Stitch FASTA reads shredded with shred.sh from BBTools back together

stitch-fasta.jl

# tested on Julialang v.1.10.2, DataStructures v0.18.16, and FASTX v2.1.4
# Usage
# $ julia stitch-fasta.jl chr20.herro.fasta.Q30.recal.shred.fasta > chr20.herro.fasta.Q30.recal.fasta
#
import Pkg; Pkg.add("FASTX")
import Pkg; Pkg.add("DataStructures")
using DataStructures
using FASTX

function process_fasta_file(filename::String)
    reader = FASTAReader(open(filename))
    sequences = Dict{String, String}()
    sequences2 = Dict{String, String}()

    for record in reader
        # Get identifier
        main_id = string(identifier(record))
        seq = sequence(record)
        sequences[main_id] = seq
    end

    close(reader)
        
    sorted_pairs = OrderedDict(sort(collect(pairs(sequences))))

    for (id, seq) in sorted_pairs
        main_id = split(id, '_')[1]
        # Aggregate sequences by the main identifier
        if haskey(sequences2, main_id)
            sequences2[main_id] *= seq
        else
            sequences2[main_id] = seq
        end
    end

    # Print the aggregated sequences
    for (id, seq) in sequences2
        println(">$id")
        println(seq)
    end
end

# Check if a filename is passed as a command line argument
if length(ARGS) < 1
    println("Usage: julia ", PROGRAM_FILE, " <filename.fasta>")
    return
end
# Example usage with command line argument
process_fasta_file(ARGS[1])