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fa2exp.py
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"""
Author: Zhang Chengsheng, @2020.06.01
输入包含FL count的fa、软件的结果前缀，输出不同水平的三代测序TPM列表
"""
import os,sys
def exp(fa,out):
"""提取fa文件中的count, 格式：>transcript/0 full_length_coverage=4;length=9621;num_subreads=22"""
with open(fa,'r') as f, open(out,'w') as o:
o.write('#ID\tFLC\tLEN\tSRC\n')
for i in f.readlines():
if not i.strip():
continue
if i.startswith('>'):
line = i.strip().split(' ')
ID = line[0].lstrip('>')
FLC = line[1].split(';')[0].split('=')[1]
LEN = line[1].split(';')[1].split('=')[1]
#SRC = line[1].split(';')[2].split('=')[1]
#o.write('{}\t{}\t{}\t{}\n'.format(ID,FLC,LEN,SRC))
o.write('{}\t{}\t{}\n'.format(ID,FLC,LEN))
return out
def expParse(expFile,FL=1):
"""FL指提取的列"""
expD = {}
with open(expFile,'r') as f:
for i in f.readlines():
if not i.strip() or i.startswith('#'):
continue
line = i.strip().split('\t')
if line[0] not in expD:
expD[line[0]] = int(line[FL])
else:
expD[line[0]] += int(line[FL])
return expD
def isoformExpCalc(stat,exp,out,out_taget):
TotalExp = sum([exp[i] for i in exp])
with open(os.path.join(out_taget,stat),'r',encoding='utf8') as f, open(out,'w') as o:
for i in f.readlines():
if not i.strip():
continue
if i.startswith('ID'):
o.write('\t'.join(i.strip().split('\t')[:9])+'\tFLC\tTPM\n')
continue
line = i.strip().split('\t')
if line[0] in exp:
FLC = exp[line[0]]
TPM = float(FLC)/TotalExp*1000000 #TPM FUNCTION
o.write('{}\t{}\t{}\n'.format('\t'.join(line[:9]),FLC,TPM))
def transcriptExpCalc(cluster,exp, out,out_taget,stat,outputdir):
TotalExp = sum([exp[i] for i in exp])
dic={}
with open(os.path.join(out_taget,cluster),'r') as f, open(out,'w') as o:
for i in f.readlines():
if not i.strip():
continue
if i.startswith('Chrom'):
o.write(i.rstrip()+'\tTPM\tFLC\n')
else:
line = i.strip().split('\t')
FLC = 0
for id in line[-1].split(','):
if id in exp:
FLC += exp[id]
TPM = float(FLC) / TotalExp * 1000000 # TPM FUNCTION
o.write('{}\t{}\t{}\n'.format(i.strip(),TPM,FLC))
trans_name=line[4].split(',')
for tmp in trans_name:
if tmp not in dic:
dic[tmp]=[str(FLC),str(TPM)]
else:
print('error')
continue
outfile=open(os.path.join(outputdir,stat+'1'),'w')
for line in open(os.path.join(out_taget,stat)):
if line.startswith('ID'):
outfile.write(line.rstrip()+'\tFLC\tTPM\n')
else:
newline=line.rstrip().split('\t')
if newline[0] in dic:
outfile.write(line.rstrip()+'\t'+'\t'.join(dic[newline[0]])+'\n')
else:
outfile.write(line.rstrip()+'\tNA\tNA\n')
#print(newline)
#print('key error')
def geneExpCalc(clusters,exp,out,out_taget):
TotalExp = sum([exp[i] for i in exp])
geneDict = {}
for file in clusters:
with open(os.path.join(out_taget,file),'r') as f:
for i in f.readlines():
if not i.strip():
continue
line = i.strip().split('\t')
gene = line[0]
ids = line[-1].split(',')
FLC = 0
for id in ids:
if id in exp:
FLC += exp[id]
if gene not in geneDict:
geneDict[gene] = FLC
else:
geneDict[gene] += FLC
with open(out,'w') as o:
o.write('Genes\tFLC\tTPM\n')
for id in geneDict:
TPM = float(geneDict[id]) / TotalExp * 1000000 # TPM FUNCTION
o.write('{}\t{}\t{}\n'.format(id,geneDict[id],TPM))
def main(fa,prefix,outputdir,out_taget):
stat = prefix + '.stat'
#cluster = [prefix+'.SM.cluster',prefix+'.NC.cluster',prefix+'.FUSION.cluster',prefix+'.GENIC.cluster']
cluster=[prefix+'.cluster.transcript']
if not os.path.exists(os.path.join(out_taget,stat)):
print('{} not found !'.format(stat))
exit(11)
if not os.path.exists(fa):
print('{} not found !'.format(stat))
exit(11)
for i in cluster:
if not os.path.exists(os.path.join(out_taget,i)):
print('{} not found !'.format(i))
exit(11)
if not os.path.exists(outputdir):
os.makedirs(outputdir)
expFile = exp(fa,os.path.join(outputdir,os.path.basename(prefix+'.readsExp.tsv')))
expD = expParse(expFile,FL=1)
isoformExpCalc(stat,expD,os.path.join(outputdir,os.path.basename(prefix+'.IsoformExp.tsv')),out_taget)
for i in cluster:
transcriptExpCalc(i,expD,os.path.join(outputdir,os.path.basename(i+'.exp')),out_taget,stat,outputdir)
geneExpCalc(cluster,expD,os.path.join(outputdir,os.path.basename(prefix+'.geneExp.tsv')),out_taget)
#merge(prefix, outputdir)
def merge(prefix,outputdir):
dic={}
for line in open(os.path.join(outputdir,prefix+'.SM.transcriptExp.tsv')):
newline=line.rstrip().split('\t')
t = newline[-1]
newline[-1] = newline[-2]
newline[-2] = t
if newline[0] not in dic:
dic[newline[0]]=[newline]
else:
dic[newline[0]].append(newline)
for line in open(os.path.join(outputdir,prefix+'.NC.transcriptExp.tsv')):
newline=line.rstrip().split('\t')
t = newline[-1]
newline[-1] = newline[-2]
newline[-2] = t
if newline[0] not in dic:
dic[newline[0]]=[newline]
else:
dic[newline[0]].append(newline)
for line in open(os.path.join(outputdir,prefix+'.GENIC.transcriptExp.tsv')):
newline=line.rstrip().split('\t')
t=newline[-1]
newline[-1]=newline[-2]
newline[-2]=t
if newline[0] not in dic:
dic[newline[0]]=[newline]
else:
dic[newline[0]].append(newline)
dic1={}
for line in open(os.path.join(outputdir,prefix+'.IsoformExp.tsv')):
newline=line.rstrip().split('\t')
if newline[3] not in dic1:
dic1[newline[3]]=newline[5]
else:
continue
outfile=open(os.path.join(outputdir,prefix+'.transcript.exp'),'w')
outfile.write('Chrom\tGene\tTranscript\tReadsCount\tReadsID\tTPM\tFLC\n')
for line in dic:
for tmp in dic[line]:
if line in dic1:
outfile.write(dic1[line]+'\t'+'\t'.join(tmp)+'\n')
else:
chr1=line.split(':')
outfile.write(chr1[0] + '\t' + '\t'.join(tmp) + '\n')
outfile.close()
def option(argv):
from argparse import ArgumentParser as AP
usages = "python3 {} -f fa -i prefix -o outputdir".format(argv[0])
p = AP(usage=usages)
p.add_argument("-f", dest="fa", metavar="[fa]", help="fasta file.",required=True)
p.add_argument("-i", dest="prefix", metavar="[prefix]", help="prefix of .annot.cluster.transcript",required=True)
p.add_argument("-o", dest="out", metavar="[outputdir]", help="outputdir path", required=True)
p.add_argument("-p", dest="out_taget", metavar="[outputdir_taget]", help="outputdir of taget path", required=True)
if len(argv) == 1:
p.print_help()
exit(1)
return p.parse_args(argv[1:])
if __name__ == '__main__':
args = option(sys.argv)
main(args.fa,args.prefix,args.out,args.out_taget)