Relative paths in db (#25)

* Don't convert fasta_files paths to absolute paths

* Prepend database directory path on to relative paths for allele fasta files in db

* Don't create db_path variable, check for existence of fasta files

* Tidy up newlines

* Added test to check MLST calling after moving a database

* Fixed issue with scheme fasta loading during calling

src/MentaLiST.jl

@@ -2,7 +2,7 @@
 using Lumberjack
 using ArgParse
 
-VERSION = "0.2.3"
+VERSION = "0.2.2"
 function parse_commandline()
     s = ArgParseSettings()
     s.epilog = "MentaLiST -- The MLST pipeline developed by the PathOGiST research group. https://github.com/WGS-TB/MentaLiST\n" *
@@ -230,6 +230,9 @@ function build_db(args)
   info("Combining results for each locus ...")
   kmer_classification = combine_loci_classification(k, results, loci)
 
+  for (index, fasta_file) in enumerate(args["fasta_files"])
+    args["fasta_files"][index] = pop!(split(dirname(fasta_file), "/")) * "/" * basename(fasta_file)
+  end
   info("Saving DB ...")
   save_db(k, kmer_classification, loci, db_file, profile, args)
   info("Done!")

src/calling_functions.jl

@@ -18,12 +18,10 @@ function run_calling_pipeline(args)
 
   # prepend base path of the kmer database on to the relative paths for allele fasta files stored in the db
   for (index, file) in enumerate(build_args["fasta_files"])
-    build_args["fasta_files"][index] = dirname(args["db"]) * "/" * file
+    build_args["fasta_files"][index] = joinpath(dirname(args["db"]), file)
   end
   # check if scheme fasta files exist
-  for fasta_file in build_args["fasta_files"]
-    check_files(fasta_file)
-  end
+  check_files(build_args["fasta_files"])
   # process each sample:
   for (sample, fq_files) in sample_files
     info("Sample: $sample. Opening fastq file(s) and counting kmers ... ")