better error reporting on parse errors

[marcelm]

From gregorym...@gmail.com on March 18, 2011 00:29:09

What steps will reproduce the problem? 1. I downloaded the latest version
2. cutadapt -O 10 -b CAGACGTGCCTCACTACGT TEE.TEST.fastq > TEE.test.trim.a1.fastq (TEE.TEST.fastq is just a standard fastq file) What is the expected output? What do you see instead? Trimmed sequences with statistics.

[kumarlab@BatLC1 TEE]$ cutadapt -O 10 -b CAGACGTGCCTCACTACGT TEE.TEST.fastq > TEE.test.trim.a1.fastq
Traceback (most recent call last):
File "/home/kumarlab/bioinfo/cutadapt-0.9.3/cutadapt", line 549, in
sys.exit(main())
File "/home/kumarlab/bioinfo/cutadapt-0.9.3/cutadapt", line 508, in main
for desc, seq, qualities in reader:
File "/home/kumarlab/bioinfo/cutadapt-0.9.3/lib/cutadapt/seqio.py", line 196, in iter
assert line[0] == '@'
AssertionError What version of the product are you using? On what operating system? 0.9.3 on linux Please provide any additional information below. I have performed this operation many times before. I got a new server and installed the latest version of cutadapt and encountered this problem.

Original issue: http://code.google.com/p/cutadapt/issues/detail?id=13

[marcelm]

From marcel.m...@tu-dortmund.de on March 18, 2011 00:57:32

Could you please send me (or attach to this issue) the first few lines of the TEE.TEST.fastq file?

[marcelm]

From gregorym...@gmail.com on March 18, 2011 11:15:13

Cutadapt runs and removes the adapter sequence but does not report statistics.

Attachment: TEE.TEST.fastq

[marcelm]

From gregorym...@gmail.com on March 18, 2011 11:26:06

The issue must have been with that file, when I ran it with the full data set it worked fine. Sorry to have bothered you. Thank you for your help.

[marcelm]

From marcel.m...@tu-dortmund.de on March 18, 2011 14:27:56

No need to be sorry, cutadapt could at least give a better error message. It seems that your test file contains two unexpected empty lines in the end, and this must have caused the assertion error. I will leave this issue open until I have added better error reporting to the routines that read in FASTQ files.

[marcelm]

From marcel.m...@tu-dortmund.de on March 18, 2011 14:28:51

Summary: better error reporting on parse errors

[marcelm]

From marcel.m...@tu-dortmund.de on April 20, 2011 09:50:08

This issue was closed by revision r133 .

Status: Fixed

[marcelm]

From marcel.m...@tu-dortmund.de on April 20, 2011 09:52:04

I've added some slightly better error reporting. Now cutadapt reports this when confronted with your file:
Error: at line 253, expected a line starting with '+'

[marcelm]

From gregorym...@gmail.com on April 20, 2011 09:55:53

Thanks! Much appreciated.