Refactor function names in R/cleanup.R

[teddyCodex]

Description

Refactored specified functions in R/cleanup.R based on issue #7

Original	Modified	User Facing
clean_string	cleanString	✅
string2accnum	extractAccessionNumber	✅
make_accnums_unique	ensureUniqueAccessionNumbers	✅
cleanup_fasta_header	cleanUpFastaHeaders	✅
remove_empty	removeEmptyRows	✅
repeat2s	condenseRepeatedDomains	✅
replaceQMs	replaceQuestionMarks	✅
remove_astrk	removeAsterisks	✅
remove_tails	removeLowFrequencyEntries	✅
cleanup_species	cleanUpSpeciesColumn	✅
cleanup_clust	cleanUpClusterData	✅
cleanup_domarch	cleanUpDomainArchitecture	✅
cleanup_gencontext	cleanUpGenomicContextColumn	✅
cleanup_GeneDesc	cleanUpGeneDescription	✅
pick_longer_duplicate	selectLongestDuplicateRecord	✅
cleanup_lineage	cleanUpLineageData	✅

Fixes issue #38

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

• I have read and followed the CONTRIBUTING.md guidelines.
• I have searched for existing content to ensure this is not a duplicate.
• I have performed a self-review of these additions (including spelling, grammar, and related).
• I have added comments to my code to help provide understanding.
• I have added a test which covers the code changes found within this PR.
• I have deleted all non-relevant text in this pull request template.
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[teddyCodex]

@jananiravi @the-mayer
File containing other occurrences of the functions. Please let me know if I should commit this file as well.

function_occurrences #38.txt