add initial draft

Author: danielle-pinto

cookbook/assets/mecA.fasta

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+>NC_007795.1:907598-908317 SAOUHSC_00935 [organism=Staphylococcus aureus subsp. aureus NCTC 8325] [GeneID=3920764] [chromosome=]
+ATGAGAATAGAACGAGTAGATGATACAACTGTAAAATTGTTTATAACATATAGCGATATCGAGGCCCGTG
+GATTTAGTCGTGAAGATTTATGGACAAATCGCAAACGTGGCGAAGAATTCTTTTGGTCAATGATGGATGA
+AATTAACGAAGAAGAAGATTTTGTTGTAGAAGGTCCATTATGGATTCAAGTACATGCCTTTGAAAAAGGT
+GTCGAAGTCACAATTTCTAAATCTAAAAATGAAGATATGATGAATATGTCTGATGATGATGCAACTGATC
+AATTTGATGAACAAGTTCAAGAATTGTTAGCTCAAACATTAGAAGGTGAAGATCAATTAGAAGAATTATT
+CGAGCAACGAACAAAAGAAAAAGAAGCTCAAGGTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACA
+AGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAA
+CTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCA
+TGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACA
+GAAGTTTATTTAAATGACTATGCTAAAATAATTATGAGTCATAACGTAACAGCTCAAGTTCGACGTTATT
+TTCCAGAGACAACTGAATAA

cookbook/index.md

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++++
+using Dates
+date = Date("2026-03-04")
+title = "BioJulia Cookbook"
+rss_descr = "Recipes for performing basic bioinformatics in julia"
++++
+
+# BioJulia Cookbook
+
+This cookbook will provide a series of "recipes" that will help get started quickly with BioJulia so you can doing some bioinformatics!
+
+We have tutorials for reading in files, performing alignments, and using tools such as BLAST,    
+as well as links to more documentation about specific BioJulia packages.
+
+{{list_dir cookbook}}

cookbook/sequences.md

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++++
+title = "Sequence Input/Output"
+rss_descr = "Reading in fasta files using FASTX.jl"
++++
+
+# Sequence Input/Output
+
+In this chapter, we'll talk about how to read in sequence files using the `FASTX.jl` module.   
+More information about the `FASTX.jl` package can be found at https://biojulia.dev/FASTX.jl/stable/  
+and with the built-in documentation. 
+
+```julia
+julia> using FASTX
+julia> ?FASTX
+```
+
+If FASTX is not already in your environment,   
+it can be easily added from the Julia Registry.
+
+To demonstrate how to this package,   
+let's try to read in some real-world data!   
+
+The `FASTX` can read in 3 file types: fasta, fastq, and fai.
+
+### FASTA files
+FASTA files are text files containing biological sequence data.       
+They have three parts: name, description, and sequence.
+
+The template of a sequence record is:
+```
+>{description}
+{sequence}
+```
+
+### FASTQ files
+FASTQ files are also text-based files that contain sequences, along with a name and description. However, they also store sequence quality information (the Q is for quality!).
+
+The template of a sequence record is:
+```
+@{description}
+{sequence}
++{description}?
+{qualities}
+```
+
+### FAI files
+
+FAI (FASTA index) files are used in conjuction with FASTA/FASTQ files.   
+They are text files with TAB-delimited columns.  
+Each line contains information about each region sequence within the FASTA/FASTQ.     
+More information about fai index files can be found [here](https://www.htslib.org/doc/faidx.html).
+
+```
+NAME	Name of this reference sequence
+LENGTH	Total length of this reference sequence, in bases
+OFFSET	Offset in the FASTA/FASTQ file of this sequence's first base
+LINEBASES	The number of bases on each line
+LINEWIDTH	The number of bytes in each line, including the newline
+QUALOFFSET	Offset of sequence's first quality within the FASTQ file
+
+```
+
+
+
+
+
+We will read in a fasta file containing the _mecA_ gene.   
+This gene was taken from NCBI [here](https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=3920764#).
+
+First we'll open the file, 
+then we'll iterate over every record in the file and  
+print out the sequence identifier, the sequence description and then the corresponding sequence.
+
+```julia
+julia> FASTAReader(open("assets/mecA.fasta")) do reader
+           for record in reader
+               println(identifier(record))
+               println(description(record))
+               println(sequence(record))
+           end
+       end
+
+NC_007795.1:907598-908317
+NC_007795.1:907598-908317 SAOUHSC_00935 [organism=Staphylococcus aureus subsp. aureus NCTC 8325] [GeneID=3920764] [chromosome=]
+ATGAGAATAGAACGAGTAGATGATACAACTGTAAAATTGTTTATAACATATAGCGATATCGAGGCCCGTGGATTTAGTCGTGAAGATTTATGGACAAATCGCAAACGTGGCGAAGAATTCTTTTGGTCAATGATGGATGAAATTAACGAAGAAGAAGATTTTGTTGTAGAAGGTCCATTATGGATTCAAGTACATGCCTTTGAAAAAGGTGTCGAAGTCACAATTTCTAAATCTAAAAATGAAGATATGATGAATATGTCTGATGATGATGCAACTGATCAATTTGATGAACAAGTTCAAGAATTGTTAGCTCAAACATTAGAAGGTGAAGATCAATTAGAAGAATTATTCGAGCAACGAACAAAAGAAAAAGAAGCTCAAGGTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCTAAAATAATTATGAGTCATAACGTAACAGCTCAAGTTCGACGTTATTTTCCAGAGACAACTGAATAA
+```
+
+In this case, there is only one sequence.
+
+Let's try reading in a larger fastq file. 
+
+```julia
+
+
+
+```
+
+
+