from sequence_handler import SequenceHandler from reagent import * import utils from user_handler import UserHandler from project_database_handler import ProjectDatabaseHandler from session import Session from exception import * dbConn = DatabaseConn() db = dbConn.databaseConnect() cursor = db.cursor() hostname = dbConn.getHostname() root_path = dbConn.getRootDir() dnaHandler = DNAHandler(db, cursor) protHandler = ProteinHandler(db, cursor) rHandler = ReagentHandler(db, cursor) oHandler = OligoHandler(db, cursor) propHandler = ReagentPropertyHandler(db, cursor) packetHandler = ProjectDatabaseHandler(db, cursor) propMapper = ReagentPropertyMapper(db, cursor) prop_Name_ID_Map = propMapper.mapPropNameID() # (prop name, prop id) prop_Category_Name_ID_Map = propMapper.mapPropCategoryNameID() # currUser is an INT user ID
def drawMap():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
root_path = dbConn.getRootDir()
form = cgi.FieldStorage(keep_blank_values="True")
#print "Content-type:text/html"
#print
#print `form`
if form.has_key("rID"):
rID = form.getvalue("rID")
else: # script executed from command line
# Worst-case scenarios
#rID = 260 # V260
#rID = 230 # V260
#rID = 80 # V80 - ok
#rID = 69661 # V2412 - not bad at all, just one of the oligos overlaps exactly with promoter (1 nt difference)
#rID = 23999 # V59541
rID = 97918
#print rID
if form.has_key("user_id_hidden"):
userID = form.getvalue("user_id_hidden")
else: # command-line execution
userID = 1 # debug
reagentID = rHandler.convertDatabaseToReagentID(rID)
uPackets = getCurrentUserProjects(userID)
#print "Content-type:text/html"
#print
#print reagentID
uPackets.sort()
#print `uPackets`
namePropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["name"], prop_Category_Name_ID_Map["General Properties"])
statusPropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["status"], prop_Category_Name_ID_Map["General Properties"])
projectPropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["packet id"], prop_Category_Name_ID_Map["General Properties"])
rName = rHandler.findSimplePropertyValue(rID, namePropID)
rTypeID = rHandler.findReagentTypeID(rID)
try:
os.remove(root_path + "Reagent/vector_maps/" + reagentID + "_Oligo_map.pdf")
except OSError:
pass
#print root_path
c = Canvas(root_path + "Reagent/vector_maps/" + reagentID + "_Oligo_map.pdf")
c.setPageSize((1500,1500))
c.setStrokeColorRGB(0,0,0)
c.saveState()
# Draw circle
origin = 0
origin_x = 750
origin_y = 750
radius = 200
c.circle(origin_x, origin_y, radius)
c.restoreState()
# Divide circle into 100-unit sectors
rSeqID = rHandler.findDNASequenceKey(rID)
rSeq = sHandler.findSequenceByID(rSeqID)
seqLen = len(rSeq)
#print "Content-type:text/html"
#print
#print `rID`
unit_angle_measure = float(360) / float(seqLen)
#print unit_angle_measure
# Mark 1 on the circle - KEEP, Karen said!
c.setLineWidth(1)
c.setStrokeColor(black)
c.setFillColor(black)
c.saveState()
path = c.beginPath()
# Draw a triangle pointing down above the circle
#path.moveTo(origin_x, origin_y+radius+7)
#path.lineTo(origin_x-5, origin_y+radius+14)
#path.lineTo(origin_x+5, origin_y+radius+14)
#path.lineTo(origin_x, origin_y+radius+7)
# Draw a triangle pointing up inside the circle
#path.moveTo(origin_x, origin_y+radius-10)
#path.lineTo(origin_x-5, origin_y+radius-14)
#path.lineTo(origin_x+5, origin_y+radius-14)
#path.lineTo(origin_x, origin_y+radius-10)
# Draw a triangle pointing right inside the circle
path.moveTo(origin_x, origin_y+radius-14)
path.lineTo(origin_x, origin_y+radius-28)
path.lineTo(origin_x+8, origin_y+radius-21)
path.lineTo(origin_x, origin_y+radius-14)
c.drawPath(path, True, True)
# label 1
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 16)
#t.setTextOrigin(origin_x-5, origin_y+radius+19) # above circle
t.setTextOrigin(origin_x-3, origin_y+radius-50) # above circle
t.textOut("1")
c.drawText(t)
c.restoreState()
# Calculate feature segment sizes
sequenceFeatures = rHandler.findReagentSequenceFeatures(rID)
#print `sequenceFeatures`
# Draw legend
ox_legend = 1280
oy_legend = 1465
prev_legend = oy_legend
# draw frame
c.setStrokeColor(darkgray)
c.setFillColor(white)
c.saveState()
featureNames = rtPropHandler.findReagentTypeAttributeNamesByCategory(rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
featureNames.sort()
if len(featureNames) > 15:
origin_spacer = -19
coeff = 12
else:
origin_spacer = 65
coeff = 15
origin_legend = prev_legend+origin_spacer-len(featureNames)*coeff
x = (990 - origin_legend) / len(featureNames)
#print x
if x < 12:
x = 12
# WHEN WANT TO ADJUST LEGEND GREY BOX HEIGHT: UPDATE THE VALUE ADDED TO legend_height AND THE VALUE SUBTRACTED FROM origin_legend
legend_height = len(featureNames)*x + 55
c.rect(ox_legend-25, origin_legend-35, 215, legend_height, 1, 1) # good for specific rtype attributes
c.restoreState()
protocolPropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["protocol"], prop_Category_Name_ID_Map["Classifiers"])
seqPropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["sequence"], prop_Category_Name_ID_Map["DNA Sequence"])
sequenceFeatures = rHandler.findAllReagentFeatures(Vector(rID), rID)
# Print reagent ID and size at the centre of the circle and print name at the top of the page
c.setFont("Helvetica-Bold", 32)
c.setFillColor(black)
c.saveState()
c.drawCentredString(origin_x, origin_y+35, reagentID)
c.drawCentredString(origin_x, origin_y+10, "nt 1 - " + `seqLen`)
if rName:
c.setFillColor(blue)
c.drawCentredString(origin_x, 1415, rName)
c.restoreState()
# find all Oligos whose protocol is 'sequencing'
# April 26, 2010: Do not include status in this query, as it might just not be recorded for the oligo at all (early entries)
cursor.execute("SELECT r.reagentID, r.groupID, s.sequence FROM Sequences_tbl s, ReagentPropList_tbl p1, ReagentPropList_tbl p2, Reagents_tbl r WHERE p1.propertyID=" + `protocolPropID` + " AND p1.propertyValue='sequencing' AND p1.reagentID=r.reagentID AND r.reagentTypeID='3' AND p1.reagentID=p2.reagentID AND p2.propertyID=" + `seqPropID` + " AND p2.propertyValue=s.seqID AND p1.status='ACTIVE' AND p2.status='ACTIVE' AND r.status='ACTIVE' AND s.status='ACTIVE'")
#print "SELECT r.reagentID, r.groupID, s.sequence FROM Sequences_tbl s, ReagentPropList_tbl p1, ReagentPropList_tbl p2, Reagents_tbl r WHERE p1.propertyID=" + `protocolPropID` + " AND p1.propertyValue='sequencing' AND p1.reagentID=r.reagentID AND r.reagentTypeID='3' AND p1.reagentID=p2.reagentID AND p2.propertyID=" + `seqPropID` + " AND p2.propertyValue=s.seqID AND p1.status='ACTIVE' AND p2.status='ACTIVE' AND r.status='ACTIVE' AND s.status='ACTIVE'"
results = cursor.fetchall()
rSeq = utils.squeeze(rSeq).lower()
#print rSeq
oligoFeatures = []
oligoIDsDict = {} # O123 => 123
oligoNamesDict = {} # 123 => "O123 Name"
oligoProjectDict = {} # 123 => 7
for result in results:
if result:
oligoID = int(result[0])
groupID = int(result[1])
oligo_lims_id = "O" + `groupID`
oligoIDsDict[oligo_lims_id] = oligoID
#print oligo_lims_id
oligoName = rHandler.findSimplePropertyValue(oligoID, namePropID)
# April 26, 2010, Karen's request: Ignore Oligos whose status is 'Failed' or 'Do Not Use'
oligoStatus = rHandler.findSimplePropertyValue(oligoID, statusPropID)
if oligoStatus:
#print oligoStatus
if oligoStatus.lower() == 'failed' or oligoStatus.lower() == 'do not use':
continue
if oligoName:
oligoNamesDict[oligoID] = oligoName
else:
oligoNamesDict[oligoID] = ""
#cursor.execute("SELECT propertyValue FROM ReagentPropList_tbl WHERE reagentID=" + `oligoID` + " AND propertyID=" + `namePropID` + " AND status='ACTIVE'")
#result2 = cursor.fetchone()
#if result2:
#oligoName = result2[0]
#oligoNamesDict[oligoID] = oligoName
#else:
#oligoNamesDict[oligoID] = ""
# PROJECT - MUST CAST TO INT
oligoPacket = int(rHandler.findSimplePropertyValue(oligoID, projectPropID))
#print oligoPacket
if oligoPacket:
if oligoPacket not in uPackets:
#print oligoPacket
continue
#cursor.execute("SELECT propertyValue FROM ReagentPropList_tbl WHERE reagentID=" + `oligoID` + " AND propertyID=" + `projectPropID` + " AND status='ACTIVE'")
#result3 = cursor.fetchone()
#if result3:
#oligoPacket = int(result3[0])
##print oligoPacket
#if oligoPacket not in uPackets:
##print oligoPacket
#continue
#oligoProjectDict[oligoID] = oligoPacket
#else:
#oligoProjectDict[oligoID] = 0
if len(result) == 3:
oligoSeq = result[2].strip().lower()
#print oligoSeq
tm = sHandler.calculateTm(oligoSeq)
# Changes made April 26, 2010: Karen caught that the sense/antisense check does not work for T3 and T7 vectors and said to check oligo sequence both ways
#if rSeq.find(oligoSeq) < 0:
#continue
if rSeq.find(oligoSeq) >= 0:
fStart = rSeq.find(oligoSeq) + 1
fEnd = fStart + len(oligoSeq) - 1
#if oHandler.isSenseOligo(oligoID):
oFeature = SequenceFeature("sequencing primer", oligo_lims_id, fStart, fEnd, 'forward', oligoSeq, tm)
#else:
#oFeature = SequenceFeature("sequencing primer", oligo_lims_id, fStart, fEnd, 'reverse', oligoSeq, tm)
else:
revSeq = sHandler.reverse_complement(oligoSeq)
if rSeq.find(revSeq) < 0:
continue
fStart = rSeq.find(revSeq) + 1
fEnd = fStart + len(revSeq)
# Note: start pos > end pos, as we're talking about reverse Oligo sequence
revStart = fEnd - 1
revEnd = fStart
# Still, record sense/antisense for displaying on the map ('forward' and 'reverse' here are just static values in Feature class, it doesn't reflect sequence orientation in our case - just use as a temporary placeholder)
#if oHandler.isSenseOligo(oligoID):
#oligoFeatures.append(oFeature)
#oFeature = SequenceFeature("sequencing primer", oligo_lims_id, revStart, revEnd, 'forward', oligoSeq, tm)
#else:
oFeature = SequenceFeature("sequencing primer", oligo_lims_id, revStart, revEnd, 'reverse', oligoSeq, tm)
oligoFeatures.append(oFeature)
sequenceFeatures.append(oFeature)
# SORT features by size, so that short features are not hidden behind the long ones
fSizes = []
sortedFeatures = []
fSortedPos = {}
fStartPos = []
fEndPos = []
for feature in sequenceFeatures:
fSize = int(feature.getFeatureSize())
if fSize > 0:
fSizes.append(fSize)
#if fSize > 150:
f_start_tmp = int(feature.getFeatureStartPos())
fStartPos.append(f_start_tmp)
fSortedPos[f_start_tmp] = feature
f_end_tmp = int(feature.getFeatureEndPos())
fEndPos.append(f_end_tmp)
fEndPos.sort()
fStartPos.sort()
#print `fStartPos`
#print `fEndPos`
fSizes.sort(reverse=True)
#print `fSizes`
for fs in fSizes:
for feature in sequenceFeatures:
fSize = feature.getFeatureSize()
# added existence check July 17/08 - different features may have same sizes so end up with duplicate features in list (e.g. cloning sizes appeared twice on the map)
if fs == fSize and feature not in sortedFeatures:
sortedFeatures.append(feature)
# Order: 5' site, 3' site, 5' linker, 3' linker, then the rest
sites_color = featureNameColorMap["5' cloning site"] # same for 3' site
# 5' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(sites_color)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "5' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# 3' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(sites_color)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "3' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# Show legend for linkers
linkers_color = featureNameColorMap["5' linker"]
# 5' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "5' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# 3' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "3' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# Output the rest of the features in alphabetical order
featureNames = featureNameColorMap.keys()
featureNames.sort()
#print `featureNames`
for featureName in featureNames:
#print featureName
if featureNameColorMap.has_key(featureName):
color = featureNameColorMap[featureName]
if featureName != "5' cloning site" and featureName != "3' cloning site" and featureName != "5' linker" and featureName != "3' linker" and color != None:
#print featureName
c.setStrokeColor(color)
c.setFillColor(color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(color)
t.setFillColor(color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + featureName.upper())
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# Sequencing Primer
oligoColor = "#7cfc00"
c.setStrokeColor(oligoColor)
c.setFillColor(oligoColor)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(oligoColor)
t.setFillColor(oligoColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "SEQUENCING PRIMER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
ox_labels = 40
oy_labels = 40
#prev_legend = oy_labels
for feature in sortedFeatures:
fType = feature.getFeatureType()
fValue = feature.getFeatureName()
fSize = feature.getFeatureSize()
#print fType
#print fValue
#print fSize
# color
if featureNameColorMap.has_key(fType):
fColor = featureNameColorMap[fType]
textColor = fColor
elif fType == 'sequencing primer':
fColor = "#7cfc00"
textColor = "black"
o_id = oligoIDsDict[fValue]
oligoName = oligoNamesDict[o_id]
if len(oligoName) > 0:
fValue += " " + oligoName
# property name
if fType == 'cdna insert':
fValue = "cDNA Insert"
elif fType == 'promoter':
fValue = fValue + " " + fType
fStart = feature.getFeatureStartPos()
fEnd = feature.getFeatureEndPos()
fDir = feature.getFeatureDirection()
# value
#if fType == 'sequencing primer':
#oligoDir = feature.getFeatureDirection()
#if oligoDir == 'forward':
#oligoType = 'Sense'
#else:
#oligoType = 'Antisense'
#fTxt = fValue + " (" + `fStart` + "-" + `fEnd` + "), " + oligoDir
#else:
fTxt = fValue + " (" + `fStart` + "-" + `fEnd` + ")"
if fSize > 0:
f_start = fStart * unit_angle_measure
#print "Start " + `fStart`
#print "End " + `fEnd`
startAngle = 90 - f_start
#print "Start angle " + `startAngle`
f_end = fEnd * unit_angle_measure
endAngle = 90 - f_end
#print "End angle " + `endAngle`
extAngle = -1*(f_end - f_start)
#print "Ext angle " + `extAngle`
x1 = origin_x - radius
y1 = origin_y - radius
x2 = origin_x + radius
y2 = origin_y + radius
p = c.beginPath()
c.setLineWidth(10)
c.setLineJoin(1)
c.setStrokeColor(fColor)
c.saveState()
p.arc(x1, y1, x2, y2, startAngle, extAngle)
c.drawPath(p)
c.restoreState()
# common to all
startAngle_rad = (startAngle * math.pi) / 180.0
endAngle_rad = (endAngle * math.pi) / 180.0
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 9)
c.saveState()
arc_x_start = origin_x + (radius+5)*math.cos(startAngle_rad)
arc_y_start = origin_y + (radius+5)*math.sin(startAngle_rad)
arc_x_end = origin_x+(radius+5)*math.cos(endAngle_rad)
arc_y_end = origin_y+(radius+5)*math.sin(endAngle_rad)
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 12)
c.saveState()
# draw line
delta = 45
if fStart < seqLen/2:
if arc_y_start > origin_y:
# THIS WORKS!!!!
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
fInd = fStartPos.index(fStart)
fY = len(fStartPos) - fInd
c.line(arc_x_start, arc_y_start, arc_x_start+math.fabs(math.sin(delta))*(fInd*10), arc_y_start+math.fabs(math.cos(delta))*(fY*10))
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(textColor)
c.setFillColor(textColor)
c.setFont("Helvetica-Bold", 8)
c.saveState()
#c.drawString(arc_x_start+math.fabs(math.sin(delta))*(fInd*10)+2, arc_y_start+math.fabs(math.cos(delta))*(fY*10)-math.cos(delta)*0.9, fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawString(arc_x_start+math.fabs(math.sin(delta))*(fInd*10)+2, arc_y_start+math.fabs(math.cos(delta))*(fY*10)-math.cos(delta)*0.9, fTxt)
c.restoreState()
else:
fInd = fStartPos.index(fStart)
fY = len(fStartPos) - fInd
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
c.line(arc_x_start, arc_y_start, arc_x_start+math.fabs(math.sin(delta))*(fY*10), arc_y_start-math.fabs(math.cos(delta))*(fInd*10))
c.restoreState()
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(textColor)
c.setFillColor(textColor)
c.setFont("Helvetica-Bold", 8)
c.saveState()
#c.drawString(arc_x_start+math.fabs(math.sin(delta))*(fY*10)+2, arc_y_start-math.fabs(math.cos(delta))*(fInd*10)-math.cos(delta)*13, fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawString(arc_x_start+math.fabs(math.sin(delta))*(fY*10)+2, arc_y_start-math.fabs(math.cos(delta))*(fInd*10)-math.cos(delta)*13, fTxt)
c.restoreState()
else:
if arc_y_start > origin_y:
fInd = fStartPos.index(fStart)
fY = len(fStartPos) - fInd
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
c.line(arc_x_start, arc_y_start, arc_x_start-math.fabs(math.sin(delta)*(fY*10)), arc_y_start+math.fabs(math.cos(delta)*(fInd*10)))
c.restoreState()
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(textColor)
c.setFillColor(textColor)
c.setFont("Helvetica-Bold", 8)
c.saveState()
#c.drawRightString(arc_x_start-math.fabs(math.sin(delta)*(fY*10))+2, arc_y_start+math.fabs(math.cos(delta)*(fInd*10)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawRightString(arc_x_start-math.fabs(math.sin(delta)*(fY*10))+2, arc_y_start+math.fabs(math.cos(delta)*(fInd*10)), fTxt)
c.restoreState()
else:
fInd = fStartPos.index(fStart)
fY = len(fStartPos) - fInd
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
c.line(arc_x_start, arc_y_start, arc_x_start-math.fabs(math.sin(delta)*(fInd*10)), arc_y_start-math.fabs(math.cos(delta)*(fY*10)))
c.restoreState()
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(textColor)
c.setFillColor(textColor)
c.setFont("Helvetica-Bold", 8)
c.saveState()
#c.drawRightString(arc_x_start-math.fabs(math.sin(delta)*(fInd*10))-2, arc_y_start-math.fabs(math.cos(delta)*(fY*10))-math.cos(delta)*12, fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawRightString(arc_x_start-math.fabs(math.sin(delta)*(fInd*10))-2, arc_y_start-math.fabs(math.cos(delta)*(fY*10))-math.cos(delta)*12, fTxt)
c.restoreState()
# print Oligo info
#prev_legend = prev_legend-10
prev_legend = 1365
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels, prev_legend-15)
t.textOut("Sequencing primers for " + reagentID + ":")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-18
fColor = "#7cfc00"
# sort oligos
tmp_oligos = {}
#print `oligoFeatures`
for oFeature in oligoFeatures:
oligoID = oFeature.getFeatureName()
#print oligoID
oligoStart = oFeature.getFeatureStartPos()
#print oligoStart
if tmp_oligos.has_key(oligoStart):
tmp_o_list = tmp_oligos[oligoStart]
else:
tmp_o_list = []
tmp_oligos[oligoStart] = oFeature
tmp_o_list.append(oFeature)
tmp_oligos[oligoStart] = tmp_o_list
oligoSeq = oFeature.getFeatureDescrType()
#print oligoSeq
#print `tmp_oligos`
for oligoStart in sorted(tmp_oligos.keys()):
oFeatures = tmp_oligos[oligoStart]
for oFeature in oFeatures:
oligoID = oFeature.getFeatureName()
#oligoSeq = oFeature.getFeatureDescrType()
oligoTm = oFeature.getFeatureDescrName()
oligoEnd = oFeature.getFeatureEndPos()
oligoDir = oFeature.getFeatureDirection()
o_rID = oligoIDsDict[oligoID]
oligoName = oligoNamesDict[o_rID]
#if oligoDir == 'forward':
#oligoType = 'Sense'
#else:
#oligoType = 'Antisense'
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
if len(oligoName) > 0:
#t.textOut(oligoID + ": " + oligoName + " (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoType)
t.textOut(oligoID + ": " + oligoName + " (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoDir)
else:
#t.textOut(oligoID + ": (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoType)
t.textOut(oligoID + ": (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoDir)
#print oligoID + ": (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoType
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.restoreState()
c.showPage()
c.save()
from sequence_handler import SequenceHandler from reagent import * import utils from user_handler import UserHandler from project_database_handler import ProjectDatabaseHandler from session import Session from exception import * dbConn = DatabaseConn() db = dbConn.databaseConnect() cursor = db.cursor() hostname = dbConn.getHostname() root_path = dbConn.getRootDir() dnaHandler = DNAHandler(db, cursor) protHandler = ProteinHandler(db, cursor) rHandler = ReagentHandler(db, cursor) oHandler = OligoHandler(db, cursor) propHandler = ReagentPropertyHandler(db, cursor) packetHandler = ProjectDatabaseHandler(db, cursor) propMapper = ReagentPropertyMapper(db, cursor) prop_Name_ID_Map = propMapper.mapPropNameID() # (prop name, prop id) prop_Category_Name_ID_Map = propMapper.mapPropCategoryNameID() # currUser is an INT user ID
def drawMap():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
root_path = dbConn.getRootDir()
form = cgi.FieldStorage(keep_blank_values="True")
#print "Content-type:text/html"
#print
#print `form`
if form.has_key("rID"):
rID = form.getvalue("rID")
else:
#rID = 148913 # V4550
rID = 29125
#rID = 72
#rID = 309
#rID = 1901 # small feature labels @ start of seq. overlap
#rID = 36415
#print rID
reagentID = rHandler.convertDatabaseToReagentID(rID)
#print "Content-type:text/html"
#print
#print reagentID
namePropID = pHandler.findReagentPropertyInCategoryID(
prop_Name_ID_Map["name"],
prop_Category_Name_ID_Map["General Properties"])
rName = rHandler.findSimplePropertyValue(rID, namePropID)
#rName = rHandler.findSimplePropertyValue(rID, prop_Name_ID_Map["name"])
rTypeID = rHandler.findReagentTypeID(rID)
try:
os.remove(root_path + "Reagent/vector_maps/" + reagentID + "_map.pdf")
except OSError:
pass
#print root_path
c = Canvas(root_path + "Reagent/vector_maps/" + reagentID + "_map.pdf")
c.setPageSize((1000, 1000))
c.setStrokeColorRGB(0, 0, 0)
c.saveState()
# Draw circle
origin = 0
origin_x = 500
origin_y = 470
radius = 200
c.circle(origin_x, origin_y, radius)
c.restoreState()
# Divide circle into 100-unit sectors
rSeqID = rHandler.findDNASequenceKey(rID)
rSeq = sHandler.findSequenceByID(rSeqID)
seqLen = len(rSeq)
#print "Content-type:text/html"
#print
#print `rID`
unit_angle_measure = float(360) / float(seqLen)
#print unit_angle_measure
# Mark 1 on the circle - KEEP, Karen said!
c.setLineWidth(1)
c.setStrokeColor(black)
c.setFillColor(black)
c.saveState()
path = c.beginPath()
path.moveTo(origin_x, origin_y + radius + 7)
path.lineTo(origin_x - 5, origin_y + radius + 14)
path.lineTo(origin_x + 5, origin_y + radius + 14)
path.lineTo(origin_x, origin_y + radius + 7)
c.drawPath(path, True, True)
# label 1
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 16)
t.setTextOrigin(origin_x - 5, origin_y + radius + 19)
t.textOut("1")
c.drawText(t)
c.restoreState()
# Calculate feature segment sizes
sequenceFeatures = rHandler.findReagentSequenceFeatures(rID)
#print `sequenceFeatures`
# Draw legend
ox_legend = 800
oy_legend = 985
prev_legend = oy_legend
# draw frame
c.setStrokeColor(darkgray)
#c.setStrokeColor(white)
#c.setFillColor(lightgrey)
c.setFillColor(white)
c.saveState()
# Output the rest of the features in alphabetical order - Moved here Jan. 26/10
#featureNames = featureNameColorMap.keys()
#print `featureNameColorMap.keys()`
#print len(featureNameColorMap.keys())
#fnames = rtPropHandler.findReagentTypeAttributeNamesByCategory(rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
#fnames.remove('expression system')
#fnames.remove('tag position')
#print `fnames`
#print len(fnames)
featureNames = rtPropHandler.findReagentTypeAttributeNamesByCategory(
rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
featureNames.sort()
#print `featureNames`
#print prev_legend-240
#print prev_legend-15-len(featureNames)*15
#c.rect(ox_legend-25, prev_legend-240, 215, 235, 1, 1)
#c.rect(ox_legend-25, prev_legend-15-len(featureNames)*15, 215, 10+len(featureNames)*15, 1, 1) # good for list of all db features
if len(featureNames) > 15:
origin_spacer = -19
coeff = 12
else:
origin_spacer = 65
coeff = 15
#origin_legend = prev_legend+65-len(featureNames)*15
origin_legend = prev_legend + origin_spacer - len(featureNames) * coeff
x = (990 - origin_legend) / len(featureNames)
#print x
if x < 12:
x = 12
legend_height = len(featureNames) * x + 15
#print legend_height
c.rect(ox_legend - 25, origin_legend - 17, 215, legend_height, 1,
1) # good for specific rtype attributes
c.restoreState()
# Order: 5' site, 3' site, 5' linker, 3' linker, then the rest
sites_color = featureNameColorMap["5' cloning site"] # same for 3' site
# 5' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
t.setStrokeColor(sites_color)
#t.setFillColor(black)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + "5' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
# 3' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(sites_color)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + "3' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
# Show legend for linkers
linkers_color = featureNameColorMap["5' linker"]
# 5' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + "5' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
# 3' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + "3' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
## Output the rest of the features in alphabetical order
#featureNames = featureNameColorMap.keys()
#featureNames.sort()
#print `featureNames`
for featureName in featureNames:
if featureNameColorMap.has_key(featureName):
color = featureNameColorMap[featureName]
#else:
#continue
if featureName != "5' cloning site" and featureName != "3' cloning site" and featureName != "5' linker" and featureName != "3' linker" and color != None:
#print featureName
c.setStrokeColor(color)
c.setFillColor(color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(color)
t.setFillColor(color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + featureName.upper())
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
#print prev_legend
# Print reagent ID and size at the centre of the circle and print name at the top of the page
c.setFont("Helvetica-Bold", 32)
c.setFillColor(black)
c.saveState()
c.drawCentredString(origin_x, origin_y + 35, reagentID)
c.drawCentredString(origin_x, origin_y + 10, "nt 1 - " + ` seqLen `)
if rName:
c.setFillColor(blue)
c.drawCentredString(origin_x, 935, rName)
c.restoreState()
# SORT features by size, so that short features are not hidden behind the long ones
fSizes = []
sortedFeatures = []
for feature in sequenceFeatures:
fSize = int(feature.getFeatureSize())
if fSize > 0:
fSizes.append(fSize)
fSizes.sort(reverse=True)
#print `fSizes`
for fs in fSizes:
for feature in sequenceFeatures:
fSize = feature.getFeatureSize()
# added existence check July 17/08 - different features may have same sizes so end up with duplicate features in list (e.g. cloning sizes appeared twice on the map)
if fs == fSize and feature not in sortedFeatures:
sortedFeatures.append(feature)
#print `sortedFeatures`
ox_labels = 40
oy_labels = 910
prev_legend = oy_labels
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels, prev_legend - 15)
t.textOut("Features shorter than 150 nt:")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 18
#for feature in sequenceFeatures:
for feature in sortedFeatures:
fType = feature.getFeatureType()
fValue = feature.getFeatureName()
fSize = feature.getFeatureSize()
#print fType
#print fValue
#print fSize
fColor = featureNameColorMap[fType]
if fType == 'cdna insert':
fValue = "cDNA Insert"
elif fType == 'promoter':
fValue = fValue + " " + fType
fStart = feature.getFeatureStartPos()
fEnd = feature.getFeatureEndPos()
fDir = feature.getFeatureDirection()
if fSize > 0:
f_start = fStart * unit_angle_measure
#print "Start " + `fStart`
#print "End " + `fEnd`
startAngle = 90 - f_start
#print "Start angle " + `startAngle`
f_end = fEnd * unit_angle_measure
endAngle = 90 - f_end
#print "End angle " + `endAngle`
extAngle = -1 * (f_end - f_start)
#print "Ext angle " + `extAngle`
x1 = origin_x - radius
y1 = origin_y - radius
x2 = origin_x + radius
y2 = origin_y + radius
p = c.beginPath()
#t = c.beginText()
c.setLineWidth(10)
c.setLineJoin(1)
fColor = featureNameColorMap[fType]
c.setStrokeColor(fColor)
c.saveState()
p.arc(x1, y1, x2, y2, startAngle, extAngle)
c.drawPath(p)
c.restoreState()
## jan. 27/10: this makes a contour for each arc
#p = c.beginPath()
#c.setLineWidth(1)
##fColor = featureNameColorMap[fType]
#c.setStrokeColor(black)
#c.setFillColor(fColor)
#c.saveState()
#p.arc(x1+5, y1+5, x2-5, y2-5, startAngle, extAngle)
#c.drawPath(p)
##c.restoreState()
##c.setLineWidth(1)
##fColor = featureNameColorMap[fType]
##c.setStrokeColor(black)
##c.setFillColor(fColor)
##c.saveState()
#p.arc(x1-5, y1-5, x2+5, y2+5, startAngle, extAngle)
#c.drawPath(p)
#c.restoreState() # jan. 27/10 modification ends here
# common to all
startAngle_rad = (startAngle * math.pi) / 180.0
endAngle_rad = (endAngle * math.pi) / 180.0
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 9)
c.saveState()
arc_x_start = origin_x + (radius + 5) * math.cos(startAngle_rad)
arc_y_start = origin_y + (radius + 5) * math.sin(startAngle_rad)
arc_x_end = origin_x + (radius + 5) * math.cos(endAngle_rad)
arc_y_end = origin_y + (radius + 5) * math.sin(endAngle_rad)
# draw label
c.setStrokeColorRGB(0, 0, 1)
c.setFillColorRGB(0, 0, 1)
c.setFont("Helvetica-Bold", 12)
c.saveState()
# draw line
delta = 45
# Rotate labels only for SMALL features (they can be crammed together)
#if fSize > 100:
#delta = 45
#else:
#delta = 32
if fStart < seqLen / 2:
if arc_y_start > origin_y:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
#if fSize <= 100:
#c.line(arc_x_start, arc_y_start, arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)))
#else:
# July 17/08: Show labels for long features only
if fSize > 150:
c.line(arc_x_start, arc_y_start,
arc_x_start + 50 * math.fabs(math.sin(delta)),
arc_y_start + 55 * math.fabs(math.cos(delta)))
c.restoreState()
# July 17/08: Show labels for long features only
if fSize > 150:
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawString(
arc_x_start + 50 * math.fabs(math.sin(delta)),
arc_y_start + 55 * math.fabs(math.cos(delta)),
fValue + " (" + ` fStart ` + "-" + ` fEnd ` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels + 5, prev_legend - 15, 15, 6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels + 25, prev_legend - 15)
t.textOut(fValue + " (" + ` fStart ` + "-" + ` fEnd ` +
")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
c.restoreState()
else:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start,
arc_x_start + 50 * math.fabs(math.sin(delta)),
arc_y_start - 55 * math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawString(
arc_x_start + 50 * math.fabs(math.sin(delta)),
arc_y_start - 55 * math.fabs(math.cos(delta)),
fValue + " (" + ` fStart ` + "-" + ` fEnd ` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels + 5, prev_legend - 15, 15, 6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels + 25, prev_legend - 15)
t.textOut(fValue + " (" + ` fStart ` + "-" + ` fEnd ` +
")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
c.restoreState()
else:
if arc_y_start > origin_y:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start,
arc_x_start - 50 * math.fabs(math.sin(delta)),
arc_y_start + 55 * math.fabs(math.cos(delta)))
#c.line(arc_x_start, arc_y_start, arc_x_start+10*math.fabs(math.sin(delta)), arc_y_start-10*math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawRightString(
arc_x_start - 50 * math.fabs(math.sin(delta)),
arc_y_start + 55 * math.fabs(math.cos(delta)),
fValue + " (" + ` fStart ` + "-" + ` fEnd ` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels + 5, prev_legend - 15, 15, 6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels + 25, prev_legend - 15)
t.textOut(fValue + " (" + ` fStart ` + "-" + ` fEnd ` +
")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
c.restoreState()
else:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start,
arc_x_start - 50 * math.fabs(math.sin(delta)),
arc_y_start - 55 * math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawRightString(
arc_x_start - 50 * math.fabs(math.sin(delta)),
arc_y_start - 55 * math.fabs(math.cos(delta)),
fValue + " (" + ` fStart ` + "-" + ` fEnd ` + ")")
c.restoreState()
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels + 5, prev_legend - 15, 15, 6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels + 25, prev_legend - 15)
t.textOut(fValue + " (" + ` fStart ` + "-" + ` fEnd ` +
")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
c.showPage()
c.save()
def drawMap():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
root_path = dbConn.getRootDir()
form = cgi.FieldStorage(keep_blank_values="True")
#print "Content-type:text/html"
#print
#print `form`
if form.has_key("rID"):
rID = form.getvalue("rID")
else:
#rID = 148913 # V4550
rID = 29125
#rID = 72
#rID = 309
#rID = 1901 # small feature labels @ start of seq. overlap
#rID = 36415
#print rID
reagentID = rHandler.convertDatabaseToReagentID(rID)
#print "Content-type:text/html"
#print
#print reagentID
namePropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["name"], prop_Category_Name_ID_Map["General Properties"])
rName = rHandler.findSimplePropertyValue(rID, namePropID)
#rName = rHandler.findSimplePropertyValue(rID, prop_Name_ID_Map["name"])
rTypeID = rHandler.findReagentTypeID(rID)
try:
os.remove(root_path + "Reagent/vector_maps/" + reagentID + "_map.pdf")
except OSError:
pass
#print root_path
c = Canvas(root_path + "Reagent/vector_maps/" + reagentID + "_map.pdf")
c.setPageSize((1000,1000))
c.setStrokeColorRGB(0,0,0)
c.saveState()
# Draw circle
origin = 0
origin_x = 500
origin_y = 470
radius = 200
c.circle(origin_x, origin_y, radius)
c.restoreState()
# Divide circle into 100-unit sectors
rSeqID = rHandler.findDNASequenceKey(rID)
rSeq = sHandler.findSequenceByID(rSeqID)
seqLen = len(rSeq)
#print "Content-type:text/html"
#print
#print `rID`
unit_angle_measure = float(360) / float(seqLen)
#print unit_angle_measure
# Mark 1 on the circle - KEEP, Karen said!
c.setLineWidth(1)
c.setStrokeColor(black)
c.setFillColor(black)
c.saveState()
path = c.beginPath()
path.moveTo(origin_x, origin_y+radius+7)
path.lineTo(origin_x-5, origin_y+radius+14)
path.lineTo(origin_x+5, origin_y+radius+14)
path.lineTo(origin_x, origin_y+radius+7)
c.drawPath(path, True, True)
# label 1
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 16)
t.setTextOrigin(origin_x-5, origin_y+radius+19)
t.textOut("1")
c.drawText(t)
c.restoreState()
# Calculate feature segment sizes
sequenceFeatures = rHandler.findReagentSequenceFeatures(rID)
#print `sequenceFeatures`
# Draw legend
ox_legend = 800
oy_legend = 985
prev_legend = oy_legend
# draw frame
c.setStrokeColor(darkgray)
#c.setStrokeColor(white)
#c.setFillColor(lightgrey)
c.setFillColor(white)
c.saveState()
# Output the rest of the features in alphabetical order - Moved here Jan. 26/10
#featureNames = featureNameColorMap.keys()
#print `featureNameColorMap.keys()`
#print len(featureNameColorMap.keys())
#fnames = rtPropHandler.findReagentTypeAttributeNamesByCategory(rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
#fnames.remove('expression system')
#fnames.remove('tag position')
#print `fnames`
#print len(fnames)
featureNames = rtPropHandler.findReagentTypeAttributeNamesByCategory(rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
featureNames.sort()
#print `featureNames`
#print prev_legend-240
#print prev_legend-15-len(featureNames)*15
#c.rect(ox_legend-25, prev_legend-240, 215, 235, 1, 1)
#c.rect(ox_legend-25, prev_legend-15-len(featureNames)*15, 215, 10+len(featureNames)*15, 1, 1) # good for list of all db features
if len(featureNames) > 15:
origin_spacer = -19
coeff = 12
else:
origin_spacer = 65
coeff = 15
#origin_legend = prev_legend+65-len(featureNames)*15
origin_legend = prev_legend+origin_spacer-len(featureNames)*coeff
x = (990 - origin_legend) / len(featureNames)
#print x
if x < 12:
x = 12
legend_height = len(featureNames)*x + 15
#print legend_height
c.rect(ox_legend-25, origin_legend-17, 215, legend_height, 1, 1) # good for specific rtype attributes
c.restoreState()
# Order: 5' site, 3' site, 5' linker, 3' linker, then the rest
sites_color = featureNameColorMap["5' cloning site"] # same for 3' site
# 5' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
t.setStrokeColor(sites_color)
#t.setFillColor(black)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "5' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# 3' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(sites_color)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "3' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# Show legend for linkers
linkers_color = featureNameColorMap["5' linker"]
# 5' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "5' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# 3' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "3' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
## Output the rest of the features in alphabetical order
#featureNames = featureNameColorMap.keys()
#featureNames.sort()
#print `featureNames`
for featureName in featureNames:
if featureNameColorMap.has_key(featureName):
color = featureNameColorMap[featureName]
#else:
#continue
if featureName != "5' cloning site" and featureName != "3' cloning site" and featureName != "5' linker" and featureName != "3' linker" and color != None:
#print featureName
c.setStrokeColor(color)
c.setFillColor(color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(color)
t.setFillColor(color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + featureName.upper())
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
#print prev_legend
# Print reagent ID and size at the centre of the circle and print name at the top of the page
c.setFont("Helvetica-Bold", 32)
c.setFillColor(black)
c.saveState()
c.drawCentredString(origin_x, origin_y+35, reagentID)
c.drawCentredString(origin_x, origin_y+10, "nt 1 - " + `seqLen`)
if rName:
c.setFillColor(blue)
c.drawCentredString(origin_x, 935, rName)
c.restoreState()
# SORT features by size, so that short features are not hidden behind the long ones
fSizes = []
sortedFeatures = []
for feature in sequenceFeatures:
fSize = int(feature.getFeatureSize())
if fSize > 0:
fSizes.append(fSize)
fSizes.sort(reverse=True)
#print `fSizes`
for fs in fSizes:
for feature in sequenceFeatures:
fSize = feature.getFeatureSize()
# added existence check July 17/08 - different features may have same sizes so end up with duplicate features in list (e.g. cloning sizes appeared twice on the map)
if fs == fSize and feature not in sortedFeatures:
sortedFeatures.append(feature)
#print `sortedFeatures`
ox_labels = 40
oy_labels = 910
prev_legend = oy_labels
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels, prev_legend-15)
t.textOut("Features shorter than 150 nt:")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-18
#for feature in sequenceFeatures:
for feature in sortedFeatures:
fType = feature.getFeatureType()
fValue = feature.getFeatureName()
fSize = feature.getFeatureSize()
#print fType
#print fValue
#print fSize
fColor = featureNameColorMap[fType]
if fType == 'cdna insert':
fValue = "cDNA Insert"
elif fType == 'promoter':
fValue = fValue + " " + fType
fStart = feature.getFeatureStartPos()
fEnd = feature.getFeatureEndPos()
fDir = feature.getFeatureDirection()
if fSize > 0:
f_start = fStart * unit_angle_measure
#print "Start " + `fStart`
#print "End " + `fEnd`
startAngle = 90 - f_start
#print "Start angle " + `startAngle`
f_end = fEnd * unit_angle_measure
endAngle = 90 - f_end
#print "End angle " + `endAngle`
extAngle = -1*(f_end - f_start)
#print "Ext angle " + `extAngle`
x1 = origin_x - radius
y1 = origin_y - radius
x2 = origin_x + radius
y2 = origin_y + radius
p = c.beginPath()
#t = c.beginText()
c.setLineWidth(10)
c.setLineJoin(1)
fColor = featureNameColorMap[fType]
c.setStrokeColor(fColor)
c.saveState()
p.arc(x1, y1, x2, y2, startAngle, extAngle)
c.drawPath(p)
c.restoreState()
## jan. 27/10: this makes a contour for each arc
#p = c.beginPath()
#c.setLineWidth(1)
##fColor = featureNameColorMap[fType]
#c.setStrokeColor(black)
#c.setFillColor(fColor)
#c.saveState()
#p.arc(x1+5, y1+5, x2-5, y2-5, startAngle, extAngle)
#c.drawPath(p)
##c.restoreState()
##c.setLineWidth(1)
##fColor = featureNameColorMap[fType]
##c.setStrokeColor(black)
##c.setFillColor(fColor)
##c.saveState()
#p.arc(x1-5, y1-5, x2+5, y2+5, startAngle, extAngle)
#c.drawPath(p)
#c.restoreState() # jan. 27/10 modification ends here
# common to all
startAngle_rad = (startAngle * math.pi) / 180.0
endAngle_rad = (endAngle * math.pi) / 180.0
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 9)
c.saveState()
arc_x_start = origin_x + (radius+5)*math.cos(startAngle_rad)
arc_y_start = origin_y + (radius+5)*math.sin(startAngle_rad)
arc_x_end = origin_x+(radius+5)*math.cos(endAngle_rad)
arc_y_end = origin_y+(radius+5)*math.sin(endAngle_rad)
# draw label
c.setStrokeColorRGB(0,0,1)
c.setFillColorRGB(0,0,1)
c.setFont("Helvetica-Bold", 12)
c.saveState()
# draw line
delta = 45
# Rotate labels only for SMALL features (they can be crammed together)
#if fSize > 100:
#delta = 45
#else:
#delta = 32
if fStart < seqLen/2:
if arc_y_start > origin_y:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
#if fSize <= 100:
#c.line(arc_x_start, arc_y_start, arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)))
#else:
# July 17/08: Show labels for long features only
if fSize > 150:
c.line(arc_x_start, arc_y_start, arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)))
c.restoreState()
# July 17/08: Show labels for long features only
if fSize > 150:
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawString(arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
t.textOut(fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.restoreState()
else:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start, arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start-55*math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawString(arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start-55*math.fabs(math.cos(delta)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
t.textOut(fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.restoreState()
else:
if arc_y_start > origin_y:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start, arc_x_start-50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)))
#c.line(arc_x_start, arc_y_start, arc_x_start+10*math.fabs(math.sin(delta)), arc_y_start-10*math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawRightString(arc_x_start-50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
t.textOut(fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.restoreState()
else:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start, arc_x_start-50*math.fabs(math.sin(delta)), arc_y_start-55*math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawRightString(arc_x_start-50*math.fabs(math.sin(delta)), arc_y_start-55*math.fabs(math.cos(delta)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.restoreState()
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
t.textOut(fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.showPage()
c.save()