changes in log

[cokelaer]

I've noticed that the log file format has changed.

For instance, in the summary section

Total basepairs processed:                505,000 bp
     Read 1:       252,500 bp
     Read 2:       252,500 bp

is now:

Total basepairs processed:                505,000 bp
     Read 1       252,500 bp
     Read 2       252,500 bp

that is there is no more ":" sign

I am parsing the output in github.com/sequana/sequana project and this obviously affect my code. This is not a big deal but I was wondering is there was any rationale to change the output with respect to cutadapt output itself. I thought it was grerat to keep the two outputs similar so that I needed only one parser ;-)

I am also parsing the remaining of the code hoping it won't change. thanks

[jdidion]

Thanks for catching this. It is an unintended change that was introduced in re-writing the code for generating the summary file. I will add the ‘:’ back in.

Also, you might want to consider parsing the JSON output instead.

On May 1, 2017, at 12:52 PM, Thomas Cokelaer notifications@github.com wrote:

I've noticed that the log file format has changed.

For instance, in the summary section

Total basepairs processed: 505,000 bp Read 1: 252,500 bp Read 2: 252,500 bp is now:

Total basepairs processed: 505,000 bp Read 1 252,500 bp Read 2 252,500 bp that is there is no more ":" sign

I am parsing the output in github.com/sequana/sequana project and this obviously affect my code. This is not a big deal but I was wondering is there was any rationale to change the output with respect to cutadapt output itself. I thought it was grerat to keep the two outputs similar so that I needed only one parser ;-)

I am also parsing the remaining of the code hoping it won't change. thanks

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[cokelaer]

ah great, so that I do not need to update my code. JSON output ? I could not find that information in the --help, does that mean we just change the extension of the output

[jdidion]

To generate JSON summary, do one of the following:

• --report-file summary.json
• --report-file summary --report-formats json

You can also generate both text and json as follows: --report-file summary --report-formats txt json

I am updating the help message and the documentation about this. I also need to update the documentation to describe the JSON format exactly, but it's pretty self-explanatory if you just look at it in a text editor.

[jdidion]

It also supports yaml and pickle if you'd prefer those instead.

[cokelaer]

brilliant. thanks

[jdidion]

It's fixed now in release 1.1.3. Please let me know if you come across any other differences that break your code.