ddurai
commented
3 years ago Dear user,
I apologise for the late reply. It seems that you are using an older version of the pipeline. We restructured certain programs. Can you please let me know when did you last pull the changes
regards Dilip A Durai
areebapatel
Hi Aeron Group,
I was using Aeron to detect fusion transcrits in Nanopore transcriptome data, after the graph building, I ran the command "snakemake --cores 10 all ", but encountered some difficulties beblow, in generateCountMatrix,
rule generateCountMatrix: input: output/matrix_CPD1906270733_transcripts_Genome_all.txt output: output/CountMatrix_CPD1906270733_transcripts_Genome.txt jobid: 7 benchmark: benchmark/generateCount_CPD1906270733_transcripts_Genome.txt wildcards: reads=CPD1906270733, transcripts=transcripts, graph=Genome
Traceback (most recent call last): File "/share/apps/biosoft/fushion/Aeron/AeronScripts/ThreePrime.py", line 24, in
if(float(ent[-2])>0.2):
ValueError: could not convert string to float: 'ENST00000391753.6'
First, I opened the file "output/matrix_CPD1906270733_transcripts_Genome_all.txt", its format was as follows:
408:1122|554f1097-d17d-4c0d-9fd9-c6bd9fe9ede1 ENST00000391753.6 0.949153 408:1122|554f1097-d17d-4c0d-9fd9-c6bd9fe9ede1 ENST00000302907.9 0.983051 408:1122|554f1097-d17d-4c0d-9fd9-c6bd9fe9ede1 ENST00000610644.4 0.960452
there were three columns, first column was Nanopore reads, second was Ensemble transcripts ID, and was the third an indentity score? It's just my guess.
and then I opened the scripts "ThreePrime.py",
for line in m: ent=line.rstrip().split("\t") if(float(ent[-2])>0.2): if(ent[0] != nam): max=0 mt[ent[0]]="" if(float(ent[-2])>max): mt[ent[0]]=[] tran=ent[1].split(".")[0] mt[ent[0]] = tran mt1[ent[0]] = float(ent[-1]) nam=ent[0] max=float(ent[-2]) elif(float(ent[-1])==max): tran=ent[1].split(".")[0] if(float(ent[-1])<float(mt1[ent[0]])): mt[ent[0]] = tran mt1[ent[0]] = float(ent[-1]) else: tmp="Hello"
My question was why using [-2] and [-1] in the scripsts, and whether the file "output/matrix_CPD1906270733_transcripts_Genome_all.txt" was correct ?
Please help me solve this problem, thanks.