Fix problem related to mkdir and time main code

main/cds.fasta

@@ -2,3 +2,5 @@
 ATGGCGAAAGAAGATAACATTGAAATGCAGGGCACCGTGCTGGAAACCCTGCCGAACACCATGTTTCGCGTGGAACTGGAAAACGGCCATGTGGTGACCGCGCATATTAGCGGCAAAATGCGCAAAAACTATATTCGCATTCTGACCGGCGATAAAGTGACCGTGGAACTGACCCCGTATGATCTGAGCAAAGGCCGCATTGTGTTTCGCAGCCGCTAA
 >aroB
 ATGGAGAGGATAGTGGTCACCCTGGGTGAGCGGTCTTATCCAATCACGATCGCTTCGGGGTTATTTAATGAGCCTGCTTCGTTCCTGCCGCTGAAATCGGGGGAGCAGGTAATGCTCGTGACAAATGAGACACTGGCCCCCCTGTATTTGGATAAAGTTAGGGGTGTCTTGGAGCAGGCAGGTGTGAACGTCGATAGTGTCATCCTGCCTGATGGCGAGCAGTATAAATCTTTAGCGGTGCTGGACACCGTGTTCACCGCACTGCTACAAAAACCGCATGGGCGCGACACTACTTTAGTCGCACTGGGGGGCGGTGTCGTTGGTGATCTGACAGGCTTCGCGGCCGCGAGTTATCAACGGGGCGTGCGGTTTATTCAGGTTCCGACCACTCTACTGAGTCAAGTTGATTCTAGTGTAGGCGGCAAAACGGCAGTCAACCATCCATTGGGCAAAAATATGATTGGTGCGTTCTACCAACCAGCTTCGGTCGTCGTGGATCTGGATTGCCTGAAGACGCTGCCGCCCCGGGAACTAGCAAGTGGTCTGGCTGAGGTTATCAAATATGGCATCATTCTGGACGGCGCATTCTTTAACTGGCTTGAAGAGAATCTGGATGCCCTACTAAGACTGGACGGTCCAGCTATGGCCTATTGTATTAGACGGTGCTGTGAGCTAAAAGCCGAGGTTGTTGCTGCGGACGAACGAGAGACTGGTCTACGTGCTTTGTTGAATCTAGGTCACACGTTTGGTCACGCCATCGAAGCCGAAATGGGTTATGGAAATTGGCTTCACGGGGAGGCGGTGGCAGCGGGGATGGTCATGGCCGCACGGACATCTGAGCGGCTGGGACAATTCTCGAGTGCCGAGACTCAAAGAATCATCACACTGTTAAAACGGGCAGGCCTGCCAGTTAATGGTCCAAGGGAAATGTCGGCCCAAGCCTACTTGCCCCACATGCTGCGGGACAAGAAAGTTCTAGCAGGGGAAATGAGGTTGATCCTTCCTCTGGCCATTGGGAAAAGTGAAGTGAGATCCGGTGTCTCGCATGAACTAGTTCTTAACGCGATAGCTGACTGTCAATCAGCGTAA
+>cysJ
+ATGACCACCCAGGTGCCGCCGAGCGCGCTGCTGCCGCTGAACCCGGAACAGCTGGCGCGCCTGCAGGCGGCGACCACCGATCTGACCCCGACCCAGCTGGCGTGGGTGAGCGGCTATTTTTGGGGCGTGCTGAACCAGCAGCCGGCGGCGCTGGCGGCGACCCCGGCGCCGGCGGCGGAAATGCCGGGCATTACCATTATTAGCGCGAGCCAGACCGGCAACGCGCGCCGCGTGGCGGAAGCGCTGCGCGATGATCTGCTGGCGGCGAAACTGAACGTGAAACTGGTGAACGCGGGCGATTATAAATTTAAACAGATTGCGAGCGAAAAACTGCTGATTGTGGTGACCAGCACCCAGGGCGAAGGCGAACCGCCGGAAGAAGCGGTGGCGCTGCATAAATTTCTGTTTAGCAAAAAAGCGCCGAAACTGGAAAACACCGCGTTTGCGGTGTTTAGCCTGGGCGATAGCAGCTATGAATTTTTTTGCCAGAGCGGCAAAGATTTTGATAGCAAACTGGCGGAACTGGGCGGCGAACGCCTGCTGGATCGCGTGGATGCGGATGTGGAATATCAGGCGGCGGCGAGCGAATGGCGCGCGCGCGTGGTGGATGCGCTGAAAAGCCGCGCGCCGGTGGCGGCGCCGAGCCAGAGCGTGGCGACCGGCGCGGTGAACGAAATTCATACCAGCCCGTATAGCAAAGATGCGCCGCTGGTGGCGAGCCTGAGCGTGAACCAGAAAATTACCGGCCGCAACAGCGAAAAAGATGTGCGCCATATTGAAATTGATCTGGGCGATAGCGGCATGCGCTATCAGCCGGGCGATGCGCTGGGCGTGTGGTATCAGAACGATCCGGCGCTGGTGAAAGAACTGGTGGAACTGCTGTGGCTGAAAGGCGATGAACCGGTGACCGTGGAAGGCAAAACCCTGCCGCTGAACGAAGCGCTGCAGTGGCATTTTGAACTGACCGTGAACACCGCGAACATTGTGGAAAACTATGCGACCCTGACCCGCAGCGAAACCCTGCTGCCGCTGGTGGGCGATAAAGCGAAACTGCAGCATTATGCGGCGACCACCCCGATTGTGGATATGGTGCGCTTTAGCCCGGCGCAGCTGGATGCGGAAGCGCTGATTAACCTGCTGCGCCCGCTGACCCCGCGCCTGTATAGCATTGCGAGCAGCCAGGCGGAAGTGGAAAACGAAGTGCATGTGACCGTGGGCGTGGTGCGCTATGATGTGGAAGGCCGCGCGCGCGCGGGCGGCGCGAGCAGCTTTCTGGCGGATCGCGTGGAAGAAGAAGGCGAAGTGCGCGTGTTTATTGAACATAACGATAACTTTCGCCTGCCGGCGAACCCGGAAACCCCGGTGATTATGATTGGCCCGGGCACCGGCATTGCGCCGTTTCGCGCGTTTATGCAGCAGCGCGCGGCGGATGAAGCGCCGGGCAAAAACTGGCTGTTTTTTGGCAACCCGCATTTTACCGAAGATTTTCTGTATCAGGTGGAATGGCAGCGCTATGTGAAAGATGGCGTGCTGACCCGCATTGATCTGGCGTGGAGCCGCGATCAGAAAGAAAAAGTGTATGTGCAGGATAAACTGCGCGAACAGGGCGCGGAACTGTGGCGCTGGATTAACGATGGCGCGCATATTTATGTGTGCGGCGATGCGAACCGCATGGCGAAAGATGTGGAACAGGCGCTGCTGGAAGTGATTGCGGAATTTGGCGGCATGGATACCGAAGCGGCGGATGAATTTCTGAGCGAACTGCGCGTGGAACGCCGCTATCAGCGCGATGTGTAT

main/main.jl

@@ -389,7 +389,7 @@ function run_file()
 
 					the_out_path = "$out_dir/$(short)_$(long)_$frame/"
 					if !(isdir(the_out_path))
-						run(`mkdir $the_out_path`)
+						run(`mkdir -p $the_out_path`)
 					end
 
 					log_io = open("$out_dir/$(short)_$(long)_$frame/log_$(rand_barcode).txt", "w+")
@@ -418,6 +418,6 @@ function run_file()
 
 end
 
-run_file()
+@time run_file()
 
 end

main/outparser.jl

@@ -0,0 +1,135 @@
+"""
+outparser: CAMEOS output parser
+"""
+
+using JLD # Should be placed here too to avoid later crash loading JLD file
+
+module main
+
+include("optimize.jl")
+include("types.jl") 
+
+using ArgParse, JLD
+
+function parse_commandline()
+	s = ArgParseSettings()
+	@add_arg_table s begin
+        "mark_gene"
+		    help = "1st positional argument, name of gene 'mark'"
+            arg_type = String
+			default = "cysJ"
+        "deg_gene"
+		    help = "2nd positional argument, name of gene 'deg'"
+            arg_type = String
+			default = "infA"
+		"runid"
+			help = "3rd positional argument, run id code created by CAMEOS"
+            arg_type = String
+            default = "LgolUs7k"
+        "--frame"
+			help = "optional argument, CAMEOS frame"
+            arg_type = String
+		    default = "p1"     
+        "--fasta"
+            help = "generate a FASTA file too"
+            action = :store_true
+        "--just-fullseq"
+            help = "the FASTA will only contain the full sequence"
+            action = :store_true
+	end
+	return parse_args(s)
+end
+
+function outparse_cameos()
+    println("=-= CAMEOS output parser =-= v0.4 - Mar 2021 =-= by LLNL =-=")
+
+    # Parse arguments
+   	parsed_args = parse_commandline()
+	mark_gene = parsed_args["mark_gene"]
+	deg_gene = parsed_args["deg_gene"]
+	runid = parsed_args["runid"]
+	frame = parsed_args["frame"]
+    fasta = parsed_args["fasta"]
+    justfullseq = parsed_args["just-fullseq"]
+
+    # Get complete path for input and output files
+    subdir = string(mark_gene, "_", deg_gene, "_", frame)
+    jld_file = string("saved_pop_", runid, ".jld")
+    csv_file = string("summary_", runid, ".csv")
+    fa_file = string("variants_", runid, ".fasta")
+    in_path = string("output/", subdir, "/", jld_file)
+    out_path = string("output/", subdir, "/", csv_file)
+    fa_path = string("output/", subdir, "/", fa_file)
+
+    # Load JLD file
+    print("Loading data from JLD file ", in_path, " ... ")
+    variants = load(in_path)["variants"];
+    println("OK!")
+
+    # Save CSV file
+    print("Saving data to CSV file ", out_path, " : ")
+    parsed = 0
+    open(out_path, "w") do io
+        println(io, string("full_seq,",
+                           mark_gene,"_psls,",
+                           mark_gene,"_seq,",
+                           deg_gene,"_psls,",
+                           deg_gene,"_seq"))
+        for var in variants
+            println(io, var.full_sequence,",",
+                    var.mark_prob,",",
+                    var.mark_seq,",", #var.mark_nuc,",",
+                    var.deg_prob,",",
+                    var.deg_seq) #,",",var.deg_nuc)
+            parsed += 1
+            if parsed % 200 == 0
+                print(".")
+            end
+        end
+    end
+    println(" OK!")
+    println(parsed, " variants parsed for ", runid)
+
+    # Save fasta file
+    if fasta
+        print("Saving data to FASTA file ", fa_path, " : ")
+        variant = 1
+        open(fa_path, "w") do io
+
+            function print2fasta(var, field::String, nucs::Bool=false)
+                # Prints header and sequence to fasta file
+                println(io, ">CAMEOS run:", runid,
+                        " mark_gene:", mark_gene,
+                        " deg_gene:", deg_gene,
+                        " variant:", variant, "/", parsed,
+                        " ", string(field))
+                if nucs
+                    println(io, getfield(getfield(var, Symbol(field)), :nucs))
+                else
+                    println(io, getfield(var, Symbol(field)))
+                end
+                return nothing
+            end
+
+            for var in variants
+                if justfullseq
+                    print2fasta(var, "full_sequence")  # equal to mark_nuc.nucs
+                else
+                    print2fasta(var, "mark_seq")
+                    print2fasta(var, "mark_nuc", true)
+                    print2fasta(var, "deg_seq")
+                    print2fasta(var, "deg_nuc", true)
+                end
+                variant += 1
+                if variant % 200 == 0
+                    print(".")
+                end
+            end
+        end
+        println(" OK!")
+        println(variant-1, " variants in FASTA file for ", runid)    
+    end
+end
+
+@time outparse_cameos()
+end

main/proteins.fasta

@@ -2,3 +2,5 @@
 MAKEDNIEMQGTVLETLPNTMFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRSR
 >aroB
 MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQAGVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASGLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAGLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADCQSA
+>cysJ
+MTTQVPPSALLPLNPEQLARLQAATTDLTPTQLAWVSGYFWGVLNQQPAALAATPAPAAEMPGITIISASQTGNARRVAEALRDDLLAAKLNVKLVNAGDYKFKQIASEKLLIVVTSTQGEGEPPEEAVALHKFLFSKKAPKLENTAFAVFSLGDSSYEFFCQSGKDFDSKLAELGGERLLDRVDADVEYQAAASEWRARVVDALKSRAPVAAPSQSVATGAVNEIHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEIDLGDSGMRYQPGDALGVWYQNDPALVKELVELLWLKGDEPVTVEGKTLPLNEALQWHFELTVNTANIVENYATLTRSETLLPLVGDKAKLQHYAATTPIVDMVRFSPAQLDAEALINLLRPLTPRLYSIASSQAEVENEVHVTVGVVRYDVEGRARAGGASSFLADRVEEEGEVRVFIEHNDNFRLPANPETPVIMIGPGTGIAPFRAFMQQRAADEAPGKNWLFFGNPHFTEDFLYQVEWQRYVKDGVLTRIDLAWSRDQKEKVYVQDKLREQGAELWRWINDGAHIYVCGDANRMAKDVEQALLEVIAEFGGMDTEAADEFLSELRVERRYQRDVY

prepare/energies_and_psls.jl

@@ -38,6 +38,44 @@ function compute_psls(prot_mat, w1, w2, nNodes, nProt)
 	return -all_scores
 end
 
+function save_energies(computed_energies, gene_name)
+    local out_file
+    try
+	    out_file = open("../main/energies/energy_$(gene_name).txt", "w")
+    catch err
+        if isa(err, SystemError)
+            out_file = open("energy_$(gene_name).txt", "w")
+            println("Warning: writting energy output to working directory")
+        else
+            rethrow()
+        end
+    finally
+	    for energy in computed_energies
+		    write(out_file, "$energy\n")
+	    end
+	    close(out_file)
+    end
+end
+
+function save_psls(computed_psls, gene_name)
+    local out_file
+    try
+	    out_file = open("../main/psls/psls_$(gene_name).txt", "w")
+    catch err
+        if isa(err, SystemError)
+            out_file = open("psls_$(gene_name).txt", "w")
+            println("Warning: writting pseudolhood output to working directory")
+        else
+            rethrow()
+        end
+    finally
+	    for psl in computed_psls
+		    write(out_file, "$psl\n")
+	    end
+	    close(out_file)
+    end  
+end
+
 function run(gene_name, jld_file, msa_file)
 	println("Reading msa file")
 	in_file = open(msa_file)
@@ -63,22 +101,14 @@ function run(gene_name, jld_file, msa_file)
 	w1 = mrf["w1"]
 	w2 = mrf["w2"]
 
-	computed_energies = compute_energies(prot_mat, w1, w2)
-	computed_psls = compute_psls(prot_mat, w1, w2, num_aa, num_prot)
+	@time computed_energies = compute_energies(prot_mat, w1, w2)
+	@time computed_psls = compute_psls(prot_mat, w1, w2, num_aa, num_prot)
 
 	#Write outputs to main directory.
 	println("Done. Saving energies/psls.")
-	out_file = open("../main/energies/energy_$(gene_name).txt", "w")
-	for energy in computed_energies
-		write(out_file, "$energy\n")
-	end
-	close(out_file)
 
-	out_file = open("../main/psls/psls_$(gene_name).txt", "w")
-	for psl in computed_psls
-		write(out_file, "$psl\n")
-	end
-	close(out_file)
+    save_energies(computed_energies, gene_name)
+    save_psls(computed_psls, gene_name)
 end
 
 function main()