Covert leading (and lagging) periods in alignments into hyphens to represent gaps

SchlossLab / Schloss_rrnAnalysis_mSphere_2021

Code Club project analyzing utility of ASVs

MIT License

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Covert leading (and lagging) periods in alignments into hyphens to represent gaps #16

Closed pschloss closed 4 years ago

pschloss commented 4 years ago

Output from mothur's commands is starting sequences with periods when the sequence doesn't start at position 1. Would like to use hyphen to represent a gap instead

In code/extract_region.sh...

Use sed to convert . to - in sequences that are outputted from mothur commands