Manual bin refinement script correction

[mlhoggard]

Script here needs correction:

https://genomicsaotearoa.github.io/metagenomics_summer_school/day2/ex9_refining_bins/#prepare-files-for-vizbin

It includes cat ${i} >> all_mock_bins.fna but there's no i variable defined earlier in the script. Should this be cat ${bin}?

[mlhoggard]

Also in the same script, it first refers to all_mock_bins.label.txt then in the script appends to all_mock_bins.label.ann (i.e. suffix changes)

[mlhoggard]

Also worth adding info to right click in VizBin and click legend to be able to tell the labels for each coloured bin (i.e. since we suggest they label their new clusters based on this)

[kmhandley]

Yes, update as follows (as indicated by Mike). This works, and add suggestion by Mike to add legend.

VizBin requires a header for annotation files

echo "label" > all_mock_bins.label.ann

Generate concatenated set of sequences and labels at the same time!

for bin in mock_bins/.fna; do
binID=$(basename ${bin} .fna)
grep '>' ${bin} | sed "s/./${binID}/g" >> all_mock_bins.label.ann
cat ${bin} >> all_mock_bins.fna
done

[JSBoey]

Fixed typos