#Importing Fasta files
#Reading in fasta file
myFasta <- read.FASTA('MT103168.fasta')
#Reading the columns of myFasta to determine names and structure of data columns
head(myFasta)## 1 DNA sequence in binary format stored in a list.
##
## Sequence length: 1560
##
## Label:
## MT103168.1 Bifidobacterium longum strain BB536 cell division...
##
## Base composition:
## a c g t
## 0.156 0.319 0.289 0.236
## (Total: 1.56 kb)str(myFasta)## List of 1
## $ MT103168.1 Bifidobacterium longum strain BB536 cell division protein FtsW (rodA) gene, complete cds: raw [1:1560] 88 18 48 88 ...
## - attr(*, "class")= chr "DNAbin"#Importing FASTQ files
#Reading in fastq file
myFastq <- read.fastq('ERR1072710.fastq')
#Reading the columns of myFastq to determine names and structure of data columns
head(myFastq)## 3 DNA sequences in binary format stored in a list.
##
## Mean sequence length: 183.667
## Shortest sequence: 146
## Longest sequence: 259
##
## Labels:
## ERR1072710.1 10317.000001315_0 length=151
## ERR1072710.2 10317.000001315_1 length=116
## ERR1072710.4 10317.000001315_3 length=151
##
## Base composition:
## a c g t
## 0.318 0.208 0.254 0.219
## (Total: 551 bases)str(myFastq)## List of 3
## $ ERR1072710.1 10317.000001315_0 length=151: raw [1:146] 18 18 88 88 ...
## $ ERR1072710.2 10317.000001315_1 length=116: raw [1:259] 18 28 18 28 ...
## $ ERR1072710.4 10317.000001315_3 length=151: raw [1:146] 28 28 88 28 ...
## - attr(*, "class")= chr "DNAbin"
## - attr(*, "QUAL")=List of 7
## ..$ ERR1072710.1 10317.000001315_0 length=151: num [1:11] 32 38 51 34 32 34 32 34 32 38 ...
## ..$ ERR1072710.2 10317.000001315_1 length=116: num [1:11] 30 30 30 30 30 30 30 30 30 30 ...
## ..$ ERR1072710.4 10317.000001315_3 length=151: num [1:42] 10 36 49 49 16 15 22 17 22 16 ...
## ..$ NA : num [1:70] 51 32 34 38 38 32 38 38 38 51 ...
## ..$ NA : num [1:67] 30 30 30 30 30 30 30 30 30 30 ...
## ..$ NA : num [1:11] 32 51 51 32 38 32 38 34 34 51 ...
## ..$ NA : num [1:11] 30 30 30 30 30 30 30 30 30 30 ...#Importing VCF files
#Reading the lines in myVCF that do NOT contain any '#' symbols
myVCF <- read.table('TwoVariants.vcf')
#Reading the lines in myVCF that DO contain any '#' symbols to identify names and structure of file
myLines <- read.csv('TwoVariants.vcf', sep = "\n")
names(myVCF) <- c('Chrom','Pos','ID','Ref','Alt','Qual','Filter','Info','Format','Values')
head(myVCF)## Chrom Pos ID Ref Alt Qual Filter Info
## 1 NZ_BCYL01000006.1 29 . A G . . AC=84;AF=1.0;SB=0.0
## 2 NZ_BCYL01000006.1 145 . A G . . AC=114;AF=1.0;SB=0.0
## Format Values
## 1 GT:AC:AF:SB:NC 1:84:1.0:0.0:+G=37,-G=47,
## 2 GT:AC:AF:SB:NC 1:114:1.0:0.0:+G=42,-G=72,str(myVCF)## 'data.frame': 2 obs. of 10 variables:
## $ Chrom : chr "NZ_BCYL01000006.1" "NZ_BCYL01000006.1"
## $ Pos : int 29 145
## $ ID : chr "." "."
## $ Ref : chr "A" "A"
## $ Alt : chr "G" "G"
## $ Qual : chr "." "."
## $ Filter: chr "." "."
## $ Info : chr "AC=84;AF=1.0;SB=0.0" "AC=114;AF=1.0;SB=0.0"
## $ Format: chr "GT:AC:AF:SB:NC" "GT:AC:AF:SB:NC"
## $ Values: chr "1:84:1.0:0.0:+G=37,-G=47," "1:114:1.0:0.0:+G=42,-G=72,"