Python related problem

[rz566]

Hi guys,

I am having a problem with the extraction part. Here is the output from extraction.err

2013-08-16 13:20:23,179 [INFO] Running
2013-08-16 13:20:23,179 [INFO] Opening Gap Objects
2013-08-16 13:20:23,182 [INFO] Loading Fasta Files
2013-08-16 13:20:36,174 [INFO] Loading References
2013-08-16 13:20:37,484 [INFO] Extracting Reads
Traceback (most recent call last):
File "~/assembly/assembler/PBJelly/Extraction.py", line 250, in <module>
me.run()
File "~/assembly/assembler/PBJelly/Extraction.py", line 206, in run
self.extractReads()
File "~/assembly/assembler/PBJelly/Extraction.py", line 117, in extractReads
self.allFasta[name][start:end] + "\n")
File "~/assembly/assembler/PBJelly/Extraction.py", line 221, in __getitem__
fn, start, numLines = self.indices[key]
KeyError: u'm130626_024929_42146_c100536682550000001823080011101390_s1_p0/59685/0_4740'

I have tried the test data (lambdaExample) and it worked fine. The KeyError message indicates that the program is unable to find the key in the .gapCans file but when I check the file, it is there!

I already check my Pacbio reads file and it looks OK. Can somebody tell me if I am doing it wrongly?

[arkilis]

fn, start, numLines = self.indices[key] is where the problem resides.

Seems like [key] here is not right. Cant tell more without your dataset.

[rz566]

fn, start, numLines = self.indices[key] is where the problem resides.

Seems like [key] here is not right. Cant tell more without your dataset.

Thanks! I already found out the problem.

The error occurred because it was expecting a key "m130626_024929_42146_c100536682550000001823080011101390_s1_p0/59685/0_4740"

but in my PacBio fasta/qual file, each reads had a RQ value beside it.

m130626_024929_42146_c100536682550000001823080011101390_s1_p0/59685/0_4740 RQ=0.85

Once I removed the RQ value from the pacbio fasta/qual, it worked perfectly.