fix typos and update mecA.fasta

Author: danielle-pinto

cookbook/assets/mecA.fasta

@@ -1,12 +1,32 @@
->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
+>NG_047945.1 Staphylococcus aureus TN/CN/1/12 mecA gene for ceftaroline-resistant PBP2a family peptidoglycan transpeptidase MecA, complete CDS
+ATGAAAAAGATAAAAATTGTTCCACTTATTTTAATAGTTGTAGTTGTCGGGTTTGGTATATATTTTTATG
+CTTCAAAAGATAAAGAAATTAATAATACTATTGATGCAATTGAAGATAAAAATTTCAAACAAGTTTATAA
+AGATAGCAGTTATATTTCTAAAAGCGATAATGGTGAAGTAGAAATGACTGAACGTCCGATAAAAATATAT
+AATAGTTTAGGCGTTAAAGATATAAACATTCAGGATCGTAAAATAAAAAAAGTATCTAAAAATAAAAAAC
+GAGTAGATGCTCAATATAAAATTAAAACAAACTACGGTAACATTGATCGCAACGTTCAATTTAATTTTGT
+TAAAGAAGATGGTATGTGGAAGTTAGATTGGGATCATAGCGTCATTATTCCAGGAATGCAGAAAGACCAA
+AGCATACATATTGAAAATTTAAAATCAGAACGTGGTAAAATTTTAGACCGAAACAATGTGGAATTGGCCA
+ATACAGGAACAGCATATGAGATAGGCATCGTTCCAAAGAATGTATCTAAAAAAGATTATAAAGCAATCGC
+TAAAGAACTAAGTATTTCTGAAGACTATATCAAACAACAAATGGATCAAAATTGGGTACAAGATGATACC
+TTCGTTCCACTTAAAACCGTTAAAAAAATGGATGAATATTTAAGTGATTTCGCAAAAAAATTTCATCTTA
+CAACTAATGAAACAAAAAGTCGTAACTATCCTCTAGAAAAAGCGACTTCACATCTATTAGGTTATGTTGG
+TCCCATTAACTCTGAAGAATTAAAACAAAAAGAATATAAAGGCTATAAAGATGATGCAGTTATTGGTAAA
+AAGGGACTCGAAAAACTTTACGATAAAAAGCTCCAACATGAAGATGGCTATCGTGTCACAATCGTTGACG
+ATAATAGCAATACAATCGCACATACATTAATAGAGAAAAAGAAAAAAGATGGCAAAGATATTCAACTAAC
+TATTGATGCTAAAGTTCAAAAGAGTATTTATAACAACATGAAAAATGATTATGGCTCAGGTACTGCTATC
+CACCCTCAAACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTATG
+GCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAACAAGTTCCAGAT
+TACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGCAATGATTGGGTTAAATAACAAAACATTAGAC
+GATAAAACAAGTTATAAAATCGATGGTAAAGGTTGGCAAAAAGATAAATCTTGGGGTGGTTACAACGTTA
+CAAGATATGAAGTGGTAAATGGTAATATCGACTTAAAACAAGCAATAGAATCATCAGATAACATTTTCTT
+TGCTAGAGTAGCACTCGAATTAGGCAGTAAGAAATTTGAAAAAGGCATGAAAAAACTAGGTGTTGGTGAA
+GATATACCAAGTGATTATCCATTTTATAATGCTCAAATTTCAAACAAAAATTTAGATAATGAAATATTAT
+TAGCTGATTCAGGTTACGGACAAGGTGAAATACTGATTAACCCAGTACAGATCCTTTCAATCTATAGCGC
+ATTAGAAAATAATGGCAATATTAACGCACCTCACTTATTAAAAGACACGAAAAACAAAGTTTGGAAGAAA
+AATATTATTTCCAAAGAAAATATCAATCTATTAACTGATGGTATGCAACAAGTCGTAAATAAAACACATA
+AAGAAGATATTTATAGATCTTATGCAAACTTAATTGGCAAATCCGGTACTGCAGAACTCAAAATGAAACA
+AGGAGAAACTGGCAGACAAATTGGGTGGTTTATATCATATGATAAAGATAATCCAAACATGATGATGGCT
+ATTAATGTTAAAGATGTACAAGATAAAGGAATGGCTAGCTACAATGCCAAAATCTCAGGTAAAGTGTATG
+ATGAGCTATATGAGAACGGTAATAAAAAATACGATATAGATGAATAACAAAACAGTGAAGCAATCCGTAA
+CGATGGTTGCTTCACTGTTTTATTATGAATTATTAATAAGTGCTGTTACTTCTCCCTTAAATACAATTTC
+TTCATTT

cookbook/sequences.md

@@ -1,26 +1,26 @@
 +++
 title = "Sequence Input/Output"
-rss_descr = "Reading in fasta files using FASTX.jl"
+rss_descr = "Reading in FASTA, FASTQ, and FAI 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. 
+and with the built-in documentation you can access directly within the Julia REPL. 
 
 ```julia
 julia> using FASTX
 julia> ?FASTX
 ```
 
-If FASTX is not already in your environment,   
+If `FASTX` is not already in your environment,   
 it can be easily added from the Julia Registry.
 
-To demonstrate how to this package,   
+To demonstrate how to use this package,   
 let's try to read in some real-world data!   
 
-The `FASTX` can read in 3 file types: fasta, fastq, and fai.
+The `FASTX` package can read in three file types: `fasta`, `fastq`, and `fai`.
 
 ### FASTA files
 FASTA files are text files containing biological sequence data.       
@@ -32,6 +32,16 @@ The template of a sequence record is:
 {sequence}
 ```
 
+The identifier is the first part of the description until the first whitespace.     
+If there is no white space, the name and description are the same.
+
+Here is an example fasta:
+```
+>chrI chromosome 1
+CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACC
+CACACACACACATCCTAACACTACCCTAACACAGCCCTAATCTA
+```
+
 ### 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!).
@@ -54,9 +64,9 @@ tcagTTAAGATGGGAT
 
 ### FAI files
 
-FAI (FASTA index) files are used in conjuction with FASTA/FASTQ files.   
+FAI (FASTA index) files are used in conjunction with FASTA/FASTQ files.   
 They are text files with TAB-delimited columns.  
-Each line contains information about each region sequence within the FASTA/FASTQ.     
+They allow the user to access specific regions of the reference FASTA/FASTQ without reading in the entire sequence into memory.      
 More information about fai index files can be found [here](https://www.htslib.org/doc/faidx.html).
 
 ```
@@ -69,15 +79,14 @@ QUALOFFSET	Offset of sequence's first quality within the FASTQ file
 
 ```
 
+We will read in a FASTA file containing the _mecA_ gene.   
+_mecA_ is an antibiotic resistance gene commonly found in Methicillin-resistant _Staphylococcus aureus_ (MRSA). 
+It helps bacteria to break down beta-lactam antibiotics like methicillin.    
+It is typically 2.1 kB long.  
+This specific reference fasta was downloaded from NCBI [here](https://www.ncbi.nlm.nih.gov/nuccore/NG_047945.1?report=fasta). More information about this reference sequence can be found [here](https://www.ncbi.nlm.nih.gov/nuccore/NG_047945.1).  
 
-
-
-
-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  
+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
@@ -86,32 +95,38 @@ julia> FASTAReader(open("assets/mecA.fasta")) do reader
                println(identifier(record))
                println(description(record))
                println(sequence(record))
+               println(length(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
+NG_047945.1
+NG_047945.1 Staphylococcus aureus TN/CN/1/12 mecA gene for ceftaroline-resistant PBP2a family peptidoglycan transpeptidase MecA, complete CDS
+ATGAAAAAGATAAAAATTGTTCCACTTATTTTAATAGTTGTAGTTGTCGGGTTTGGTATATATTTTTATGCTTCAAAAGATAAAGAAATTAATAATACTATTGATGCAATTGAAGATAAAAATTTCAAACAAGTTTATAAAGATAGCAGTTATATTTCTAAAAGCGATAATGGTGAAGTAGAAATGACTGAACGTCCGATAAAAATATATAATAGTTTAGGCGTTAAAGATATAAACATTCAGGATCGTAAAATAAAAAAAGTATCTAAAAATAAAAAACGAGTAGATGCTCAATATAAAATTAAAACAAACTACGGTAACATTGATCGCAACGTTCAATTTAATTTTGTTAAAGAAGATGGTATGTGGAAGTTAGATTGGGATCATAGCGTCATTATTCCAGGAATGCAGAAAGACCAAAGCATACATATTGAAAATTTAAAATCAGAACGTGGTAAAATTTTAGACCGAAACAATGTGGAATTGGCCAATACAGGAACAGCATATGAGATAGGCATCGTTCCAAAGAATGTATCTAAAAAAGATTATAAAGCAATCGCTAAAGAACTAAGTATTTCTGAAGACTATATCAAACAACAAATGGATCAAAATTGGGTACAAGATGATACCTTCGTTCCACTTAAAACCGTTAAAAAAATGGATGAATATTTAAGTGATTTCGCAAAAAAATTTCATCTTACAACTAATGAAACAAAAAGTCGTAACTATCCTCTAGAAAAAGCGACTTCACATCTATTAGGTTATGTTGGTCCCATTAACTCTGAAGAATTAAAACAAAAAGAATATAAAGGCTATAAAGATGATGCAGTTATTGGTAAAAAGGGACTCGAAAAACTTTACGATAAAAAGCTCCAACATGAAGATGGCTATCGTGTCACAATCGTTGACGATAATAGCAATACAATCGCACATACATTAATAGAGAAAAAGAAAAAAGATGGCAAAGATATTCAACTAACTATTGATGCTAAAGTTCAAAAGAGTATTTATAACAACATGAAAAATGATTATGGCTCAGGTACTGCTATCCACCCTCAAACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTATGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAACAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGCAATGATTGGGTTAAATAACAAAACATTAGACGATAAAACAAGTTATAAAATCGATGGTAAAGGTTGGCAAAAAGATAAATCTTGGGGTGGTTACAACGTTACAAGATATGAAGTGGTAAATGGTAATATCGACTTAAAACAAGCAATAGAATCATCAGATAACATTTTCTTTGCTAGAGTAGCACTCGAATTAGGCAGTAAGAAATTTGAAAAAGGCATGAAAAAACTAGGTGTTGGTGAAGATATACCAAGTGATTATCCATTTTATAATGCTCAAATTTCAAACAAAAATTTAGATAATGAAATATTATTAGCTGATTCAGGTTACGGACAAGGTGAAATACTGATTAACCCAGTACAGATCCTTTCAATCTATAGCGCATTAGAAAATAATGGCAATATTAACGCACCTCACTTATTAAAAGACACGAAAAACAAAGTTTGGAAGAAAAATATTATTTCCAAAGAAAATATCAATCTATTAACTGATGGTATGCAACAAGTCGTAAATAAAACACATAAAGAAGATATTTATAGATCTTATGCAAACTTAATTGGCAAATCCGGTACTGCAGAACTCAAAATGAAACAAGGAGAAACTGGCAGACAAATTGGGTGGTTTATATCATATGATAAAGATAATCCAAACATGATGATGGCTATTAATGTTAAAGATGTACAAGATAAAGGAATGGCTAGCTACAATGCCAAAATCTCAGGTAAAGTGTATGATGAGCTATATGAGAACGGTAATAAAAAATACGATATAGATGAATAACAAAACAGTGAAGCAATCCGTAACGATGGTTGCTTCACTGTTTTATTATGAATTATTAATAAGTGCTGTTACTTCTCCCTTAAATACAATTTCTTCATTT
+2107
 ```
+We confirmed that the length of the gene matches what we'd expect for _mecA_. 
+In this case, there is only one sequence that spans the entire length of the gene.   
+After this gene was sequenced, all of the reads were assembled together into a single consensus sequence.      
+_mecA_ is a well-characterized gene, so there are no ambiguous regions, and there is no need for there to be multiple contigs  
+(AKA for the gene to be broken up into multiple pieces, as we know exactly how the reads should be assembled together.).  
 
-In this case, there is only one sequence.
 
-Let's try reading in a larger fastq file. 
+Let's try reading in a larger FASTQ file. 
 
-The raw reads for a Staphylococcus aureus isolate was sequenced with Pac-Bio and uploaded to NCBI [here](https://trace.ncbi.nlm.nih.gov/Traces/?run=SRR12147540).   
-The link to download the raw fastq's can be found [here](https://trace.ncbi.nlm.nih.gov/Traces/?run=SRR12147540).
+The raw reads for a _Staphylococcus aureus_ isolate were sequenced with PacBio and uploaded to NCBI [here](https://trace.ncbi.nlm.nih.gov/Traces/?run=SRR12147540).     
+The link to download the raw FASTQ files can be found [here](https://trace.ncbi.nlm.nih.gov/Traces/?run=SRR12147540).
 
-The biosample ID for this sample is `SAMN14830786`.
+The BioSample ID for this sample is `SAMN14830786`.
 This ID refers to the physical bacterial isolate.  
 
-The SRA sample accession number (an internal value used within Sequence Read Archive) is `SRS6947643`.    
+The SRA sample accession number (an internal value used within the Sequence Read Archive) is `SRS6947643`.    
 
 Both values correspond to one another and are helpful identifiers. 
 
 The SRR (sample run accession number) is the unique identifier within SRA   
-and corresponds to the specific sequencing run within SRA. 
+and corresponds to the specific sequencing run. 
 
-In a later tutorial, we will discuss how we can download this file within julia with the SRR.
+In a later tutorial, we will discuss how to download this file in Julia using the SRR.
 
 But for now, the file can be downloaded using curl 
 
@@ -164,10 +179,11 @@ julia> records[1:10]
  All of the nucleotides in all of the reads have a quality score of `$`, which corresponds to a probabilty of error of 0.50119.  
  More information about how to convert ASCII values to quality scores [here](https://people.duke.edu/~ccc14/duke-hts-2018/bioinformatics/quality_scores.html).  
  This would be quite poor if we were looking at Illumia data.  
- However, because of how Pacbio chemistry works,  
- the quality scores are often flattened and there is simply a placeholder value on this line.  
- This does not mean our reads are trash!  
+ However, because of how PacBio chemistry works,  
+ quality scores are often flattened and there is simply a placeholder value on this line.  
+ This does not mean our reads are low quality!  
  Now that we've learned how to read files in and manipulate them a bit,  
-let's see if we can align the mecA gene to the Staphylococcus aureus genome.  
+let's see if we can align the _mecA_ gene to the _Staphylococcus aureus_ genome.  
+This will tell us if this _S. aureus_ is MRSA.