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Comments on "incomplete final line" warning

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hyginn 2017-10-12 21:50:30 -04:00
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commit edb245f818
1 changed files with 41 additions and 18 deletions
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FND-Genetic_code.R
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@ -3,15 +3,15 @@
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the FND-Genetic_code unit. # R code accompanying the FND-Genetic_code unit.
# #
# Version: 1.0 # Version: 1.0.1
# #
# Date: 2017 09 28 # Date: 2017 10 12
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.0.1 Comment on "incomplete final line" warning in FASTA
# 1.0 First live version # 1.0 First live version
# #
#
# TODO: # TODO:
# #
# #
@ -22,20 +22,22 @@
# going on. That's not how it works ... # going on. That's not how it works ...
# #
# ============================================================================== # ==============================================================================
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ---------------------------------------------------------- #TOC> ----------------------------------------------------------
#TOC> 1 Storing the genetic code 41 #TOC> 1 Storing the genetic code 43
#TOC> 1.1 Genetic code in Biostrings 59 #TOC> 1.1 Genetic code in Biostrings 61
#TOC> 2 Working with the genetic code 86 #TOC> 2 Working with the genetic code 88
#TOC> 2.1 Translate a sequence. 115 #TOC> 2.1 Translate a sequence. 117
#TOC> 3 An alternative representation: 3D array 176 #TOC> 3 An alternative representation: 3D array 199
#TOC> 3.1 Print a Genetic code table 209 #TOC> 3.1 Print a Genetic code table 232
#TOC> 4 Tasks 235 #TOC> 4 Tasks 258
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
# = 1 Storing the genetic code ============================================ # = 1 Storing the genetic code ============================================
@ -121,6 +123,19 @@ c(names(GENETIC_CODE)[GENETIC_CODE == "M"],
# read it # read it
mbp1 <- readLines("./data/S288C_YDL056W_MBP1_coding.fsa") mbp1 <- readLines("./data/S288C_YDL056W_MBP1_coding.fsa")
# You will notice that this generates a Warning message:
# Warning message:
# In readLines("./data/S288C_YDL056W_MBP1_coding.fsa") :
# incomplete final line found on './data/S288C_YDL056W_MBP1_coding.fsa'
# The reason for this is that the last character of the file is the letter "A"
# and not a "\n" line break. This file is exactly how it was sent from the
# server; I think good, defensive programming practice would have been to
# include some kind of an end-marker in the file, like a final "\n". This helps
# us recognize an incomplete transmission. Let's parse the actual sequence from
# the file, and then check for completeness.
head(mbp1) head(mbp1)
# drop the first line (header) # drop the first line (header)
@ -130,16 +145,18 @@ head(mbp1)
# concatenate it all to a single string # concatenate it all to a single string
mbp1 <- paste(mbp1, sep = "", collapse = "") mbp1 <- paste(mbp1, sep = "", collapse = "")
# how long ist it? # how long is it?
nchar(mbp1) nchar(mbp1)
# how many codons? # how many codons?
nchar(mbp1)/3 nchar(mbp1)/3
# That looks correct for the 833 aa sequence plus 1 stop codon. # That looks correct for the 833 aa sequence plus 1 stop codon. This gives us a
# first verification that the file we read is complete, the nucleotides of a
# complete ORF should be divisible by 3.
# Extract the codons. There are many ways to split a long string into chunks # Extract the codons. There are many ways to split a long string into chunks
# of three characters. Here we use Biostrings codons() function. codons() # of three characters. Here we use the Biostrings codons() function. codons()
# requires an object of type DNAstring - a special kind of string with # requires an object of type DNAstring - a special kind of string with
# attributes that are useful for Biostrings. Thus we convert the sequence first # attributes that are useful for Biostrings. Thus we convert the sequence first
# with DNAstring(), then split it up, then convert it into a plain # with DNAstring(), then split it up, then convert it into a plain
@ -155,11 +172,17 @@ for (i in seq_along(mbp1Codons)) {
mbp1AA[i] <- GENETIC_CODE[mbp1Codons[i]] mbp1AA[i] <- GENETIC_CODE[mbp1Codons[i]]
} }
head(mbp1Codons)
head(mbp1AA) head(mbp1AA)
tail(mbp1Codons)
tail(mbp1AA) # Note the stop! tail(mbp1AA) # Note the stop!
# We can work with this vector, for example if we want to tabulate the amino # The TAA "ochre" stop codon is our second verification that the nucleotide
# acid frequencies: # sequence is complete: a stop codon can't appear internally in an ORF.
# We can work with the mbp1AA vector, for example to tabulate the
# amino acid frequencies:
table(mbp1AA) table(mbp1AA)
sort(table(mbp1AA), decreasing = TRUE) sort(table(mbp1AA), decreasing = TRUE)