Add logs to filtering

[fgvieira]

Add log info on filtered sequences

[shenwei356]

Thanks for this PR, but I think there's no need to log all removed sequences, as they would be a lot. Also, to be consistent with previous quiet behaviour, outputting such a lot extra logs should be optional with some flags like (--verbose).

And if you do want to know which sequences are filtered out, you can use seqkit grep -v -f <(seqkit seq -ni result.fx) input.fx | seqkit seq -ni to get the list.

[fgvieira]

I agree, but I thought that the idea was to be verbose by default and, if not, the user could specify the --quiet option.

[shenwei356]

seqkit seq -m is frequently used, it's better not to freak users out with tens or hundreds of log info when they (including me) use previous commands (without --quiet) as usual.

I prefer outputting these logs optional with a new flag --verbose just for seqkit seq.

[fgvieira]

Sure, that would work also. thanks for your help!

[fgvieira]

Add log info on filtered sequences

[shenwei356]

Thanks for this PR, but I think there's no need to log all removed sequences, as they would be a lot. Also, to be consistent with previous quiet behaviour, outputting such a lot extra logs should be optional with some flags like (--verbose).

And if you do want to know which sequences are filtered out, you can use seqkit grep -v -f <(seqkit seq -ni result.fx) input.fx | seqkit seq -ni to get the list.

[fgvieira]

I agree, but I thought that the idea was to be verbose by default and, if not, the user could specify the --quiet option.

[shenwei356]

seqkit seq -m is frequently used, it's better not to freak users out with tens or hundreds of log info when they (including me) use previous commands (without --quiet) as usual.

I prefer outputting these logs optional with a new flag --verbose just for seqkit seq.

[fgvieira]

Sure, that would work also. thanks for your help!

[fgvieira]

Add log info on filtered sequences

[shenwei356]

Thanks for this PR, but I think there's no need to log all removed sequences, as they would be a lot. Also, to be consistent with previous quiet behaviour, outputting such a lot extra logs should be optional with some flags like (--verbose).

And if you do want to know which sequences are filtered out, you can use seqkit grep -v -f <(seqkit seq -ni result.fx) input.fx | seqkit seq -ni to get the list.

[fgvieira]

I agree, but I thought that the idea was to be verbose by default and, if not, the user could specify the --quiet option.

[shenwei356]

seqkit seq -m is frequently used, it's better not to freak users out with tens or hundreds of log info when they (including me) use previous commands (without --quiet) as usual.

I prefer outputting these logs optional with a new flag --verbose just for seqkit seq.

[fgvieira]

Sure, that would work also. thanks for your help!

[fgvieira]

Add log info on filtered sequences

[shenwei356]

Thanks for this PR, but I think there's no need to log all removed sequences, as they would be a lot. Also, to be consistent with previous quiet behaviour, outputting such a lot extra logs should be optional with some flags like (--verbose).

And if you do want to know which sequences are filtered out, you can use seqkit grep -v -f <(seqkit seq -ni result.fx) input.fx | seqkit seq -ni to get the list.

[fgvieira]

I agree, but I thought that the idea was to be verbose by default and, if not, the user could specify the --quiet option.

[shenwei356]

seqkit seq -m is frequently used, it's better not to freak users out with tens or hundreds of log info when they (including me) use previous commands (without --quiet) as usual.

I prefer outputting these logs optional with a new flag --verbose just for seqkit seq.

[fgvieira]

Sure, that would work also. thanks for your help!

[fgvieira]

Add log info on filtered sequences

[shenwei356]

Thanks for this PR, but I think there's no need to log all removed sequences, as they would be a lot. Also, to be consistent with previous quiet behaviour, outputting such a lot extra logs should be optional with some flags like (--verbose).

And if you do want to know which sequences are filtered out, you can use seqkit grep -v -f <(seqkit seq -ni result.fx) input.fx | seqkit seq -ni to get the list.

[fgvieira]

I agree, but I thought that the idea was to be verbose by default and, if not, the user could specify the --quiet option.

[shenwei356]

seqkit seq -m is frequently used, it's better not to freak users out with tens or hundreds of log info when they (including me) use previous commands (without --quiet) as usual.

I prefer outputting these logs optional with a new flag --verbose just for seqkit seq.

[fgvieira]

Sure, that would work also. thanks for your help!

[fgvieira]

Add log info on filtered sequences

[shenwei356]

Thanks for this PR, but I think there's no need to log all removed sequences, as they would be a lot. Also, to be consistent with previous quiet behaviour, outputting such a lot extra logs should be optional with some flags like (--verbose).

And if you do want to know which sequences are filtered out, you can use seqkit grep -v -f <(seqkit seq -ni result.fx) input.fx | seqkit seq -ni to get the list.

[fgvieira]

I agree, but I thought that the idea was to be verbose by default and, if not, the user could specify the --quiet option.

[shenwei356]

seqkit seq -m is frequently used, it's better not to freak users out with tens or hundreds of log info when they (including me) use previous commands (without --quiet) as usual.

I prefer outputting these logs optional with a new flag --verbose just for seqkit seq.

[fgvieira]

Sure, that would work also. thanks for your help!

[fgvieira]

Add log info on filtered sequences

[shenwei356]

Thanks for this PR, but I think there's no need to log all removed sequences, as they would be a lot. Also, to be consistent with previous quiet behaviour, outputting such a lot extra logs should be optional with some flags like (--verbose).

And if you do want to know which sequences are filtered out, you can use seqkit grep -v -f <(seqkit seq -ni result.fx) input.fx | seqkit seq -ni to get the list.

[fgvieira]

I agree, but I thought that the idea was to be verbose by default and, if not, the user could specify the --quiet option.

[shenwei356]

seqkit seq -m is frequently used, it's better not to freak users out with tens or hundreds of log info when they (including me) use previous commands (without --quiet) as usual.

I prefer outputting these logs optional with a new flag --verbose just for seqkit seq.

[fgvieira]

Sure, that would work also. thanks for your help!

[fgvieira]

Add log info on filtered sequences

[shenwei356]

Thanks for this PR, but I think there's no need to log all removed sequences, as they would be a lot. Also, to be consistent with previous quiet behaviour, outputting such a lot extra logs should be optional with some flags like (--verbose).

And if you do want to know which sequences are filtered out, you can use seqkit grep -v -f <(seqkit seq -ni result.fx) input.fx | seqkit seq -ni to get the list.

[fgvieira]

I agree, but I thought that the idea was to be verbose by default and, if not, the user could specify the --quiet option.

[shenwei356]

seqkit seq -m is frequently used, it's better not to freak users out with tens or hundreds of log info when they (including me) use previous commands (without --quiet) as usual.

I prefer outputting these logs optional with a new flag --verbose just for seqkit seq.

[fgvieira]

Sure, that would work also. thanks for your help!