51 lines
1.3 KiB
R
51 lines
1.3 KiB
R
#=================================================
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# Data for Logo MSA plots
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#=================================================
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cat("\n=========================================="
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, "\nLogo MSA Plots Data: ALL params"
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, "\n=========================================")
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#msa1 = read.csv("/home/tanu/git/Data/cycloserine/output/gid_msa.csv", header = F)
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#head(msa1)
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#msa_seq= msa1$V1
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#head(msa_seq)
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#msa2 = read.csv("/home/tanu/git/Data/cycloserine/input/gid.1fasta", header = F)
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#head(msa2)
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#wt_seq = msa2$V1
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#head(wt_seq)
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# BOTH WORK
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#LogoPlotMSA(msa_seq, wt_seq)
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#LogoPlotMSA(msa1, msa2)
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#####################################
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#================
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# MSA file: muts
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#================
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in_filename_msa = paste0(tolower(gene), "_msa.csv")
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infile_msa = paste0(outdir, "/", in_filename_msa)
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cat("\nInput file for MSA plots: ", infile_msa, "\n")
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msa1 = read.csv(infile_msa, header = F)
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head(msa1)
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cat("\nLength of MSA:", nrow(msa1))
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msa_seq = msa1$V1
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head(msa_seq)
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#================
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# fasta file: wt
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#================
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#in_filename_fasta = paste0(tolower(gene), ".1fasta")
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in_filename_fasta = paste0(tolower(gene), "2_f2.fasta")
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infile_fasta = paste0(indir, "/", in_filename_fasta)
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cat("\nInput fasta file for WT: ", infile_fasta, "\n")
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msa2 = read.csv(infile_fasta, header = F)
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head(msa2)
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cat("\nLength of WT fasta:", nrow(msa2))
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wt_seq = msa2$V1
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head(wt_seq)
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