile.close()
except:
pass
try:
reportlib.finish_nonps(reportFile)
except:
pass
db.useOneConnection(0)
sys.exit(status)
开发者ID:mgijax,项目名称:vocload,代码行数:27,代码来源:GOremoveannot.py
示例2: printReport
def printReport(fp):
# Same Strains and the Marker/Allele associations
db.sql('''
select s._Strain_key, a._Marker_key, a._Allele_key
into temporary table strains2
from strains s, PRB_Strain_Marker a
where s._Strain_key = a._Strain_key
''', None)
db.sql('create index strains2_idx1 on strains2(_Strain_key)', None)
# Strains that do not have the same Allele
db.sql('''
select s.* into temporary table strainsToProcess from strains s
where not exists (select 1 from strains2 ss where s._Strain_key = ss._Strain_key
and s._Allele_key = ss._Allele_key)
''', None)
# Retrieve MGI ids of the Genotypes
mgiIDs = {}
results = db.sql('''
select s._Strain_key, a.accID
from strainsToProcess s, ACC_Accession a
where s._Genotype_key = a._Object_key
and a._MGIType_key = 12
and a._LogicalDB_key = 1
and a.preferred = 1
''', 'auto')
for r in results:
key = r['_Strain_key']
value = r['accID']
if not mgiIDs.has_key(key):
mgiIDs[key] = []
mgiIDs[key].append(value)
# Process
rows = 0
results = db.sql('select distinct _Strain_key, accID, strain from strainsToProcess order by strain', 'auto')
for r in results:
key = r['_Strain_key']
fp.write(r['accID'] + reportlib.TAB)
fp.write(r['strain'] + reportlib.TAB)
fp.write(string.join(mgiIDs[key], ',') + reportlib.CRT)
fp.write('\n(%d rows affected)\n' % (len(results)))
db.sql('drop table strains', None)
db.sql('drop table strains2', None)
db.sql('drop table strainsToProcess', None)
reportlib.finish_nonps(fp)
开发者ID:mgijax,项目名称:qcreports_db,代码行数:54,代码来源:PRB_StrainJAX3.py
示例3: processMGI_8columns
def processMGI_8columns():
#
# process MGI-oriented reports with 8 columns
#
# iterate thru files
for b in column8Files:
value = os.environ[b]
inFile, htmlFile = initFiles(value)
# print html header
htmlFile.write(tableStart + CRT)
htmlFile.write('<TD>Marker</TD>')
htmlFile.write('<TD>Symbol</TD>')
htmlFile.write('<TD>Chromosome</TD>')
htmlFile.write('<TD>Entrez Gene</TD>')
htmlFile.write('<TD>Associated Sequences</TD>')
htmlFile.write('<TD>Marker Type</TD>' + CRT)
# iterate thru input file
for line in inFile.readlines():
tokens = string.split(line, TAB)
if len(tokens) < 3:
continue
mgiID = tokens[0]
mgiSymbol = tokens[1]
mgiChromosome = tokens[2]
egID = tokens[3]
sequences = tokens[6]
markerType = tokens[7]
htmlFile.write('<TR><TD>' + mgiAnchor(mgiID) + '</TD>')
htmlFile.write('<TD>' + mgiSymbol + '</TD>')
htmlFile.write('<TD>' + mgiChromosome + '</TD>')
htmlFile.write('<TD>' + externalAnchor(egID, EG_URL_KEY) + '</TD>')
htmlFile.write('<TD>' + idAnchors(sequences) + '</TD>')
htmlFile.write('<TD>' + markerType + '</TD></TR>')
htmlFile.write(CRT)
htmlFile.write(tableEnd)
inFile.close()
reportlib.finish_nonps(htmlFile, isHTML = 1)
开发者ID:mgijax,项目名称:egload,代码行数:50,代码来源:formatreports.py
示例4: writeReport
def writeReport(resultsDict, rptName, category):
fp = reportlib.init(rptName, outputdir = os.environ['QCOUTPUTDIR'], printHeading = None)
if category == 1004: # expressed component, has properties
fp.write('Action%sCategory%sOrganizer ID%sOrganizer symbol%sRelationship ID%sRelationship Name%sParticipant ID%sParticipant Name%sQualifier%sAbbreviation%sEvidence Code%sjnum_id%sCurator ID%sNotes%sProperty:Non-mouse_Organism%sProperty:Non-mouse_Gene_Symbol%sProperty:Non-mouse_NCBI_Gene_ID%s' % (TAB, TAB, TAB, TAB, TAB, TAB, TAB, TAB, TAB, TAB,TAB, TAB, TAB, TAB, TAB, TAB, CRT))
else: # 1003 mutation involves, no properties
fp.write('Action%sCategory%sOrganizer ID%sOrganizer symbol%sRelationship ID%sRelationship Name%sParticipant ID%sParticipant Name%sQualifier%sAbbreviation%sEvidence Code%sjnum_id%sCurator ID%sNotes%s' % (TAB, TAB, TAB, TAB, TAB, TAB,TAB, TAB, TAB, TAB, TAB, TAB, TAB, CRT))
nmOrgVal = ''
nmGSVal = ''
nmGIVal = ''
for r in resultsDict:
# Each record in this list represents the same feature,
# but with different properties
resultsList = resultsDict[r]
cat = resultsList[0]['category']
aId = resultsList[0]['alleleId']
aSym = resultsList[0]['alleleSymbol']
rvId = resultsList[0]['rvId']
rel = resultsList[0]['relationship']
mId = resultsList[0]['markerId']
mSym = resultsList[0]['markerSymbol']
qual = resultsList[0]['qualifier']
evid = resultsList[0]['evidence']
jnum = resultsList[0]['JNum']
curator = resultsList[0] ['login']
notes = resultsList[0]['note']
if notes == None:
notes = ''
if category == 1004: # expresses component, get properties
nmOrgVal = ''
nmGSVal = ''
nmGIVal = ''
for res in resultsList:
propName = res['propName']
propValue = res['propValue']
if propName == None:
continue
elif propName == NON_MOUSE_ORG:
nmOrgVal = propValue
elif propName == NON_MOUSE_GS:
nmGSVal = propValue
elif propName == NON_MOUSE_GI:
nmGIVal = propValue
fp.write('%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s' % (cat, TAB, aId, TAB, aSym, TAB, rvId, TAB, rel, TAB, mId, TAB, mSym, TAB, qual, TAB, evid, TAB, jnum, TAB, curator, TAB, notes, TAB, nmOrgVal, TAB, nmGSVal, TAB, nmGIVal, CRT) )
else: # mutation involves
fp.write('%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s' % (cat, TAB, aId, TAB, aSym, TAB, rvId, TAB, rel, TAB, mId, TAB, mSym, TAB, qual, TAB, evid, TAB, jnum, TAB, curator, TAB, notes, CRT) )
reportlib.finish_nonps(fp) # non-postscript file
开发者ID:mgijax,项目名称:qcreports_db,代码行数:50,代码来源:PHENO_Features.py
示例5: printReport
def printReport(fp):
db.sql('create index idx1 on strains(_Strain_key)', None)
db.sql('create index idx2 on strains(_Genotype_key)', None)
genotypes = {}
results = db.sql('''
select distinct s._Strain_key, a.accID, a.numericPart
from strains s, ACC_Accession a
where s._Genotype_key = a._Object_key
and a._MGIType_key = 12
and a._LogicalDB_key = 1
and a.prefixPart = 'MGI:'
and a.preferred = 1
order by a.numericPart''', 'auto')
for r in results:
key = r['_Strain_key']
value = r['accID']
if not genotypes.has_key(key):
genotypes[key] = []
genotypes[key].append(value)
results = db.sql('''
(
select distinct s._Strain_key, s.strain, s.accID, s.numericPart
from strains s
where not exists (select 1 from PRB_Strain_Genotype g where s._Strain_key = g._Strain_key and s._Genotype_key = g._Genotype_key)
and exists (select 1 from VOC_Annot va where va._AnnotType_key = 1002 and s._Genotype_key = va._Object_key)
union
select distinct s._Strain_key, s.strain, s.accID, s.numericPart
from strains s
where not exists (select 1 from PRB_Strain_Genotype g where s._Strain_key = g._Strain_key and s._Genotype_key = g._Genotype_key)
and exists (select 1 from VOC_Annot va where va._AnnotType_key = 1020 and s._Genotype_key = va._Object_key)
)
order by numericPart''', 'auto')
for r in results:
fp.write(r['accID'] + TAB)
fp.write(r['strain'] + TAB)
fp.write(string.join(genotypes[r['_Strain_key']], ',') + CRT)
fp.write('\n(%d rows affected)\n' % (len(results)))
reportlib.finish_nonps(fp)
开发者ID:mgijax,项目名称:qcreports_db,代码行数:42,代码来源:PRB_StrainJAX2.py
示例6: processMGI_2columns
def processMGI_2columns():
#
# process MGI-oriented reports w/ 2 columns
#
# iterate thru files
for b in column2Files:
value = os.environ[b]
inFile, htmlFile = initFiles(value)
# print html header
htmlFile.write(tableStart + CRT)
htmlFile.write('<TD>Marker</TD>' + CRT)
htmlFile.write('<TD>EG ID</TD>')
# iterate thru input file
for line in inFile.readlines():
tokens = string.split(line, TAB)
if len(tokens) < 2:
continue
egID = tokens[0]
mgiID = tokens[1]
htmlFile.write('<TR><TD>' + mgiAnchor(mgiID) + '</TD>')
htmlFile.write('<TD>' + egID + '</TD>')
htmlFile.write(CRT)
htmlFile.write(tableEnd)
inFile.close()
reportlib.finish_nonps(htmlFile, isHTML = 1)
开发者ID:mgijax,项目名称:egload,代码行数:37,代码来源:formatreports.py
示例7:
# retrieve all UniProt ID associated with mouse markers
sequence = {}
results = db.sql('select a.accID ' + \
'from MRK_Marker m, ACC_Accession a ' + \
'where m._Organism_key = 1 ' + \
'and m._Marker_key = a._Object_key ' + \
'and a._MGIType_key = 2 ' + \
'and a._LogicalDB_key = 13 ' + \
'order by a.accID', 'auto')
count = 1
for r in results:
fpLinkOut.write(2 * TAB + '<Query>' + r['accID'] + '[pacc]</Query>' + CRT)
count = count + 1
fpLinkOut.write(''' </ObjectList>
</ObjectSelector>
<ObjectUrl>
<Base>&base;</Base>
<Rule>&lo.pacc;</Rule>
</ObjectUrl>
</Link>
</LinkSet>
''')
reportlib.finish_nonps(fpLinkOut)
db.useOneConnection(0)
开发者ID:mgijax,项目名称:reports_db,代码行数:29,代码来源:protein_linkout.py
示例8:
fp2.write(string.join(mpDO1[genotype], '|') + TAB)
if mpOMIM1.has_key(genotype):
fp2.write(string.join(mpOMIM1[genotype], '|'))
fp2.write(CRT)
#
# DO report 2
#
if mpDO2.has_key(genotype):
fp3.write(mpDisplay[genotype] + TAB)
fp3.write(string.join(mpAlleles[genotype], '|') + TAB)
if mpAlleleIDs.has_key(genotype):
fp3.write(string.join(mpAlleleIDs[genotype], '|'))
fp3.write(TAB)
fp3.write(mpStrain[genotype] + TAB)
fp3.write(mpID[term] + TAB)
if mpRef.has_key(refKey):
fp3.write(string.join(mpRef[refKey], '|'))
fp3.write(TAB + string.join(mpMarker[genotype], '|') + TAB)
fp3.write(string.join(mpDO2[genotype], '|') + TAB)
if mpOMIM2.has_key(genotype):
fp3.write(string.join(mpOMIM2[genotype], '|'))
fp3.write(CRT)
reportlib.finish_nonps(fp1) # non-postscript file
reportlib.finish_nonps(fp2) # non-postscript file
reportlib.finish_nonps(fp3) # non-postscript file
开发者ID:mgijax,项目名称:reports_db,代码行数:29,代码来源:MGI_GenePheno.py
示例9: processJournal
#.........这里部分代码省略.........
db.sql('create index markers1_idx1 on markers1(_Refs_key)', None)
db.sql('''WITH ref_counts1 AS (
SELECT _Refs_key, count(*) AS markerCount
FROM markers1
GROUP BY _Refs_key
)
select m.*, r.markerCount
into mcount1
from markers1 m , ref_counts1 r
where m._Refs_key = r._Refs_key
''', None)
db.sql('create index mcount1_idx1 on mcount1(_Refs_key)', None)
# get the set of references not coded with high priority,
# add newGeneCount column to be updated later
results = db.sql('''
select distinct a.jnumID, i._Refs_key, i.markerCount,
i.conditional, i.priority,
a.short_citation,
0 as newGeneCount
into temporary table final
from mcount1 i, BIB_Citation_Cache a
where i._Refs_key = a._Refs_key
''', None)
#
# new genes
#
# the set of references/markers = high/medium priorty
# and references/markers are not referenced in the assay module
#
db.sql('''
select distinct i._Refs_key, i._Marker_key
into temporary table markers2
from GXD_Index i, BIB_Refs b
where i._Refs_key = b._Refs_key
and b.journal in ('%s')
and i._Priority_key in (74714, 74715) /* high/medium */
and not exists (select 1 from GXD_Assay a where i._Refs_key = a._Refs_key)
and not exists (select 1 from GXD_Assay a where i._Marker_key = a._Marker_key)
''' % journalTitle, None)
db.sql('create index markers2_idx1 on markers2(_Refs_key)', None)
#
# by reference, get the count
#
db.sql('''WITH ref_counts2 AS (
SELECT _Refs_key, count(*) AS newGeneCount
FROM markers2
GROUP BY _Refs_key
)
select m.*, r.newGeneCount
into mcount2
from markers2 m , ref_counts2 r
where m._Refs_key = r._Refs_key
''', None)
db.sql('create index mcount2_idx1 on mcount2(_Refs_key)', None)
#
# by reference, set final.newGeneCount = mcount2.newGeneCount
#
db.sql('''
update final
set newGeneCount = m.newGeneCount
from mcount2 m
where final._Refs_key = m._Refs_key
''', None)
# now write the report
results = db.sql('select * from final order by priority, newGeneCount desc, markerCount desc', 'auto')
for r in results:
fp.write(string.ljust(str(r['jnumID']), 30))
fp.write(SPACE)
fp.write(string.ljust(str(r['markerCount']), 12))
fp.write(SPACE)
fp.write(string.ljust(str(r['newGeneCount']), 12))
fp.write(SPACE)
fp.write(string.ljust(str(r['conditional']), 20))
fp.write(SPACE)
fp.write(string.ljust(str(r['priority']), 10))
fp.write(SPACE)
fp.write(string.ljust(str(r['short_citation']), 50))
fp.write(CRT)
fp.write('%s(%d rows affected)%s%s' % (CRT, len(results), CRT, CRT))
# drop all the temp tables because we are looping
db.sql('drop table markers1', None)
db.sql('drop table mcount1', None)
db.sql('drop table final', None)
db.sql('drop table markers2', None)
db.sql('drop table mcount2', None)
reportlib.finish_nonps(fp)
开发者ID:mgijax,项目名称:qcreports_db,代码行数:101,代码来源:GXD_FullCode.py
示例10: process
#.........这里部分代码省略.........
displayNotes1 = displayNotes1 + topType1 + separatorTopBottom + bottomType1 + notenewline
displayNotes2 = displayNotes2 + topType2 + separatorTopBottom + bottomType2 + notenewline
elif compound == 'Top':
# new top, new group: process old group
if foundBottom >= 1:
displayNotes1 = displayNotes1 + topType1 + separatorTopBottom + bottomType1 + notenewline
displayNotes2 = displayNotes2 + topType2 + separatorTopBottom + bottomType2 + notenewline
topType1 = ''
topType2 = ''
bottomType1 = ''
bottomType2 = ''
foundTop = 0
foundBottom = 0
# new top, same group: need space to separate tops + existing information
if foundTop >= 1:
topType1 = topType1 + separatorBottom + allele1
topType2 = topType2 + ' \Allele(' + mgiID1 + '|' + allele1 + '|)'
# if there is no top, then copy in existing information
else:
topType1 = allele1
topType2 = '\Allele(' + mgiID1 + '|' + allele1 + '|)'
foundTop = foundTop + 1
elif compound == 'Bottom':
# new bottom, same group: need space to separate bottoms + existing information
if foundBottom >= 1:
bottomType1 = bottomType1 + separatorBottom + allele1
bottomType2 = bottomType2 + separatorBottom
if allele1WildType == 1:
bottomType2 = bottomType2 + '\AlleleSymbol(' + mgiID1 + '|0)'
else:
bottomType2 = bottomType2 + '\Allele(' + mgiID1 + '|' + allele1 + '|)'
# if there is no bottom, then copy in existing information
else:
bottomType1 = allele1
if allele1WildType == 1:
bottomType2 = '\AlleleSymbol(' + mgiID1 + '|0)'
else:
bottomType2 = '\Allele(' + mgiID1 + '|' + allele1 + '|)'
foundBottom = foundBottom + 1
if foundTop >= 1 and foundBottom >= 1:
displayNotes1 = displayNotes1 + topType1 + separatorTopBottom + bottomType1 + notenewline
displayNotes2 = displayNotes2 + topType2 + separatorTopBottom + bottomType2 + notenewline
#print displayNotes1
#print displayNotes2
if mode == 'sql':
#
# initialize the MGI_Note._Note_key primary key
#
cmd = 'begin transaction;\n'
cmd = cmd + 'create temp table noteKeyMax on commit drop as select max(_Note_key) + 1 as noteKey from MGI_Note;\n'
cmd = cmd + processNote(g, displayNotes1, combNoteType1)
cmd = cmd + processNote(g, displayNotes2, combNoteType2)
cmd = cmd + processNote(g, displayNotes2, combNoteType3)
print processNote(g, displayNotes1, combNoteType1)
print processNote(g, displayNotes1, combNoteType2)
print processNote(g, displayNotes1, combNoteType3)
#print cmd
cmd = cmd + "commit transaction;\n"
db.sql(cmd, None)
else:
fp1.write(r['genotypeID'] + reportlib.TAB + displayNotes1 + reportlib.CRT)
fp2.write(r['genotypeID'] + reportlib.TAB + displayNotes2 + reportlib.CRT)
fp3.write(r['genotypeID'] + reportlib.TAB + displayNotes2 + reportlib.CRT)
if DEBUG:
print 'finished with genotype\n'
sys.stdout.flush()
if DEBUG:
print '\nfinished running allele combination\n'
sys.stdout.flush()
if mode == 'bcp':
reportlib.finish_nonps(fp1) # non-postscript file
reportlib.finish_nonps(fp2) # non-postscript file
reportlib.finish_nonps(fp3) # non-postscript file
db.commit()
开发者ID:mgijax,项目名称:allcacheload,代码行数:101,代码来源:allelecombination.py
示例11: iphone_do
#.........这里部分代码省略.........
value = r
if not refs2.has_key(key):
refs2[key] = []
refs2[key].append(value)
#
# DO/Human Marker by Marker
#
results = db.sql('''
select distinct m._term_key, a.accid
from diseaseontology m, VOC_Annot aa, ACC_Accession a
where m._term_key = aa._term_key
and aa._annottype_key = 1022
and aa._object_key = a._object_key
and a._mgitype_key = 2
and a._logicaldb_key = 55
and a.preferred = 1
''', 'auto')
markerannots2 = {}
for r in results:
key = r['_term_key']
value = r['accid']
if not markerannots2.has_key(key):
markerannots2[key] = []
markerannots2[key].append(value)
#
# report
#
results = db.sql('select * from diseaseontology', 'auto')
for r in results:
key = r['_term_key']
fp.write(r['accid'] + TAB)
fp.write(r['term'] + TAB)
# DO (_annottype_key = 1022)
# MGI Ref ID (MGI:xxx|MGI:xxx|...)
if refs1.has_key(key):
i=0
for n in refs1[key]:
if i>0:
fp.write('|'+str(n['mgiid']))
else:
fp.write(str(n['mgiid']))
i=1
fp.write(TAB)
else:
fp.write('0' + TAB)
# DO (_annottype_key = 1022)
# MGI Genotype ID (MGI:xxx|MGI:xxx|...)
if genoannots1.has_key(key):
fp.write(string.join(genoannots1[key], '|') + TAB)
else:
fp.write('0' + TAB)
# DO (_annottype_key = 1022)
# MGI Marker ID (MGI:xxx|MGI:xxx|...)
if markerannots1.has_key(key):
fp.write(string.join(markerannots1[key], '|') + TAB)
else:
fp.write('0' +TAB)
# DO (_annottype_key = 1022)
# MGI Allele ID (MGI:xxx|MGI:xxx|...)
if alleleannots1.has_key(key):
fp.write(string.join(alleleannots1[key], '|') + TAB)
else:
fp.write('0' + TAB)
# DO (_annottype_key = 1022)
# MGI Ref ID (MGI:xxx|MGI:xxx|...)
if refs2.has_key(key):
i=0
for n in refs2[key]:
if i>0:
fp.write('|'+str(n['mgiid']))
else:
fp.write(str(n['mgiid']))
i=1
fp.write(TAB)
else:
fp.write('0' + TAB)
# DO (_annottype_key = 1022)
# EntrezGene ID (xxx|xxx|...)
if markerannots2.has_key(key):
fp.write(string.join(markerannots2[key], '|'))
else:
fp.write('0')
fp.write(CRT)
reportlib.finish_nonps(fp)
# re-create a symbolic link between the new file and the current file
os.chdir(reportDir)
os.symlink(reportWithDate + '.rpt', currentReport)
开发者ID:mgijax,项目名称:reports_db,代码行数:101,代码来源:MGI_iphone_app.py
示例12: iphone_genes
#.........这里部分代码省略.........
for n in refs[key]:
if i>0:
fp.write('|'+str(n['mgiid']))
else:
fp.write(str(n['mgiid']))
i=1;
fp.write(TAB)
else:
fp.write('0' + TAB)
# MGI Allele ID (MGI:xxx|MGI:xxx|...)
if alleles.has_key(key):
fp.write(string.join(alleles[key], '|') + TAB)
else:
fp.write('0' + TAB)
# GO ID (C group): (GO:xxxx|GO:xxxx|...)
if goCannots.has_key(key):
i=0
for n in goCannots[key]:
if i>0:
fp.write('|'+str(n['accid']))
else:
fp.write(str(n['accid']))
i=1
fp.write(TAB)
else:
fp.write('0' + TAB)
# GO ID (F group): (GO:xxxx|GO:xxxx|...)
if goFannots.has_key(key):
i=0
for n in goFannots[key]:
if i>0:
fp.write('|'+str(n['accid']))
else:
fp.write(str(n['accid']))
i=1
fp.write(TAB)
else:
fp.write('0' +TAB)
# GO ID (P group): (GO:xxxx|GO:xxxx|...)
if goPannots.has_key(key):
i=0
for n in goPannots[key]:
if i>0:
fp.write('|'+str(n['accid']))
else:
fp.write(str(n['accid']))
i=1
fp.write(TAB)
else:
fp.write('0' +TAB)
# MP ID: (MP:xxxx|MP:xxxx|...)
if phenoannots.has_key(key):
i=0
for n in phenoannots[key]:
if i>0:
fp.write('|'+str(n['accid']))
else:
fp.write(str(n['accid']))
i=1
fp.write(TAB)
else:
fp.write('0' +TAB)
# DO ID: (xxxx|xxxx|...)
if dogenotype.has_key(key):
i=0
for n in dogenotype[key]:
if i>0:
fp.write('|'+str(n['accid']))
else:
fp.write(str(n['accid']))
i=1
fp.write(TAB)
else:
fp.write('0' + TAB)
# DO ID: (xxxx|xxxx|...)
if dohuman.has_key(key):
i=0
for n in dohuman[key]:
if i>0:
fp.write('|'+str(n['accid']))
else:
fp.write(str(n['accid']))
i=1
#fp.write(TAB)
else:
fp.write('0')
fp.write(CRT)
reportlib.finish_nonps(fp)
# re-create a symbolic link between the new file and the current file
os.chdir(reportDir)
os.symlink(reportWithDate + '.rpt', currentReport)
开发者ID:mgijax,项目名称:reports_db,代码行数:101,代码来源:MGI_iphone_app.py
示例13: processEG
def processEG():
#
# process EG-oriented reports
#
try:
inFile = open(egFileName, 'r')
head, tail = os.path.split(egFileName)
# initialize output (html) file
htmlFile = reportlib.init(tail, \
outputdir = os.environ['RPTDIR'], printHeading = None, isHTML = 1)
egmgiFile = reportlib.init(egmgiFileName, fileExt = '.txt', \
outputdir = os.environ['RPTDIR'], printHeading = None)
egnomgiFile = reportlib.init(egnomgiFileName, fileExt = '.txt', \
outputdir = os.environ['RPTDIR'], printHeading = None)
except:
print 'Problem with file: %s' % (egFileName)
print 'Problem with file: %s' % (egmgiFileName)
print 'Problem with file: %s' % (egnomgiFileName)
sys.exit(1)
# print html header
htmlFile.write(tableStart + CRT)
htmlFile.write('<TD>Entrez Gene</TD>')
htmlFile.write('<TD>Symbol</TD>')
htmlFile.write('<TD>Chromosome</TD>')
htmlFile.write('<TD>Associated Sequences</TD>' + CRT)
# iterate thru input file
for line in inFile.readlines():
tokens = string.split(line, TAB)
if len(tokens) < 3:
continue
egID = tokens[0]
egSymbol = tokens[1]
egChromosome = tokens[2];
sequences = tokens[3];
htmlFile.write('<TR><TD>' + externalAnchor(egID, EG_URL_KEY) + '</TD>')
htmlFile.write('<TD>' + egSymbol + '</TD>')
htmlFile.write('<TD>' + egChromosome + '</TD>')
htmlFile.write('<TD>' + idAnchors(sequences) + '</TD></TR>')
htmlFile.write(CRT)
# if file does not contains MGIids...
if string.find(sequences, 'MGIID=[-]') > 0:
egnomgiFile.write(egID + TAB)
egnomgiFile.write(egSymbol + TAB)
egnomgiFile.write(egChromosome + TAB)
egnomgiFile.write(sequences + CRT)
# if file does contains MGIids...
else:
seqs = string.split(sequences, ',')
# only print sequences with MGI ids
for s in seqs:
if string.find(s, 'MGIID=[') >= 0:
s = string.replace(s, 'MGIID=[', '')
s = string.replace(s, ']', '')
s = string.replace(s, '{', '')
s = string.replace(s, '}', '')
s = string.replace(s, ' ', '')
s = string.replace(s, '\n', '')
egmgiFile.write(egID + TAB)
egmgiFile.write(egSymbol + TAB)
egmgiFile.write(egChromosome + TAB)
egmgiFile.write(s + CRT)
htmlFile.write(tableEnd)
egmgiFile.close()
egnomgiFile.close()
inFile.close()
reportlib.finish_nonps(htmlFile, isHTML = 1)
开发者ID:mgijax,项目名称:egload,代码行数:85,代码来源:formatreports.py
示例14: writeHTML
imsrTAB.setdefault(accID, []).append(strain)
value = string.replace(strain, '<', 'beginss')
value = string.replace(value, '>', 'endss')
value = string.replace(value, 'beginss', '<sup>')
value = string.replace(value, 'endss', '</sup>')
value = '%s%s%s' % (reportlib.create_imsrstrain_anchor(strain), value, reportlib.close_accession_anchor())
imsrHTML.setdefault(accID, []).append(value)
#
# process results
#
results = db.sql('select * from cre order by driverNote', 'auto')
for r in results:
writeHTML(r, imsrHTML)
writeTAB(r, imsrTAB)
#
# clean up
#
fpHTML.write('</TABLE>')
fpHTML.write('<pre>')
reportlib.finish_nonps(fpHTML, isHTML = 1) # non-postscript file
reportlib.finish_nonps(fpTAB) # non-postscript file
db.useOneConnection(0)
开发者ID:mgijax,项目名称:reports_db,代码行数:30,代码来源:MGI_Recombinase_Full.py
示例15: runQueries
results = db.sql('select * from results order by hstatus desc, mstatus desc, msymbol', 'auto')
for r in results:
key = r['m_Marker_key']
fp.write(string.ljust(r['msymbol'], 32) + \
string.ljust(r['mstatus'], 12) + \
string.ljust(r['hsymbol'], 32) + \
string.ljust(r['hstatus'], 15))
fp.write(CRT)
fp.write('\n(%d rows affected)\n' % (len(results)))
#
# Main
#
fp1 = reportlib.init('HMD_SymbolDiffs1', outputdir = os.environ['QCOUTPUTDIR'])
runQueries(includeRiken = 0)
report1(fp1, includeRiken = 0)
reportlib.finish_nonps(fp1)
fp3 = reportlib.init('HMD_SymbolDiffs3', outputdir = os.environ['QCOUTPUTDIR'])
runQueries(includeRiken = 1)
report1(fp3, includeRiken = 1)
reportlib.finish_nonps(fp3)
开发者ID:mgijax,项目名称:qcreports_db,代码行数:27,代码来源:HMD_SymbolDiffs.py
示例16: writeRecordF
db.sql('''select o.*, 'yes' as isGO
into temporary table fpE
from domarkers o, markers m
where o._Marker_key = m._Marker_key
union
select o.*, 'no' as isGO
from domarkers o
where not exists
(select 1 from VOC_Annot a where o._Marker_key = a._Object_key and a._AnnotType_key = 1000)
''', None)
# number of unique MGI gene
results = db.sql('select distinct _Marker_key from fpE', 'auto')
fpE.write('Number of unique MGI Gene IDs: %s\n' % (len(results)))
# total number of rows
results = db.sql('select * from fpE', 'auto')
fpE.write('Total number of rows: %s\n\n' % (len(results)))
fpE.write('mgi ID' + TAB + \
'symbol' + TAB + \
'GO?' + CRT*2)
results = db.sql('select * from fpE order by symbol', 'auto')
for r in results:
writeRecordF(fpE, r)
reportlib.finish_nonps(fpD, isHTML = 1) # non-postscript file
reportlib.finish_nonps(fpE) # non-postscript file
开发者ID:mgijax,项目名称:qcreports_db,代码行数:29,代码来源:MRK_GOIEA.py
示例17: exists
results = db.sql('''
select a.accID, i.jnumID, i.figureLabel, i.paneLabel, i.cdate
from images i, ACC_Accession a
where not exists (select 1 from specimen s
where i._Refs_key = s._Refs_key
and i._ImagePane_key = s._ImagePane_key)
and not exists (select 1 from gel s
where i._Refs_key = s._Refs_key
and i._ImagePane_key = s._ImagePane_key)
and i._Image_key = a._Object_key
and a._MGIType_key = 9
and a._LogicalDB_key = 1
order by a.accID, i.jnumID, i.figureLabel
''', 'auto')
for r in results:
fp.write(r['accID'] + TAB)
fp.write(r['jnumID'] + TAB)
fp.write(r['figureLabel'] + TAB)
if (r['paneLabel'] == None):
fp.write('None' + TAB)
else:
fp.write(r['paneLabel'] + TAB)
fp.write(r['cdate'] + CRT)
fp.write(CRT + '(%d rows affected)' % (len(results)) + CRT)
reportlib.finish_nonps(fp) # non-postscript file
开发者ID:mgijax,项目名称:qcreports_db,代码行数:28,代码来源:GXD_ImagesUnused.py
示例18: reportClose
def reportClose():
global fpD
reportlib.finish_nonps(fpD, isHTML = 1)
开发者ID:mgijax,项目名称:qcreports_db,代码行数:4,代码来源:MRK_NoGO.py
示例19: str
fp.write(string.ljust('Month', 10))
fp.write(string.ljust('Assays', 10))
fp.write(string.ljust('Results', 10) + CRT)
fp.write(string.ljust('----------', 30))
fp.write(string.ljust('----', 10))
fp.write(string.ljust('-----', 10))
fp.write(string.ljust('------', 10))
fp.write(string.ljust('-------', 10) + CRT)
fp.write(string.ljust(r['assayType'], 30))
fp.write(string.ljust(str(int(r['year'])), 10))
fp.write(string.ljust(str(int(r['month'])), 10))
fp.write(string.ljust(str(int(r['assays'])), 10))
fp.write(string.ljust(str(int(r['results'])), 10) + CRT)
prevAssay = r['assayType']
fp.write(CRT + 'Total Assays: ' + str(asummary[prevAssay]) + CRT)
fp.write('Total Results: ' + str(rsummary[prevAssay]) + CRT)
########
# #
# Main #
# #
########
fp = reportlib.init(sys.argv[0], outputdir = os.environ['QCOUTPUTDIR'], sqlLogging = 1)
monthlyCounts()
reportlib.finish_nonps(fp)
开发者ID:mgijax,项目名称:qcreports_db,代码行数:29,代码来源:GXD_StatsMonthly.py
示例20: closeFiles
def closeFiles():
# write out all annotations
for n in newannot.keys():
inferredFrom = '|'.join(newannot[n])
annotFile.write(annotLine % (n[0], n[1], n[2], n[3], inferredFrom, n[4], n[5], n[6], n[7]))
# write out unique pubmed ids that are not found in MGI
for p in pubmedUnique:
pubmedErrorFile.write(p + '\n')
# write out evidence code counts for unique pubmed ids that are not found in MGI
for p in pubmedEvidence.keys():
pubmedeviErrorFile.write(p + ':\t' + str(pubmedEvidence[p]) + '\n')
reportlib.finish_nonps(unresolvedAErrorFile)
reportlib.finish_nonps(unresolvedBErrorFile)
reportlib.finish_nonps(unresolvedCErrorFile)
reportlib.finish_nonps(mgiErrorFile)
reportlib.finish_nonps(multiGeneErrorFile)
reportlib.finish_nonps(nopubmedFile)
reportlib.finish_nonps(paintFile)
reportlib.finish_nonps(pubmedAnnotFile)
reportlib.finish_nonps(pubmedErrorFile)
reportlib.finish_nonps(pubmedeviErrorFile)
reportlib.finish_nonps(dupErrorFile)
reportlib.finish_nonps(gafFile)
reportlib.finish_nonps(gpadFile)
reportlib.finish_nonps(annotFile)
reportlib.finish_nonps(uberonTextFile)
reportlib.finish_nonps(propertiesErrorFile)
return 0
开发者ID:mgijax,项目名称:goload,代码行数:33,代码来源:goamouse.py
注:本文中的reportlib.finish_nonps函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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