chloe_main

Author: arabidopsis

Project.toml

@@ -4,7 +4,7 @@ authors = [
     "Ian Small <[email protected]>",
     "Ian Castleden <[email protected]>",
 ]
-version = "0.1.12"
+version = "0.1.14"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

RECIPES.md

@@ -1,51 +1,90 @@
 # Recipies
 
-## Creating a Project
+## Creating a Julia Project
 
 ```bash
-julia -e 'using Pkg; Pkg.generate("myproject")' \
-    && cd myproject \
-    && julia --project=. -e 'using Pkg; Pkg.add("https://github.com/ian-small/chloe.git")'
+# create a Julia project in directory myproject
+julia -e 'using Pkg; Pkg.generate("myproject")'
+cd myproject
+# add Chloe to the project
+julia --project=. -e 'using Pkg; Pkg.add("https://github.com/ian-small/chloe.git")'
+# get Chloe database (This can be placed anywhere you want really)
+git clone https://github.com/ian-small/chloe_references
+```
+
+## CommandLine
+
+Annotate a fasta file from the command line.
+
+```bash
+# note the '--'
+julia --project=. -e 'using Chloe; chloe_main()' -- annotate NC_011032.1.fa
 ```
 
 ## Simple
 
-Annotate a single FASTA file
+Annotate a single FASTA file.
 
 ```julia
 import Chloe
-import Logging
-
+# to quieten Chloe set the logging level:
+# import Logging
 # Logging.disable_logging(Logging.Info) # Disable debug and info
 
-# cd && git clone https://github.com/ian-small/chloe_references
-db = Chloe.ReferenceDbFromDir("~/chloe_references")
+references = Chloe.ReferenceDbFromDir("chloe_references")
 
-outfile, uid = Chloe.annotate(db,  "NC_011032.1.fa")
+outfile, uid = Chloe.annotate(references,  "NC_011032.1.fa")
 
 println(outfile)
 ```
+
+Write to buffer instead of to a file.
+
+```julia
+import Chloe
+references = Chloe.ReferenceDbFromDir("chloe_references")
+io, uid = Chloe.annotate(references, "NC_011032.1.fa", nothing, IOBuffer())
+# show .sff content
+println(String(take!(io)))
+```
+
+Read from an already open fasta file.
+
+
+```julia
+import Chloe
+references = Chloe.ReferenceDbFromDir("chloe_references")
+outfile, uid = open("NC_011032.1.fa", "r") do io
+    Chloe.annotate(references, io)
+end
+```
 ## Distributed
 
+It's easy to annotate multiple fasta files in parallel
+
 ```julia
 using Distributed
 # add workers
 addprocs(2)
 
 @everywhere begin
     import Chloe
+    # to quieten Chloe set the logging level:
     # import Logging
     # Logging.disable_logging(Logging.Info) # Disable debug and info
-    references = Chloe.ReferenceDbFromDir("~/chloe_references")
+    references = Chloe.ReferenceDbFromDir("chloe_references")
 end
 
 fasta_directory = "fastas"
 
 pmap = f -> l -> map(f, l)
+# find all fasta files in a directory
 fastas = readdir(dir) |> filter(f -> endswith(f, r"\.fa")) |> pmap(f -> joinpath(fasta_directory, f))
-outputs = @distributed (vcat) for fname = fastas
-    # note that references in on a worker process
-    output, uid = Chloe.annotate(references, fname, nothing, fname * ".sff")
+
+# outputs is the list of output files
+outputs = @distributed (vcat) for fasta = fastas
+    # note that `references` in on the worker process
+    output, uid = Chloe.annotate(references, fasta, nothing, fasta * ".sff")
     [output]
 end
 ```
@@ -55,8 +94,8 @@ using Distributed
 addprocs(4)
 @everywhere  begin
     using Chloe
-    db = ReferenceDbFromDir("~/chloe_references")
+    references = ReferenceDbFromDir("~/chloe_references")
 end
-r = fetch(@spawnat :any annotate(db, "NC_011032.1.fa"))
+r = fetch(@spawnat :any annotate(references, "NC_011032.1.fa"))
 println(r)
 ```

src/Chloe.jl

@@ -2,7 +2,7 @@ module Chloe
 
 export annotate, annotate_batch, ReferenceDbFromDir, ReferenceDb, ChloeConfig, AbstractReferenceDb
 # export MayBeIO, MayBeString
-export cmd_main
+export chloe_main
 export distributed_main, chloe_distributed, run_broker, broker_main, get_distributed_args, maybe_launch_broker
 export set_global_logger
 export annotate_one_task
@@ -19,7 +19,7 @@ include("dist/chloe_distributed.jl")
 
 # import .ChloeDistributed: distributed_main, chloe_distributed, run_broker, get_distributed_args, maybe_launch_broker
 import .Annotator: annotate_batch, annotate, ReferenceDb, ReferenceDbFromDir, AbstractReferenceDb, ChloeConfig
-import .CmdLine: cmd_main
+import .CmdLine: chloe_main
 import .Broker: broker_main
 import .ZMQLogging: set_global_logger
 end

src/dist/chloe_cmd.jl

@@ -1,6 +1,6 @@
 
 module CmdLine
-export cmd_main
+export chloe_main
 
 import ArgParse: ArgParseSettings, @add_arg_table!, parse_args
 import Logging
@@ -150,7 +150,7 @@ function getargs(args::Vector{String}=ARGS)
     parse_args(args, cmd_args; as_symbols=true)
 end
 
-function cmd_main(args::Vector{String} = ARGS)
+function chloe_main(args::Vector{String} = ARGS)
     parsed_args = getargs(args)
     level = lowercase(parsed_args[:level])
     Logging.with_logger(Logging.ConsoleLogger(stderr,