def plot(pictureFileName,
sbjctLen,
sbjctAcc,
blHits,
sizeX=700,
fontsize=4,
typePlot='png'):
""" picture output """
# blHits: list of split (blast m8 line)
# blHits = [qry, sbjct, % identity, aln length, mismatches, gap, q. start, q. end, s. start, s. end, e-value, bit score]
gdPlot = genoGd.genoGD(fontsize=fontsize, sizeX=sizeX, nbQuery=len(blHits))
gdPlot.plotSeq(seqlen=sbjctLen,
start=0,
stop=sizeX,
header=sbjctAcc,
color='red',
up=True)
gdPlot._nbligneP()
rpt = float(sizeX) / sbjctLen
nbhit = 0
for blh in blHits:
head = True
# if len(blLine[0])<= 10:
# header = blLine[0]
# else:
# header = blLine[0][0:10]+'..'
header = blh[0][8:18] + '..'
if int(blh[8]) < int(blh[9]):
gdPlot.plotHit(int(int(blh[8]) * rpt),
int(int(blh[9]) * rpt),
header,
_blastScoreVsColor(float(blh[10])),
delta=2,
head=head)
nbhit += 1
gdPlot._nbligneP()
else:
gdPlot.plotHit(int(int(blh[9]) * rpt),
int(int(blh[8]) * rpt),
header,
_blastScoreVsColorInv(float(blh[10])),
delta=2,
head=head)
nbhit += 1
gdPlot._nbligneP()
head = False
gdPlot._nbligneP()
gdPlot.plotSeq(seqlen=sbjctLen,
start=0,
stop=sizeX,
header=sbjctAcc,
color='red',
up=False)
gdPlot.legend()
gdPlot.legendInv()
if typePlot == 'png' and nbhit > 0:
picturefh = open(pictureFileName, "w")
gdPlot.picture.writePng(picturefh)
picturefh.close()
def plotMergeFewPlus(pictureFileName,
sbjctLen,
sbjctAcc,
blHits,
sizeX=700,
fontsize=4,
typePlot='png'):
""" picture output """
# blHits: list of split (blast m8 line)
# blHits = [qry, sbjct, % identity, aln length, mismatches, gap, q. start, q. end, s. start, s. end, e-value, bit score]
gdPlot = genoGd.genoGD(fontsize=fontsize,
sizeX=sizeX,
nbQuery=len(blHits) / 60)
gdPlot.plotSeq(seqlen=sbjctLen,
start=0,
stop=sizeX,
header=sbjctAcc,
color='red',
up=True)
gdPlot._nbligneP()
gdPlot._nbligneP()
rpt = float(sizeX) / sbjctLen
nbhit = 1
i = 0
nmax = 0
while i < len(blHits):
head = False
header = ''
end = int(blHits[i][9])
gdPlot.plotHit(int(int(blHits[i][8]) * rpt),
int(int(blHits[i][9]) * rpt),
'',
_blastScoreVsColor(float(blHits[i][11])),
delta=2,
head=False)
n = 0
while (i < len(blHits) - 1) and (int(blHits[i + 1][8]) < end):
gdPlot._nbligneP()
gdPlot.plotHit(int(int(blHits[i + 1][8]) * rpt),
int(int(blHits[i + 1][9]) * rpt),
header,
_blastScoreVsColor(float(blHits[i + 1][11])),
delta=2,
head=head)
i += 1
n += 1
if n > nmax:
nmax = n
gdPlot.nbligne -= n
i += 1
gdPlot.nbligne += nmax
# gdPlot.plotSeq(seqlen=sbjctLen, start=0, stop=sizeX, header=sbjctAcc, color='red', up = False)
# gdPlot._nbligneP()
gdPlot.legendMerge()
if typePlot == 'png' and nbhit > 0:
picturefh = open(pictureFileName, "w")
gdPlot.picture.writePng(picturefh)
picturefh.close()
def plotMerge(pictureFileName,
sbjctLen,
sbjctAcc,
blHits,
sizeX=700,
fontsize=4,
typePlot='png'):
""" picture output """
# blHits: list of split (blast m8 line)
# blHits = [qry, sbjct, % identity, aln length, mismatches, gap, q. start, q. end, s. start, s. end, e-value, bit score]
gdPlot = genoGd.genoGD(fontsize=fontsize, sizeX=sizeX, nbQuery=1)
gdPlot.plotSeq(seqlen=sbjctLen,
start=0,
stop=sizeX,
header=sbjctAcc,
color='red',
up=True)
gdPlot._nbligneP()
gdPlot._nbligneP()
rpt = float(sizeX) / sbjctLen
# if sbjctLen > float(sizeX):
# rpt = float(sizeX) / sbjctLen
# else:
# rpt = 1
nbhit = 1
for blh in blHits:
head = False
header = ''
if int(blh[11]) < int(blh[12]):
gdPlot.plotHit(int(int(blh[11]) * rpt),
int(int(blh[12]) * rpt),
header,
'lightred',
delta=2,
head=head)
else:
gdPlot.plotHit(int(int(blh[12]) * rpt),
int(int(blh[11]) * rpt),
header,
'blue',
delta=2,
head=head)
head = False
gdPlot._nbligneP()
# gdPlot.plotSeq(seqlen=sbjctLen, start=0, stop=sizeX, header=sbjctAcc, color='red', up = False)
# gdPlot._nbligneP()
gdPlot.legendMerge()
if typePlot == 'png' and nbhit > 0:
picturefh = open(pictureFileName, "w")
gdPlot.picture.writePng(picturefh)
picturefh.close()
