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denovo_plot.py
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denovo_plot.py
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import matplotlib
matplotlib.use('Agg')
import pysam
import matplotlib.pyplot as plt
def plot_n100(outpath,minlen):
ctglen=open(outpath+'contig_length_info','r').read().split('\n')[:-1]
ctglen=[int(c.split('\t')[1]) for c in ctglen if int(c.split('\t')[1]) >= minlen]
n100=[]
x100=[]
ctglen.sort(reverse=True)
totallen=sum(ctglen)
addlen=0
lastlen=0
for i in range(100):
x100+=[i+1]
while addlen < (i+1)/100.0*totallen:
try:
lastlen=ctglen.pop(1)
addlen+=lastlen
except:
break
n100+=[lastlen]
plt.plot(x100,n100,linewidth=2)
plt.xlabel('N1-N100')
plt.ylabel('Contig Length /bp')
plt.savefig(outpath+'plot_n1n100.pdf')
print ('end n100')
return 0
def plot_na100(outpath):
samfile=pysam.AlignmentFile(outpath+'contig_to_ref.sam','r')
allread=samfile.fetch()
alignlen=[]
for align in allread:
if align.flag==4:
continue
alignlen+=[align.query_alignment_length]
n100=[]
x100=[]
alignlen.sort(reverse=True)
totallen=sum(alignlen)
addlen=0
lastlen=0
for i in range(100):
x100+=[i+1]
while addlen < (i+1)/100.0*totallen:
try:
lastlen=alignlen.pop(1)
addlen+=lastlen
except:
break
n100+=[lastlen]
plt.plot(x100,n100,linewidth=2)
plt.xlabel('NA1-NA100')
plt.ylabel('Contig Length /bp')
plt.savefig(outpath+'plot_na1na100.pdf')
print ('end na100')
return 0
def findpos(c,ctglength,step,startrefpos,ctgstartpos):
temppos=[]
ctgname=c.query_name
refpos=c.reference_start
cigar=c.cigarstring
if 'S' not in cigar.split('M')[0].split('=')[0] and 'H' not in cigar.split('M')[0].split('=')[0]:
ctgpos=0
else:
ctgpos=int(cigar.split('M')[0].split('=')[0].split('S')[0].split('H')[0])
currpos=ctgpos
num=''
for m in cigar:
num+=m; continue
if m in 'M=X':
ctgpos+=int(num); refpos+=int(num); num=''
if m=='I':
ctgpos+=int(num);num=''
if m =='D':
refpos+=int(num); num='';continue
if m in 'SH':
if refpos>c.reference_start:
break
else:
num=''
while ctgpos>=currpos+step:
if ctgpos>=currpos+step*2:
temppos+=[[currpos+step,refpos+startrefpos,ctgname]]
else:
temppos+=[[ctgpos,refpos+startrefpos,ctgname]]
currpos+=step
if c.flag in [16,2064]:
temppos=[ [ctglength-mm[0],mm[1],mm[2]] for mm in temppos]
updatestart=[]
for mm in temppos :
updatestart+=[[mm[0]+ctgstartpos,mm[1],mm[2]]]
return updatestart
def plot_dotplot(outpath):
print ('start dot plot')
samfile=pysam.AlignmentFile(outpath+'contig_to_ref.bam','rb')
allchrom=samfile.references
allchromlen=samfile.lengths
maxreflen=max(allchromlen)
idex=allchromlen.index(maxreflen)
maxchrom=allchrom[idex]
print (maxchrom)
allread=samfile.fetch(maxchrom)
if maxreflen >= 10000000:
step=10000
elif maxreflen>=1000000:
step=1000
else:
step=100
ctgleninfo=open(outpath+'contig_length_info','r').read().split('\n')[:-1]
ctglen={}
for c in ctgleninfo:
ctglen[c.split('\t')[0]]=int(c.split('\t')[1])
alignedctg={}
for align in allread:
if align.query_name not in alignedctg:
alignedctg[align.query_name]=align.query_alignment_length
else:
alignedctg[align.query_name]+=align.query_alignment_length
longalignctg=[c for c in alignedctg if alignedctg[c] >= maxreflen/100.0]
print (len(longalignctg))
startpos=0
contig_startpos={}
for c in longalignctg:
contig_startpos[c]=startpos
startpos+=ctglen[c]
allpos=[]
allread=samfile.fetch(maxchrom)
for align in allread:
if align.query_name not in longalignctg:
continue
temppos=[]
ctglength=ctglen[align.query_name]
ctgstart=contig_startpos[align.query_name]
temppos=findpos(align,ctglength,step,0,ctgstart)
allpos+=temppos
plotx=[c[0] for c in allpos]
ploty=[c[1] for c in allpos]
plotcolor=[c[2] for c in allpos]
allcolor=set(plotcolor)
colors={}
i=1
for c in allcolor:
colors[c]=i
i+=10
plotcolor2=[colors[c] for c in plotcolor]
size=[1]*len(plotcolor2)
plt.scatter(plotx,ploty,s=size,c=plotcolor2)
plt.xlabel('Reference Position')
plt.ylabel('Contig Position')
plt.savefig(outpath+'plot_synteny.pdf')
return 0