4. Inspecting and Manipulating Text Data with Unix Tools - Part 2¶

Lesson Objectives

insertion, deletion, search and replace(substitution) with sed
Use specialised language awk to do a variety of text-processing tasks
Quick overview of bioawk (an extension of awk to process common biological data formats)

sed¶

The streamline editor or sed command is a stream editor that reads one or more text files, makes changes or edits according to editing script, and writes the results to standard output. First, we will discuss sed command with respect to search and replace function.

Find and Replace¶

Most common use of sed is to substitute text, matching a pattern. The syntax for doing this in sed is as follows:

sed 'OPERATION/REGEXP/REPLACEMENT/FLAGS' FILENAME

Here, / is the delimiter (you can also use _ (underscore), | (pipe) or : (colon) as delimiter as well)
OPERATION specifies the action to be performed (sometimes if a condition is satisfied).
- The most common and widely used operation is s which does the substitution operation
- Other useful operators include y for transformation, i for insertion, d for deletion etc.).
REGEXP and REPLACEMENT specify search term and the substitution term respectively for the operation that is being performed.
FLAGS are additional parameters that control the operation. Some common FLAGS include:
- g replace all the instances of REGEXP with REPLACEMENT (globally)
- N where N is any number, to replace Nth instance of the REGEXP with REPLACEMENT
- p if substitution was made, then prints the new pattern space
- i ignores case for matching REGEXP
- w file If substitution was made, write out the result to the given file
- d when specified without REPLACEMENT, deletes the found REGEXP

Some find and replace examples

Find and replace all chr to chromosome in the example.bed file and append the the edit to a new file names example_chromosome.bed

sed 's/chr/chromosome/g' example.bed > example_chromosome.bed

Find and replace chr to chromosome, only if you also find 40 in the line

This will follow the format sed '/SEARCH_STRING/OPERATION/REGEXP/REPLACEMENT/FLAGS' FILENAME where SEARCH_STRING is 40
```
sed '/40/s/chr/chromosome/g' example.bed > example_40.bed
```

Find and replace directly on the input, but save an old version too

sed -i.old 's/chr/chromosome/g' example.bed

-i to edit files in-place instead of printing to standard output

Print specific lines of the file

To print a specific line you can use the address function. Note that by default, sed will stream the entire file, so when you are interested in specific lines only, you will have to suppress this feature using the option -n

-n, --quiet, --silent = suppress automatic printing of pattern space

print 5^th line of example.bed

sed -n '5p' example.bed

We can provide any number of additional lines to print using -e option. This tells sed to execute the next command line argument as sed program Let's print line 2 and 5,

sed -n -e '2p' -e '5p' example.bed

It also accepts range, using ,. Let's print line 2-6,

sed -n '2,6p' example.bed

Also, we can create specific pattern, like multiples of a number using ~. Let's print every tenth line of Mus_musculus.GRCm38.75_chr1.bed starting from 10, 20, 30.. to end of the file

sed -n '10~10p' Mus_musculus.GRCm38.75_chr1.bed

Exercise 4.4

Can you use the above ~ trick to extract all the odd numbered lines from Mus_musculus.GRCm38.75_chr1.bed and append the output to a new file odd_sed.bed

One of the powerful features is that we can combine these ranges or multiples in any fashion. Example: fastq files have header on first line and sequence in second, next two lines will have the quality and a blank extra line (four lines make one read). Sometimes we only need the sequence and header

code

sed -n '1~4p;2~4p' SRR097977.fastq

Sanity Check

It's not a bad practice validate some of these commands by comparing the output from another command. For an example, above sed -n '1~4p;2~4p' SRR097977.fastq should print exactly half the number of lines in the file as it is removing two lines per read. Do a quick sanity check with sed -n '1~4p;2~4p' SRR097977.fastq | wc -l & cat SRR097977.fastq | wc -l

We can use the above trick to convert the .fastq to .fasta

sed -n '1~4p;2~4p' SRR097977.fastq  | sed 's/^@/>/g' > SRR097977.fasta

Optional (Advanced) -Let's say that we want capture all the transcript names from the last column (9^th column) from .gtf file. We can write something similar to:

code

grep -v "^#" Mus_musculus.GRCm38.75_chr1.gtf | head -n 3 | sed -E 's/.*transcript_id "([^"]+)".*/\1/'

-E option to enable POSIX Extended Regular Expressions (ERE)

POSIX Regular and Exetended Regular Expressions

POSIX Basic Regular Expressions

POSIX or “Portable Operating System Interface for uniX” is a collection of standards that define some of the functionality that a (UNIX) operating system should support. One of these standards defines two flavors of regular expressions. Commands involving regular expressions, such as grep and egrep, implement these flavors on POSIX-compliant UNIX systems. Several database systems also use POSIX regular expressions.

The Basic Regular Expressions or BRE flavor standardizes a flavor similar to the one used by the traditional UNIX grep command. This is pretty much the oldest regular expression flavor still in use today. One thing that sets this flavor apart is that most meta-characters require a backslash to give the metacharacter its flavor. Most other flavors, including POSIX ERE, use a backslash to suppress the meaning of metacharacters. Using a backslash to escape a character that is never a metacharacter is an error.

POSIX Extended Regular Expressions

The Extended Regular Expressions or ERE flavor standardizes a flavor similar to the one used by the UNIX egrep command. “Extended” is relative to the original UNIX grep, which only had bracket expressions, dot, caret, dollar and star. An ERE support these just like a BRE. Most modern regex flavors are extensions of the ERE flavor. By today’s standard, the POSIX ERE flavor is rather bare bones. The POSIX standard was defined in 1986, and regular expressions have come a long way since then.

The developers of egrep did not try to maintain compatibility with grep, creating a separate tool instead. Thus egrep, and POSIX ERE, add additional metacharacters without backslashes. You can use backslashes to suppress the meaning of all metacharacters, just like in modern regex flavors. Escaping a character that is not a meta-character is an error.

Output is not really what we are after,

1  pseudogene  gene    3054233 3054733 .   +   .   gene_id "ENSMUSG00000090025"; gene_name "Gm16088"; gene_source "havana"; gene_biotype "pseudogene";
ENSMUST00000160944
ENSMUST00000160944

The is due to sed default behaviour where it prints every line, making replacements to matching lines. .i.e Some lines of the last column of Mus_musculus.GRCm38.75_chr1.gtf don't contain transcript_id. So, sed prints the entire line rather than captured group. One way to solve this would be to use grep transcript_id before sed to only work with lines containing the string transcript_id . However, sed offers a cleaner way. First, disable sed from outputting all lines with -n ( can use --quiet or --silent as well .i.e. suppress automatic printing of pattern space). Then, by appending p (Print the current pattern space) after the last slash sed will print all lines it’s made a replacement on. The following is an illustration of -n used with p:

code

grep -v "^#" Mus_musculus.GRCm38.75_chr1.gtf | head -n 3 | sed -E -n 's/.*transcript_id "([^"]+)".*/\1/p'

This example uses an important regular expression idiom: capturing text between delimiters (in this case, quotation marks). This is a useful pattern, so let’s break it down:

First, match zero or more of any character ( .* ) before the string "transcript_id" .
Then, match and capture (because there are parentheses around the pattern) one or more characters that are not a quote. This is accomplished with [^"]+ , the important idiom in this example. In regular extension jargon, the brackets make up a character class. Character classes specify what characters the expression is allowed to match. Here, we use a caret ( ^ ) inside the brackets to match anything except what’s inside these brackets (in this case, a quote). The end result is that we match and capture one or more nonquote characters (because there’s a trailing + ). This approach is nongreedy; often beginners make the mistake of taking a greedy approach and use .* . Consider:

Aho, Weinberger, Kernighan = AWK¶

Awk is a scripting language used for manipulating data and generating reports. The awk command programming language requires no compiling and allows the user to use variables, numeric functions, string functions, and logical operators.

Awk is a utility that enables a programmer to write tiny but effective programs. These take the form of statements that define text patterns that are to be searched for in each line of a document, and the action that is to be taken when a match is found within a line.

Awk is mostly used for pattern scanning and processing. It searches one or more files to see if they contain lines that match with the specified patterns and then perform the associated actions.

WHAT CAN WE DO WITH AWK?

AWK Operations:
- Scans a file line by line
- Splits each input line into fields
- Compares input line/fields to pattern
- Performs action(s) on matched lines
Useful For:
- Transform data files
- Produce formatted reports
Programming Constructs:
- Format output lines
- Arithmetic and string operations
- Conditionals and loops

There are two key parts for understanding the Awk language: how Awk processes records, and pattern-action pairs. The rest of the language is quite simple.

Awk processes input data a record (line) at a time. Each record is composed of fields (column entries) that Awk automatically separates. Awk assigns the entire record to the variable $0, field one’s value to $1, field two’s value to $2, etc.
We build Awk programs using one or more of the following structures: pattern { action }. Each pattern is an expression or regular expression pattern. In Awk lingo, these are pattern-action pairs and we can chain multiple pattern-action pairs together (separated by semicolons). If we omit the pattern, Awk will run the action on all records. If we omit the action but specify a pattern, Awk will print all records that match the pattern.

Syntax:

awk options 'selection_criteria {action}' input-file >  output-file

Options

-f program-file OR --file program-file: Reads the AWK program source from the file program-file, instead of from the first command line argument.

-F fsOR --field-separator fs : Use fs for the input field separator

Default behaviour of awk is to print every line of data from the specified file. .i.e. mimics cat

awk '{print}' example.bed

Output

chromosome1 26  39
chromosome1 32  47
chromosome3 11  28
chromosome1 40  49
chromosome3 16  27
chromosome1 9   28
chromosome2 35  54
chromosome1 10  19

Print lines which match the given pattern

awk '/chromosome1/{print}' example.bed

chromosome1    26  39
chromosome1    32  47
chromosome1    40  49
chromosome1    9   28
chromosome1    10  19

awk can be used to mimic functionality of cut

awk '{print $2 "\t" $3}' example.bed

\t for tab separated ( Refer to Special meanings of certain escaped characters in supplementary )

Output

Here, we’re making use of Awk’s string concatenation. Two strings are concatenated if they are placed next to each other with no argument. So for each record, $2"\t"$3 concatenates the second field, a tab character, and the third field. However, this is an instance where using cut is much simpler as the equivalent of above is cut -f 2,3 example.bed

Let’s look at how we can incorporate simple pattern matching. Suppose we wanted to write a filter that only output lines where the length of the feature (end position - start position) was greater than 18. Awk supports arithmetic with the standard operators + , - , * , / , % (remainder), and ^ (exponentiation). We can subtract within a pattern to calculate the length of a feature, and filter on that expression:

awk '$3 - $2 > 18' example.bed

chromosome1    9   28
chromosome2    35  54

awk Comparison and Logical operations

Comparison	Description
`a == b`	a is equal to b
`a != b`	a is not equal to b
`a < b`	a is less than b
`a > b`	a is greater than b
`a <= b`	a is less than or equal to b
`a >= b`	a is greater than or equal to b
`a ~ b`	a matches regular expression pattern b
`a !~ b`	a does not match regular expression pattern b
`a && b`	logical a and b
`a \\|\\| b`	logical or a and b
`!a`	not a (logical negation)

We can also chain patterns, by using logical operators && (AND), || (OR), and ! (NOT). For example, if we wanted all lines on chromosome 1 with a length greater than 10:

code

awk '$1 ~ /chromosome1/ && $3 - $2 > 10' example.bed

chromosome1    26  39
chromosome1    32  47
chromosome1    9   28

First pattern, $1 ~ /chr1 specifies the regular expression (All Regular expressions are in slashes). We are matching the first field, $1 against the regular expression chr1.
Tilde ~ means match.
To do the inverse of match, we can use !~ OR !($1 ~ /chromosome1/)

Built-In Variables and special patterns In Awk

Awk’s built-in variables include the field variables $1, $2, $3, and so on ($0 is the entire line) — that break a line of text into individual words or pieces called fields.
- NR: keeps a current count of the number of input records. Remember that records are usually lines. Awk command performs the pattern/action statements once for each record in a file.
- NF: keeps a count of the number of fields within the current input record.
- FS: contains the field separator character which is used to divide fields on the input line. The default is “white space”, meaning space and tab characters. FS can be reassigned to another character (typically in BEGIN) to change the field separator.
- RS: stores the current record separator character. Since, by default, an input line is the input record, the default record separator character is a newline.
- OFS: stores the output field separator, which separates the fields when Awk prints them. The default is a blank space. Whenever print has several parameters separated with commas, it will print the value of OFS in between each parameter.
- ORS: stores the output record separator, which separates the output lines when Awk prints them. The default is a newline character. print automatically outputs the contents of ORS at the end of whatever it is given to print.
Also, there are two special patterns BEGIN & END
- BEGIN - specifies what to do before the first record is read in. Useful to initialise and set up variables
- END - what to do after the last record's processing is complete. Useful to print data summaries at the end of file processing

Examples

We can use NR to extract ranges of lines, too; for example, if we wanted to extract all lines between 3 and 5 (inclusive):

awk 'NR >= 3 && NR <=5' example.bed

    chr3   11  28
    chr1   40  49
    chr3   16  27

suppose we wanted to calculate the mean feature length in example.bed. We would have to take the sum feature lengths, and then divide by the total number of records. We can do this with:

awk 'BEGIN{s = 0}; {s += ($3-$2)}; END{ print "mean: " s/NR};' example.bed 

  mean: 14

Explain please

In this example, we’ve initialized a variable s to 0 in BEGIN (variables you define do not need a dollar sign). Then, for each record we increment s by the length of the feature. At the end of the records, we print this sum s divided by the number of records NR , giving the mean.

awk makes it easy to convert between bioinformatics files like BED and GTF. Can you generate a three-column BED file from Mus_muscu‐lus.GRCm38.75_chr1.gtf: ?

Follow this link for a quick recap on annotation formats
Note that the start site of features in the .bed file is 1 less than the start site of features in the .gtf file: .bed uses 0-indexing and .gtf uses 1-indexing .i.e. "chr 1 100" in a GTF/GFF is "chr 0 100" in BED
Let's build the command based on awk options 'selection_criteria {action}' input-file
- What is the selection_criteria ? ( hint- it evolves around a symbol. )
- There is a possibility of needing the "inverse of match" function in awk here which can be invoked with !
- For {action}, we will need the field IDs of the three columns. Based on pre-existing knowledge of annotation formats, it will be feild 1, 4 and 5. Don't foget the above note on 0 vs 1 indexing of start site

Help !

awk '!/^#/ { print $1 "\t" $4-1 "\t" $5}' Mus_musculus.GRCm38.75_chr1.gtf | head -n 3

1  3054232 3054733
1  3054232 3054733
1  3054232 3054733

Optional (Advanced) - awk also has a very useful data structure known as an associative array. Associative arrays behave like Python’s dictionaries or hashes in other languages. We can create an associative array by simply assigning a value to a key.

For example, suppose we wanted to count the number of features (third column) belonging to the gene “Lypla1.” We could do this by incrementing their values in an associative array:

awk '/Lypla1/ {feature[$3] += 1}; END {for (k in feature) print k "\t" feature[k]}' Mus_musculus.GRCm38.75_chr1.gtf

exon   69
CDS    56
UTR    24
gene   1
start_codon    5
stop_codon 5
transcript 9

Quick Intro to Arrays

The awk language provides one-dimensional arrays for storing groups of related strings or numbers. Every awk array must have a name. Array names have the same syntax as variable names; any valid variable name would also be a valid array name. But one name cannot be used in both ways (as an array and as a variable) in the same awk program.

Arrays in awk superficially resemble arrays in other programming languages, but there are fundamental differences. In awk, it isn’t necessary to specify the size of an array before starting to use it. Additionally, any number or string, not just consecutive integers, may be used as an array index.

In most other languages, arrays must be declared before use, including a specification of how many elements or components they contain. In such languages, the declaration causes a contiguous block of memory to be allocated for that many elements. Usually, an index in the array must be a nonnegative integer. For example, the index zero specifies the first element in the array, which is actually stored at the beginning of the block of memory. Index one specifies the second element, which is stored in memory right after the first element, and so on. It is impossible to add more elements to the array, because it has room only for as many elements as given in the declaration. (Some languages allow arbitrary starting and ending indices—e.g., ‘15 .. 27’—but the size of the array is still fixed when the array is declared.)

A contiguous array of four elements might look like below, conceptually, if the element values are eight, "foo", "", and 30.

Only the values are stored; the indices are implicit from the order of the values. Here, eight is the value at index zero, because eight appears in the position with zero elements before it.

Arrays in awk are different—they are associative. This means that each array is a collection of pairs—an index and its corresponding array element value:

The pairs are shown in jumbled order because their order is irrelevant

One advantage of associative arrays is that new pairs can be added at any time. For example, suppose a tenth element is added to the array whose value is "number ten". The result is:

Now the array is sparse, which just means some indices are missing. It has elements 0–3 and 10, but doesn’t have elements 4, 5, 6, 7, 8, or 9.

It’s worth noting that there’s an entirely Unix way to count features of a particular gene: grep , cut , sort , and uniq -c

code

grep "Lypla1" Mus_musculus.GRCm38.75_chr1.gtf | cut -f 3 | sort | uniq -c

However, if we needed to also filter on column-specific information (e.g., strand), an approach using just base Unix tools would be quite messy. With Awk, adding an additional filter would be trivial: we’d just use && to add another expression in the pattern.

Optional - `bioawk`¶

bioawk is an extension of awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original awk.

The original awk requires a YACC-compatible parser generator (e.g. Byacc or Bison). bioawk further depends on zlib so as to work with gzip'd files.

YACC

A parser generator is a program that takes as input a specification of a syntax, and produces as output a procedure for recognizing that language. Historically, they are also called compiler-compilers. YACC (yet another compiler-compiler) is an LALR(LookAhead, Left-to-right, Rightmost derivation producer with 1 lookahead token) parser generator. YACC was originally designed for being complemented by Lex.

Lex (A Lexical Analyzer Generator) helps write programs whose control flow is directed by instances of regular expressions in the input stream. It is well suited for editor-script type transformations and for segmenting input in preparation for a parsing routine.

bioawk features

It can automatically recognize some popular formats and will parse different features associated with those formats. The format option is passed to bioawk using -c arg flag. Here arg can be bed, sam, vcf, gff or fastx (for both fastq and FASTA). It can also deal with other types of table formats using the -c header option. When header is specified, the field names will used for variable names, thus greatly expanding the utility.`
There are several built-in functions (other than the standard awk built-ins), that are specific to biological file formats. When a format is read with bioawk, the fields get automatically parsed. You can apply several functions on these variables to get the desired output. Let’s say, we read fasta format, now we have $name and $seq that holds sequence name and sequence respectively. You can use the print function (awk built-in) to print $name and $seq. You can also use bioawk built-in with the print function to get length, reverse complement etc by using '{print length($seq)}'. Other functions include reverse, revcomp, trimq, and, or, xor etc.

Variables for each format

For the -c you can either specify bed, sam, vcf, gff, fastx or header. bioawk will parse these variables for the respective format. If -c header is specified, the field names (first line) will be used as variables (spaces and special characters will be changed to under_score).

bed	sam	vcf	gff	fastx
chrom	qname	chrom	seqname	name
start	flag	pos	source	seq
end	rname	id	feature	qual
name	pos	ref	start	comment
score	mapq	alt	end
strand	cigar	qual	score
thickstart	rnext	filter	filter
thickend	pnext	info	strand
rgb	tlen	group
blockcount	seq	attribute
blocksizes	qual
blockstarts

bioawk is not a default linux/unix utility. .i.e. Has to be installed. This is available as a module on NeSI HPC platforms which can be loaded with

code

module load bioawk/1.0

The basic idea of Bioawk is that we specify what bioinformatics format we’re working with, and Bioawk will automatically set variables for each field (just as regular Awk sets the columns of a tabular text file to $1, $1, $2, etc.). For Bioawk to set these fields, specify the format of the input file or stream with -c. Let’s look at Bioawk’s supported input formats and what variables these formats set:

code

bioawk

usage: bioawk [-F fs] [-v var=value] [-c fmt] [-tH] [-f progfile | 'prog'] [file ...]

bioawk -c help

bed:
   1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts 
sam:
   1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual 
vcf:
   1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info 
gff:
   1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute 
fastx:
   1:name 2:seq 3:qual 4:comment

As an example of how this works, let’s read in example.bed and append a column with the length of the feature (end position - start position) for all protein coding genes:

code

bioawk -c gff '$3 ~ /gene/ && $2 ~ /protein_coding/ {print $seqname,$end-$start}' Mus_musculus.GRCm38.75_chr1.gtf | head -n 4

Bioawk is also quite useful for processing FASTA/FASTQ files. For example, we could use it to turn a FASTQ file into a FASTA file:

code

bioawk -c fastx '{print ">"$name"\n"$seq}' SRR097977.fastq | head -n 4

>SRR097977.1
TATTCTGCCATAATGAAATTCGCCACTTGTTAGTGT
>SRR097977.2
GGTTACTCTTTTAACCTTGATGTTTCGACGCTGTAT

Note that Bioawk detects whether to parse input as FASTQ or FASTA when we use -c fastx.

Bioawk can also serve as a method of counting the number of FASTQ/FASTA entries:

bioawk -c fastx 'END{print NR}' SRR097977.fastq

Bioawk’s function revcomp() can be used to reverse complement a sequence:

bioawk -c fastx '{print ">"$name"\n"revcomp($seq)}' SRR097977.fastq | head -n 4

>SRR097977.1
ACACTAACAAGTGGCGAATTTCATTATGGCAGAATA
>SRR097977.2
ATACAGCGTCGAAACATCAAGGTTAAAAGAGTAACC

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4. Inspecting and Manipulating Text Data with Unix Tools - Part 2¶

sed¶

Find and Replace¶

Aho, Weinberger, Kernighan = AWK¶

Optional - bioawk¶

Optional - `bioawk`¶