Python reportlib.init函数代码示例

def mmrrc():

    mmrrcfp = reportlib.init(sys.argv[0], outputdir = os.environ['QCOUTPUTDIR'], fileExt = '.mmrrc.rpt')

    title = 'MMRRC Strains w/ Genotype Associations where the Markers/Alleles of the Strain record\n' + \
	    'do not exactly match the Markers/Alleles of the Genotype record.'

    mmrrcfp.write(title + '\n\n')
    mmrrcfp.write('MMRRC#' + reportlib.TAB)
    mmrrcfp.write('Strain' + reportlib.TAB)
    mmrrcfp.write('Genotypes' + reportlib.TAB)
    mmrrcfp.write(reportlib.CRT)

    # MMNC Strains w/ Genotype Associations; exclude wild type alleles
    db.sql('''
	    select distinct sa.accID, s.strain, g._Genotype_key, g._Strain_key, a._Marker_key, a._Allele_key 
	    into temporary table strains 
	    from PRB_Strain s, PRB_Strain_Genotype g, GXD_AlleleGenotype a, ALL_Allele aa, ACC_Accession sa 
	    where s.strain like '%/Mmnc'
	    and s._Strain_key = g._Strain_key 
	    and g._Genotype_key = a._Genotype_key 
	    and a._Allele_key = aa._Allele_key 
	    and aa.isWildType = 0 
	    and s._Strain_key = sa._Object_key 
	    and sa._MGIType_key = 10 
	    and sa._LogicalDB_key = 38 
	    and sa.preferred = 1 
	    ''', None)
    db.sql('create index strains_idx2 on strains(_Strain_key)', None)

    printReport(mmrrcfp)

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

def initFiles(value):
    #
    # open input, html files
    #

    # open input (text) file

    try:
        inFile = open(value, 'r')
        head, tail = os.path.split(value)

        # initialize output (html) file

        htmlFile = reportlib.init(tail, outputdir = os.environ['RPTDIR'], printHeading = None, isHTML = 1)

    except:

	print 'Cannot open file: %s' % (value)
	sys.exit(1)

    return inFile, htmlFile

def mmrrc():

    title = 'Public MMRRC strains whose Alleles are used in a Genotype'
    title = title + ' but there is no corresponding Strain/Genotype association\n'
    title = title + '(where Genotypes have been created within the last week)'


    mmrrcfp = reportlib.init(sys.argv[0], title, \
			outputdir = os.environ['QCOUTPUTDIR'], fileExt = '.mmrrc.' + os.environ['DATE'] + '.rpt')

    mmrrcfp.write('MMRRC' + TAB)
    mmrrcfp.write('Strain' + TAB)
    mmrrcfp.write('Genotypes' + CRT*2)
    
    # Retrieve all Strains that have a MMRRC ID and whose Alleles are used in a Genotype

    db.sql('drop table strains', None)

    db.sql('''
	select distinct s._Strain_key, 
			substring(s.strain,1,70) as strain, 
			a.accID, 
			a.numericPart,
			g._Genotype_key 
	into temporary table strains 
	from PRB_Strain s, ACC_Accession a, PRB_Strain_Marker sm, GXD_Genotype g, GXD_AlleleGenotype ag 
	where s.private = 0 
	and s._Strain_key = a._Object_key 
	and a._MGIType_key = 10 
	and a._LogicalDB_key = 38 
	and s._Strain_key = sm._Strain_key 
	and sm._Allele_key = ag._Allele_key 
	and ag._Genotype_key = g._Genotype_key
	and g.creation_date between %s and current_date
	''' % (fromDate), None)

    printReport(mmrrcfp)

import string
import reportlib
import db

db.setTrace()

CRT = reportlib.CRT
SPACE = reportlib.SPACE
TAB = reportlib.TAB
PAGE = reportlib.PAGE

#
# Main
#

fp1 = reportlib.init(sys.argv[0], outputdir = os.environ['REPORTOUTPUTDIR'], printHeading = None)
fp2 = reportlib.init('MGI_Geno_DiseaseDO', outputdir = os.environ['REPORTOUTPUTDIR'], printHeading = None)
fp3 = reportlib.init('MGI_Geno_NotDiseaseDO', outputdir = os.environ['REPORTOUTPUTDIR'], printHeading = None)

#
# select all MP annotations
#

db.sql('''select distinct a._Object_key, a._Term_key, e._Refs_key 
	into temporary table mp 
	from VOC_Annot a, VOC_Evidence e, VOC_Term t 
	where a._AnnotType_key = 1002 
	and a._Qualifier_key = t._Term_key 
	and t.term is null 
	and a._Annot_key = e._Annot_key
	''', None)

column1 = ''     # chromosome
column4 = ''     # startCoordinate
column5 = ''     # endCoordinate
column7 = ''     # strand

# template for column nine
column9 = 'Creator %s; Sequence_tag_ID %s; GenBank_ID %s; DBxref %s; Type %s'

# components of column 9
creator = ''
seqTagID = ''
seqID = ''
mgiID = ''
seqType = 'DNA'

fp = reportlib.init(sys.argv[0], fileExt = '.gff', outputdir = \
   outputDir, printHeading = None)

print 'Writing gff file ...'
sys.stdout.flush()

for seqKey in gtCoordDictBySeqKey:
    if alleleKeyDictBySeqKey.has_key(seqKey):
	coordList = gtCoordDictBySeqKey[seqKey]
	column1 = coordList[3]
	column4 = str(coordList[0])
	column5 = str(coordList[1])
	column7 = coordList[2]
	alleleKey = alleleKeyDictBySeqKey[seqKey]
	seqTagID = seqTagIdsDictBySeqKey[seqKey]
	seqID = seqIdDictBySeqKey[seqKey]
	

import re
import reportlib
import db

db.setTrace()

CRT = reportlib.CRT
SPACE = reportlib.SPACE
TAB = reportlib.TAB
PAGE = reportlib.PAGE

#
# Main
#

fp = reportlib.init(sys.argv[0], 'References with GO status "Full-coded" where there is no GO annotation', os.environ['QCOUTPUTDIR'])

fp.write('''
 	The reference must be:
 	     group = GO, status = 'Full-coded'
	     No GO annotation
''')

results = db.sql('''select distinct a.accid as jnumID, b.isDiscard, 
	to_char(b.creation_date, 'MM/dd/yyyy') as cdate
    from BIB_Workflow_status wf, ACC_Accession a, BIB_Refs b
    where wf._Group_key = 31576666
    and wf.isCurrent = 1
    and wf._Status_key = 31576674
    and wf._Refs_key = a._Object_key
    and a._MGIType_key = 1

#       - TR12427/Disease Ontology (DO)
#
'''

import sys
import os
import string
import reportlib
import db

db.setTrace()

TAB = reportlib.TAB
CRT = reportlib.CRT

fp = reportlib.init(sys.argv[0], 'Obsolete/Missing OMIM terms in DO as xrefs', outputdir = os.environ['QCOUTPUTDIR'])

results = db.sql('''
	(
	select a1.accID as doid, a2.accID as omimid
	from ACC_Accession a1, ACC_Accession a2
	where a1._MGIType_key = 13
	and a1._LogicalDB_key = 191 
	and a1._Object_key = a2._Object_key
	and a1.preferred = 1 
	and a2._LogicalDB_key = 15
	and a2.accID not like 'OMIM:PS%'
	and not exists (select 1 from ACC_Accession a3, VOC_Term t
		where a2.accID = a3.accID
		and a3._MGIType_key = 13
		and a3._LogicalDB_key = 15

import reportlib
import db

db.setTrace()

CRT = reportlib.CRT
SPACE = reportlib.SPACE
TAB = reportlib.TAB
PAGE = reportlib.PAGE

gpiSet = ['PR', 'EMBL', 'ENSEMBL', 'RefSeq']
gpiFileName = os.environ['PUBREPORTDIR'] + '/output/mgi.gpi'
gpiFile = open(gpiFileName, 'r')
gpiLookup = []

fp = reportlib.init(sys.argv[0], '', os.environ['QCOUTPUTDIR'])

fp.write('Marker used in Annotation differs from Marker used in Protein Isoform Ontology\n\n')
fp.write('value\tannotation\tontology\n\n')

results = db.sql('''select p.value, m.symbol as annotation, pm.symbol as isoformlookup
        from VOC_Annot a, VOC_Evidence e, VOC_Evidence_Property p, VOC_Term t, MRK_Marker m,
                ACC_Accession pa1, VOC_Annot pa, MRK_Marker pm
        where a._AnnotType_key = 1000
        and a._Object_key = m._Marker_key
        and a._Annot_key = e._Annot_key
        and e._AnnotEvidence_key = p._AnnotEvidence_key
        and p._PropertyTerm_key = t._Term_key
        and t.term = 'gene product'
        and p.value like 'PR:%'
        and p.value = pa1.accID

import db

db.setTrace()

DB_PREFIX = 'MGI'
SPECIES = 'taxon:10090'
DBTYPE_MARKER = 'gene'
DBTYPE_ISOFORM = 'protein'
DBTYPE_RNA = 'transcript'

TAB = reportlib.TAB
CRT = reportlib.CRT

db.useOneConnection(1)

fp = reportlib.init('mgi', fileExt = '.gpi', outputdir = os.environ['REPORTOUTPUTDIR'], printHeading = None)

fp.write('!gpi-version: 1.2\n')
fp.write('!date: %s $\n' % (mgi_utils.date("%m/%d/%Y")))
fp.write('!\n')
fp.write('! from Mouse Genome Database (MGD) & Gene Expression Database (GXD)\n')
fp.write('!\n')
fp.write('!  DB                     required  1             1             MGI\n')
fp.write('!  DB_Object_ID           required  1             2/17          MGI:87870\n')
fp.write('!  DB_Object_Symbol       required  1             3             Acat1\n')
fp.write('!  DB_Object_Name         optional  0 or greater  10            acetyl-Coenzyme A acetyltransferase 1\n')
fp.write('!  DB_Object_Synonym(s)   optional  0 or greater  11            Acat|6330585C21Rik\n')
fp.write('!  DB_Object_Type         required  1             12            gene\n')
fp.write('!  Taxon                  required  1             13            taxon:10090\n')
fp.write('!  Parent_Object_ID       optional  0 or 1        -             if DB_Object_ID = Isoform, then MGI:id of the Isoform\n')
fp.write('!  DB_Xref(s)             optional  0 or greater  -             if DB_Object_ID = Isoform, then UniProtKB:id of the Isoform\n')

def process(mode):
    # Purpose: process data using either 'sql' or 'bcp' mode
    # Returns:
    # Assumes:
    # Effects:
    # Throws:

    global notenewline

    if mode == 'bcp':
	fp1 = reportlib.init('allelecombnotetype1', printHeading = None)
	fp2 = reportlib.init('allelecombnotetype2', printHeading = None)
	fp3 = reportlib.init('allelecombnotetype3', printHeading = None)
    else:
	notenewline = '\n'

    # delete existiing Allele Combination notes for Genotypes we're processing

    if DEBUG:
        print '\ndeleting existing allele combination\n'
	sys.stdout.flush()

    db.sql('''delete from MGI_Note 
	using toprocess p 
	where p._Genotype_key = MGI_Note._Object_key 
	and MGI_Note._MGIType_key = %s 
	and MGI_Note._NoteType_key in (%s,%s,%s)
	''' % (mgiTypeKey, combNoteType1, combNoteType2, combNoteType3), None)

    if DEBUG:
        print 'finished deleting existing allele combination\n'
	sys.stdout.flush()

    # read in appropriate records

    if DEBUG:
        print '\nselecting existing allele combination\n'
	sys.stdout.flush()

    cmd = '''(
	    select p._Genotype_key,
	    p.genotypeID,
	    t1.term as alleleState, 
	    t2.term as compound, 
	    a1.symbol as allele1, 
	    a2.symbol as allele2, 
	    a1.isWildType as allele1WildType, 
	    a2.isWildType as allele2WildType, 
	    c1.accID as mgiID1, 
	    c2.accID as mgiID2, 
	    g.sequenceNum, m.chromosome 
	    from toprocess p, 
	    GXD_AllelePair g LEFT OUTER JOIN MRK_Marker m on (g._Marker_key = m._Marker_key),
	    VOC_Term t1, VOC_Term t2, ALL_Allele a1, ALL_Allele a2, 
	    ACC_Accession c1, ACC_Accession c2
	    where p._Genotype_key = g._Genotype_key 
	    and g._PairState_key = t1._Term_key 
	    and g._Compound_key = t2._Term_key 
	    and g._Allele_key_1 = a1._Allele_key 
	    and g._Allele_key_2 = a2._Allele_key 
	    and g._Allele_key_1 = c1._Object_key 
	    and c1._MGIType_key = 11 
	    and c1._LogicalDB_key = 1 
	    and c1.prefixPart = 'MGI:' 
	    and c1.preferred = 1 
	    and g._Allele_key_2 = c2._Object_key 
	    and c2._MGIType_key = 11 
	    and c2._LogicalDB_key = 1 
	    and c2.prefixPart = 'MGI:' 
	    and c2.preferred = 1 
	    union 
	    select p._Genotype_key,
	    p.genotypeID,
	    t1.term as alleleState, 
	    t2.term as compound, 
	    a1.symbol as allele1,
	    null as allele2, 
	    a1.isWildType as allele1WildType, 
	    0 as allele2WildType, 
	    c1.accID as mgiID1, 
	    null as mgiID2, 
	    g.sequenceNum, m.chromosome 
	    from toprocess p, 
	    GXD_AllelePair g LEFT OUTER JOIN MRK_Marker m on (g._Marker_key = m._Marker_key),
	    VOC_Term t1, VOC_Term t2, ALL_Allele a1, ACC_Accession c1
	    where p._Genotype_key = g._Genotype_key 
	    and g._PairState_key = t1._Term_key 
	    and g._Compound_key = t2._Term_key 
	    and g._Allele_key_1 = a1._Allele_key 
	    and g._Allele_key_2 is null 
	    and g._Allele_key_1 = c1._Object_key 
	    and c1._MGIType_key = 11 
	    and c1._LogicalDB_key = 1 
	    and c1.prefixPart = 'MGI:' 
	    and c1.preferred = 1 
	    )
	    order by _Genotype_key, sequenceNum;\n'''

    results = db.sql(cmd, 'auto')

#.........这里部分代码省略.........

try:
        optlist, args = getopt.getopt(sys.argv[1:], 'K:')
except:
        showUsage()

for opt in optlist:
        if opt[0] == '-K':
                markerKey = opt[1]
        else:
                showUsage()

if markerKey is None:
        showUsage()

db.useOneConnection(1)
fp = reportlib.init(sys.argv[0], printHeading = None)

marker()
accession()
miscellaneous()
allele()
goAnnotations()
history()
mapping()
probes()
gxd()

db.useOneConnection(0)
reportlib.finish_nonps(fp)	# non-postscript file

import re
import reportlib
import db

db.setTrace()

CRT = reportlib.CRT
SPACE = reportlib.SPACE
TAB = reportlib.TAB
PAGE = reportlib.PAGE

#
# Main
#

fp = reportlib.init(sys.argv[0], 'Supplemental Data Needed', os.environ['QCOUTPUTDIR'])

fp.write('\tReferences where:\n')
fp.write('\t- has J#\n')
fp.write('\t- is not Discard\n')
fp.write('\t- is-reviewe-article = No\n')
fp.write('\t- supplemental in:\n')
fp.write('\t\tDb found supplement\n')
fp.write('\t\tCurator found supplement\n')
fp.write('\t- Status in (Chosen, Indexed)\n')
fp.write('\t- Journal not in "Elife"\n')
fp.write('\t- Sorted by Curator/pm2geneload, Status, J#\n\n')
fp.write('\tbecause the J: assignment triggered a search for:\n')
fp.write('\t- supplemental\n')
fp.write('\t- supplementary\n')
fp.write('\t- additional file\n')

'''

import sys
import os
import string
import reportlib
import db

db.setTrace()

CRT = reportlib.CRT
SPACE = reportlib.SPACE
TAB = reportlib.TAB
PAGE = reportlib.PAGE

fp = reportlib.init(sys.argv[0], 'References that are marked as "MGI discard" and have data associated with them', os.environ['QCOUTPUTDIR'])

results = db.sql('''select distinct a.accid as jNum, a.numericPart
    from BIB_Refs b, MRK_Reference m, ACC_Accession a
    where b.isDiscard = 1
    and b._Refs_key = m._Refs_key
    and m._Refs_key = a._Object_key
    and a._MGIType_key = 1
    and a._LogicalDB_key = 1
    and a.preferred = 1
    and prefixPart = 'J:' ''', 'auto')
for r in results:
    fp.write('%s%s' % (r['jNum'], CRT))

fp.write('Total: %s' % len(results))
reportlib.finish_nonps(fp)      # non-postscript file

import reportlib
import db

db.setTrace()

CRT = reportlib.CRT
SPACE = reportlib.SPACE
TAB = reportlib.TAB
PAGE = reportlib.PAGE

#
# Main
#

title = 'Genes without Sequence with GXD Annotations'
fp = reportlib.init(sys.argv[0], title = title, outputdir = os.environ['QCOUTPUTDIR'])

fp.write('    includes "official"\n')
fp.write('    excludes "DNA Segment"\n\n')

fp.write(string.ljust('Gene Symbol', 30) + \
 	 string.ljust('Marekr Type', 30) + \
	 string.ljust('GXD Refs', 30) + \
 	 CRT)

fp.write(string.ljust('-----------', 30) + \
 	 string.ljust('-----------', 30) + \
	 string.ljust('--------', 30) + \
 	 CRT)

#