question: insert <tab> char with --rename?

[eboyden]

Hi - is there a means to use --rename to insert a tab character? I tried \t and "\t", to no avail. This would be useful, for example, when extracting multiple pieces of information with Cutadapt and putting them all into separate SAM tags in the fastq comment, then using a compatible aligner to move the entire comment into the bam file. (The space after the read ID is fine, but every subsequent separator needs to be a tab.) If there's a convenient way to do this inside of Cutadapt then please let me know, if not it would be great to add this feature (e.g. {tab}). Thanks!

[y9c]

You can insert tab into the command line, rather \t, and the output will contain tab.

In linux shell, use Ctrl+V TAB to insert a tab.

[marcelm]

Sorry for not responding earlier, this issue got lost among other notifications. @y9c is correct, but I agree it would be nicer with direct support for this in Cutadapt. I have therefore just added support for writing \t within the --rename template string. That should also be more readable in scripts than having a literal tab character in the file. Thank you for the suggestion!

This will be in Cutadapt 4.3.

[eboyden]

Excellent, thanks! And yeah I know you can insert a literal TAB on the command line with Ctrl+V, and that does indeed work, but I agree that more explicit support is cleaner. TABs aren't always interpreted properly by text parsers, and if someone copy-pasted code and wasn't careful about it, it could become a string of spaces that would break things.