Patterns, Filters, and Pipes

Pattern Matching

Wildcards (special characters) can be used in several ways:

  • Standard wildcards (globbing) – matching to work on a set of files
  • Regular expressions – matching to work within files

Standard Expansion Patterns

Standard wildcards are used for globbing files – pulling together files to perform an action on them.

Wildcard Represents
*

0 or more characters

  • a*e would match ae, a103e, apple
?

Any single character

  • a?e would match a1e, ape, are
[]

Any one of the characters within the brackets (comma separated list)

  • m[a,3,n]s would match mas, m3s, mns
  • [1-3]a would match 1a, 2a, 3a
{}

Any term within the brackets (comma separated list)

  • ls {*.doc, *.pdf} would list all files ending in .doc and .pdf
[!]

Anything except (negate) the character within the brackets (comma separated list)

  • ls *[!A,B].txt would match 123.txt, ZNEBF.txt, C.txt
\

“Escapes” the following character, to treat it as a non-special character

  • ls *\.*.txt would match this.file.txt, NOT this.txt

Let’s try some examples in our shell-lesson-data directory.

Q&A: How can we list all files in shell-lesson-data/north-pacific-gyre that end with .txt?

# change into directory 
cd ~/Desktop/shell-lesson-data/north-pacific-gyre

# use * wildcard to list all ending in .txt
ls *.txt
NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
NENE01751A.txt
NENE01751B.txt
NENE01812A.txt
NENE01843A.txt
NENE01843B.txt
NENE01971Z.txt
NENE01978A.txt
NENE01978B.txt
NENE02018B.txt
NENE02040A.txt
NENE02040B.txt
NENE02040Z.txt
NENE02043A.txt
NENE02043B.txt
this.file.txt
this.txt

Q&A: List the files in shell-lesson-data/north-pacific-gyre that do not end with .txt.

# change into directory 
cd ~/Desktop/shell-lesson-data/north-pacific-gyre

# use ! to with the [] to negate all files ending in .txt
ls *[!.txt]
goodiff.sh
goostats.sh

Q&A: List the files in shell-lesson-data/north-pacific-gyre with the last two positions before the suffix are a number lower than 5, followed by not Z.

# change into directory 
cd ~/Desktop/shell-lesson-data/north-pacific-gyre

# use ! to with the [] to negate all files ending in .txt
ls *[0-4][!Z].*
NENE01751A.txt
NENE01751B.txt
NENE01812A.txt
NENE01843A.txt
NENE01843B.txt
NENE02040A.txt
NENE02040B.txt
NENE02043A.txt
NENE02043B.txt

Regular Expressions (regex)

A complex form of pattern matching that combines “wildcards” to create powerful patterns for text matching and manipulation in files.

Tip

Used with grep to search for text – which we’ll explain in a bit.

  • regex symbols are interpreted by the commands above
What makes a pattern?

To efficiently represent a pattern, we need to develop a language that specifies

  • atom – the actual character that we want to match
  • positions – the location of this atom
  • number of times – how many times we see the atom
  • groups – groups of matched atoms or non-matched
Representing Atoms

Character classes are used to represent atoms.

Character class – Example Matches
Non-special characters – a a matches a
Dot – . . matches ANYTHING
Range – [a-z] [a-z] matches any letter from a through z
Character set – [abc] [abc] matches a, b, or c
Character set – [[:alnum:]] [[:alnum:]] matches any alpha-numeric character
Character set – [[:lower:]] [[:lower:]] matches any lowercase letter
Character set – [[:space:]] [[:space:]] matches any whitespace
Character set – [[:digit:]] | [[:digit:]] matches any digit |
Negated character set – [^abc] [^abc] matches anything except a, b, or c
Whitespace – \s \s matches any whitespace character
Non-whitespace – \S \S matches any non-whitespace character
Word – \w \w an entire word (continuous alpha-numeric or underscores)
Non-word – \W \W not a word
Digit – \d \d any digit
Non-digit – \D \D not a digit
Positions

Anchors are used to specify the location of characters or set of characters – so the pattern will only match if the position also matches.

Anchor Example(s)
Start of line/string – ^ ^a matches the a in apple, but not sandal
End of line/string – $ a$ matches the a in spa, but not space
Number of times

Quantifiers are used to specify the number of times preceeding characters or sets of characters are repeated.

Quantifier Example(s)
0 or 1 time – ? re?d matches rd, red, NOT reed, read
0 or more times – * re*d matches rd, red, reed, NOT read
1 or more times – + re+d matches red, reed, NOT rd, read
Specified number of times – {} re{1}d matches red, NOT rd, reed, read
Range of times – {1,3} re{1,3}d matches red, reed, NOT rd, read
Or – | re(e|a)d matches reed, read, NOT rd, red
Groups and Reference

Matched atoms can be grouped together and referenced later.

Grouping/Reference Example(s)
Capture the group – () (re)d groups re together
Reference the group – \1 \1 references the first group captured
Practicing with Regex

Learning regex takes time and practice!

Question 1:

Which expression will select only the in the following?

“The great thing about learning is that the experience itself teaches you something, though it may not be the thing you wanted to learn.”

  1. the
  2. (T|t)e
  3. [Tt]he
  4. *he
  1. Yes. This will match the.
  2. No. This will also match The.
  3. No. This will also match The.
  4. No. This will also match The.

Question 2:

Which expression will select all of the following?

foxes boxes loxes
  1. .oxes
  2. [fbl]oxes
  3. (f|b|l)oxes
  4. *oxes
  1. Yes. . will match anything for the first character.
  2. Yes. Uses character set matching.
  3. Yes. Uses or matching.
  4. No. * is a quantifier and references nothing.

Question 3:

Which expression will select all of the following?

nd ned need
  1. ne+d
  2. ne?d
  3. ne*d
  4. ne.d
  1. No. + matches e 1 or more times.
  2. No. ? matches e 0 or 1 times.
  3. Yes. * matches e 0 or more times.
  4. No. . matches anything one time exactly.

For more practice, I recommend RegexOne

Using regex with grep

Regular expressions are most effective when used with specific commands.

grep – globally search a regular expression and print

Searches for a pattern within a file and returns the line containing the pattern.

Tip

By default, grep returns the line containing the pattern and is case-sensitive.

A few of the useful options are below:

  • use -i to peform case-insensitive matching
  • use -v to return the non-matching lines
  • use -w to return the word instead of the line that matches
  • use -A to return the line after the matching line
  • use -B to return the line before the matching line
  • use -E to use extended regular expressions
  • use -c to return the number of times a match is seen
  • use -n to output the line number that matches
Command Options/Flags Arguments
grep flags pattern /path/to/file

Let’s try this on a few files in our shell-lesson-data/exercise-data/creatures directory.

If we take a look at top 5 lines of each file (head command) we see:

# cd into the directory
cd ~/Desktop/shell-lesson-data/exercise-data/creatures

# print the first 5 lines each file 
head -n 5 *
==> basilisk.dat <==
COMMON NAME: basilisk
CLASSIFICATION: basiliscus vulgaris
UPDATED: 1745-05-02
CCCCAACGAG
GAAACAGATC

==> minotaur.dat <==
COMMON NAME: minotaur
CLASSIFICATION: bos hominus
UPDATED: 1765-02-17
CCCGAAGGAC
CGACATCTCT

==> unicorn.dat <==
COMMON NAME: unicorn
CLASSIFICATION: equus monoceros
UPDATED: 1738-11-24
AGCCGGGTCG
CTTTACCTTA

Using grep, let’s pull out the common names line of all of the creatures.

# cd into the directory
cd ~/Desktop/shell-lesson-data/exercise-data/creatures

# grep COMMON NAME from all files ending in .dat 
grep 'COMMON NAME' *.dat
basilisk.dat:COMMON NAME: basilisk
minotaur.dat:COMMON NAME: minotaur
unicorn.dat:COMMON NAME: unicorn

Using grep, let’s check how many times the CCC is seen in each creatures genomic sequence.

# cd into the directory
cd ~/Desktop/shell-lesson-data/exercise-data/creatures

# grep COMMON NAME from all files ending in .dat 
grep -c 'CCC' *.dat
basilisk.dat:22
minotaur.dat:18
unicorn.dat:22

What if we want just the first line following the common name unicorn?

# cd into the directory
cd ~/Desktop/shell-lesson-data/exercise-data/creatures

# grep COMMON NAME from all files ending in .dat 
grep -A 1 'unicorn' *.dat
unicorn.dat:COMMON NAME: unicorn
unicorn.dat-CLASSIFICATION: equus monoceros

What if we wanted anything updates in the 1740’s? We need to use -E option to use the extended regular expressions we covered earlier.

# cd into the directory
cd ~/Desktop/shell-lesson-data/exercise-data/creatures

# grep COMMON NAME from all files ending in .dat 
grep -E '174\d-\d{2}-\d{2}' *.dat
basilisk.dat:UPDATED: 1745-05-02

As we can see, grep and pattern matching is useful, but it becomes even more powerful it we combine it with filtering.

Filtering

In unix, we can filter data in many ways. Here we’ll cover a few light, but useful commands to do so.

cut – filtering data from each line, cutting columns/fields out

Filter data (“cut”) based upon a separator.

Command Options/Flags Arguments
cut flags file/input
Tip

The cut command separates fields by tabs by default.

Some useful flags are below:

  • use -d to set the delimeter between fields to another character
  • use -f to list the fields to cut (can create a list -f 2,3 cuts field 2 and 3. -f 3-5 cuts field 3 to 5.)

Let’s take a look at the animals.csv file in shell-lesson-data/exercise-data/animal-counts.

# cd to directory
cd ~/Desktop/shell-lesson-data/exercise-data/animal-counts

# look at file
head -n 3 animals.csv
2012-11-05,deer,5
2012-11-05,rabbit,22
2012-11-05,raccoon,7

Let’s keep only the animals and counts – fields 2 and 3 if we consider the comma as the field separator.

# cd to directory
cd ~/Desktop/shell-lesson-data/exercise-data/animal-counts

# cut to keep the second field (-f), using comma as a field separator (-d)
cut -f2,3 -d ',' animals.csv
deer,5
rabbit,22
raccoon,7
rabbit,19
deer,2
fox,4
rabbit,16
bear,1

uniq – report or filter out repeated lines

Filters out repeated ADJACENT lines, but also allows for counting them, or ignoring a specific number of them.

Command Options/Flags Arguments
uniq flags input/file output/file
Tip

The uniq command is case sensitive by default and removes all duplicated adjacent lines. Thus, sorting prior is recommended.

Some useful flags are below:

  • use -c add the count of the number of times the line occurs
  • use -i to ignore case

If a file looked like this:

$ cat animals.txt
bear
deer
deer
fox
rabbit
rabbit
rabbit
raccoon

Then uniq, with counts would output

uniq -c animals.txt
   1 bear
   2 deer
   1 fox
   3 rabbit
   1 raccoon

sort – order lines of a file

Sorts a file or input in a highly customizable way.

Command Options/Flags Arguments
sort flags file/input
Tip

The sort command is case sensitive by default sorts lexiconically

Some useful flags are below:

  • use -t to specify the field separator
  • use -i to ignore case
  • use -c to check if a file is sorted
  • use -k to specify a field to sort on
  • use -u to keep unique lines
  • use -n to perform a numberic sort

Let’s sort the animals file by the second field (-k), using the commma as the field separator (-t).

# cd to directory
cd ~/Desktop/shell-lesson-data/exercise-data/animal-counts

# cut to keep the second field (-f), using comma as a field separator (-d)
sort -t , -k 2 animals.csv
2012-11-07,bear,1
2012-11-06,deer,2
2012-11-05,deer,5
2012-11-06,fox,4
2012-11-07,rabbit,16
2012-11-06,rabbit,19
2012-11-05,rabbit,22
2012-11-05,raccoon,7

grep – globally search a regular expression and print

Returns filtered lines, can also negate lines.

Command Options/Flags Arguments
grep flags pattern /path/to/file 
# cd to directory
cd ~/Desktop/shell-lesson-data/exercise-data/animal-counts

# give me the lines that do not have an animal that ends in r
grep -Ev ',\w+r,' animals.csv
2012-11-05,rabbit,22
2012-11-05,raccoon,7
2012-11-06,rabbit,19
2012-11-06,fox,4
2012-11-07,rabbit,16

Pipes

Pipes (|) are used to quickly connect unix commands by “piping” output of one command to the input of another.

command1 | command2 | command3

Download the gtf

We will download the file with wget or curl.

In the terminal, type which wget, and which curl.

  • If you see a path returned when you type one of those commands and press enter, then you have that command.
#check for wget
which wget

#check for curl
which curl
/Users/csifuentes/miniconda3/bin/wget
/usr/bin/curl

You can download the file as below, depending on the command you want to use.

# cd to ~/Desktop/shell-lesson-data
cd ~/Desktop/shell-lesson-data

# wget file (using capital -O as the flag to create a gzipped file named example.gtf.gz)
wget -O example.gtf.gz ftp://ftp.ensemblgenomes.org/pub/release-39/fungi/gtf/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/Cryptococcus_neoformans_var_grubii_h99.CNA3.39.gtf.gz
# cd to ~/Desktop/shell-lesson-data
cd ~/Desktop/shell-lesson-data

# wget file (using lowercase -o as the flag to create a gzipped file name example.gtf.gz)
curl -o example.gtf.gz ftp://ftp.ensemblgenomes.org/pub/release-39/fungi/gtf/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/Cryptococcus_neoformans_var_grubii_h99.CNA3.39.gtf.gz

You can unzip the file as below, depending on the command you want to use.

# cd to ~/Desktop/shell-lesson-data
cd ~/Desktop/shell-lesson-data

# gunzip file
gunzip example.gtf.gz
# cd to ~/Desktop/shell-lesson-data
cd ~/Desktop/shell-lesson-data

# view it
head example.gtf
#!genome-build CNA3
#!genome-version CNA3
#!genome-date 2015-11
#!genome-build-accession GCA_000149245.3
#!genebuild-last-updated 2015-11
1   ena gene    100 5645    .   -   .   gene_id "CNAG_04548"; gene_source "ena"; gene_biotype "protein_coding";
1   ena transcript  100 5645    .   -   .   gene_id "CNAG_04548"; transcript_id "AFR92135"; gene_source "ena"; gene_biotype "protein_coding"; transcript_source "ena"; transcript_biotype "protein_coding";
1   ena exon    5494    5645    .   -   .   gene_id "CNAG_04548"; transcript_id "AFR92135"; exon_number "1"; gene_source "ena"; gene_biotype "protein_coding"; transcript_source "ena"; transcript_biotype "protein_coding"; exon_id "AFR92135-1";
1   ena CDS 5494    5645    .   -   0   gene_id "CNAG_04548"; transcript_id "AFR92135"; exon_number "1"; gene_source "ena"; gene_biotype "protein_coding"; transcript_source "ena"; transcript_biotype "protein_coding"; protein_id "AFR92135"; protein_version "1";
1   ena start_codon 5643    5645    .   -   0   gene_id "CNAG_04548"; transcript_id "AFR92135"; exon_number "1"; gene_source "ena"; gene_biotype "protein_coding"; transcript_source "ena"; transcript_biotype "protein_coding";

GTF files contain the following information, as columns (fields)

  • chromosome name
  • annotation source
  • feature-type
  • genomic start
  • genomic end
  • score
  • strand
  • genomic phase
  • additonal information (gene_id, etc.)

Analysis

Using the commands we’ve learned thus far, let’s explore the example.gtf file to answer the following:

  1. How many chromosomes does the organism have?
  2. How many unique gene ids does the organism have?
  3. Which chromosome has the most genes?
How many chromosomes does the organism have?
# cd to directory
cd ~/Desktop/shell-lesson-data

# print the file to the screen to pipe it into grep
# remove the lines with #! because they'll get in the way
# cut to keep the first column (chromosomes)
# sort the chromosomes numerically, removing duplicates
cat example.gtf | grep -v '^#' | cut -f1 | sort -nu 
Mt
1
2
3
4
5
6
7
8
9
10
11
12
13
14

This organism has 14 + Mt chromosomes.

How many genes does the organism have?
# cd to directory
cd ~/Desktop/shell-lesson-data

# print the file to the screen to pipe it into grep
# remove the lines with #! because they'll get in the way
# cut to keep the third column (biotype)
# sort values
# keep unique values, specifying counts of each unique value
cat example.gtf | grep -v '^#' | cut -f3 | sort | uniq -c
49063 CDS
52036 exon
6923 five_prime_utr
8497 gene
7860 start_codon
3167 stop_codon
7034 three_prime_utr
9348 transcript

This organism has 8497 genes.

Which chromosome has the most genes?
# cd to directory
cd ~/Desktop/shell-lesson-data

# print the file to the screen to pipe it into grep
# remove the lines with #! because they'll get in the way
# cut to keep the first and third columns (chromosome, biotype)
# sort values
# keep unique values, specifying counts of each unique value to get totals of biotypes by chromosome
# pull out gene biotype totals
cat example.gtf | grep -v '^#' | cut -f1,3 | sort | uniq -c | grep 'gene'
1033 1  gene
 474 10 gene
 663 11 gene
 326 12 gene
 322 13 gene
 417 14 gene
 706 2  gene
 725 3  gene
 503 4  gene
 812 5  gene
 640 6  gene
 641 7  gene
 639 8  gene
 554 9  gene
  42 Mt gene

Chromosome 1 has the most genes, 1033. Mt has the least, 42.

As we can see, piping commands together allows us to easily perform analyses as a set of commands. In the next lesson, we’ll learn about how we can use loops and scripts to do this even more efficiently.