refactor function names in R/pre-msa-tree and R/reverse-operons.R

[teddyCodex]

Description

Refactored specified function names in R/pre-msa-tree.R and R/reverse_operons.R based on issue #7

R/pre-msa-tree.R

Original	Modified	User Facing
RepresentativeAccNums	createRepresentativeAccNum	✅
write.MsaAAMultipleAlignment	writeMSA_AA2FA	✅
get_accnums_from_fasta_file	getAccNumFromFA	✅

R/reverse_operons.R

Original	Modified	User Facing
reveql	straightenOperonSeq	✅
reverse_operon	reverseOperonSeq	✅

Fixes issue #52

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

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[the-mayer]

Thank you. In addition to the rebase I went ahead and maintained function name consistency across CHANGED-pre-msa-tree.R and pre-msa-tree.R until a decision is made on #78

Thanks!