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Find

A big part of data science is making sure what you expect in a particular file is what you have in that file. This is fairly easy when your files are small but is challenging when the files are much larger than your screen.

To explore this topic in more detail, navigate to the data/MiSeq/ directory.

cd ~/MiSeq
ls

FASTQ format

This directory contains multiple FASTQ files. A FASTQ file normally uses four lines per sequence.

  • Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).
  • Line 2 is the raw sequence letters.
  • Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
  • Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.

A FASTQ file containing a single sequence might look like this:

Info

An example FASTQ file

@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

We can use the cat command to print fastq files to the screen, but thousands of lines of text would crowd your screen. Instead, we will use the head command to view the first 8 lines of the file. You can copy the file name below and paste it into the console or you can type and use tab complete to pick a particular file.

head -n 4 F3D0_S188_L001_R1_001.fastq
@M00967:43:000000000-A3JHG:1:1101:18327:1699 1:N:0:188
NACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG
+
AABABBFFFGGGGGGGGGGGGGGGGHHHHHHHGGGHHHHHGHGGGGGGGHGGGG[email protected]DHHGHEGGGGGGBFGGEGGGGGGGG.DFEFFFFFFFDCFFFFFFFFFFFFFFFFFFFFFFFFFFDFDFFFEFFCFF?FDFFFFFFFFAFFFFFFFFFFFBDDFFFFFEFADFFFFFBAFFFA?EFFFBFF
@M00967:43:000000000-A3JHG:1:1101:14069:1827 1:N:0:188
TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG
+
3AA?ABBDBFFBEGGEGGGGAFFGGGGGHHHCGGGGGGHFGHGGCFDEFGGG[email protected][email protected]@BGGGEGCEBFFFBFFB;[email protected]FFDDFAFFFFF.AF9/FBBBBB.EAFFE?F

head prints the first ten lines of a file out onto your screen. Similarly, the tail command prints the last 10 lines of a file.

tail -4 F3D0_S188_L001_R1_001.fastq
@M00967:43:000000000-A3JHG:1:1105:19125:28016 1:N:0:188
TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGGGGGGGGCAAAAA
+
>AAAAFFBBBBDGFGGGEGFG[email protected][email protected]@EF/BFFF9//9FF;B.;.:F//9A.;9.9;B/////BFDB9FF.AAB/:?B-;[email protected];EA/;B99BE99B///B:9.;:9F..;9=-FD.9A-;@BB----?F..
@M00967:43:000000000-A3JHG:1:1105:20429:28046 1:N:0:188
TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACA
+
BBBBBBBBBFFFGGGFFGGGGGGGGGGGHHHHHHHGGGHGHHHGHGGGGGGGHGGEGGFGGHGHHHHHHHHHGHHHHEHHGGGGGGHHHHHHHGGGGGHHHGFHHHHGGHHHHHGGGGGHFGH?GHHGHHHHGG<CDFHGGGGGHCFGHHHHEHFHCGCGEFFGGGGGGEGGEFGGGFFFFGGG/FDCFFFFFADFFFFFDFFFFFFFFFABFFFFF?DFFFE.EEFFFEFFFFAAFADFFFFECDEFB..

FASTA format

FASTQ files should not be confused with FASTA files. FASTQ files contain information about the quality of the sequence, but FASTA files only contain the sequence and an identifier.

Info

An Example FASTA file

> SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH

Let's look at a synthetic FASTA file.

head -4 HMP_MOCK.v35.fasta 
> A.baumannii.1 
TGGGGAATATTGGACAATGGGGGGAACCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGCCTTATGGTTGTAAAGCACTTTAAGCGAGGAGGAGGCTACTTTAGTTAATACCTAGAGATAGTGGACGTTACTCGCAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGATGTCTACTAGCCGTTGGGGCCTTTGAGGCTTTAGTGGCGCAGCTAACGCGATAAGTAGACCGCCTGGGGAGTACGGTC
> A.odontolyticus.1
TGGGGAATATTGCACAATGGGCGAAAGCCTGATGCAGCGACGCCGCGTGAGGGATGGAGGCCTTCGGGTTGTAAACCTCTTTCGCTCATGGTCAAGCCGCAACTCAAGGTTGTGGTGAGGGTAGTGGGTAAAGAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGTTGGGCACTAGGTGTGGGGGCCACCCGTGGTTTCTGCGCCGTAGCTAACGCTTTAAGTGCCCCGCCTGGGGAGTACGGCC

FASTQ and FASTA files are often used in combination to map reads to a genome or transcription. You have seen three ways to read large files. Next, we will learn how to use and manipulate the files.

Wildcards

Sometimes you know a file or directory exists, but you cannot find it. Sometimes you want to find many files with similar properties. This is where the wildcard (*) comes in handy. What do the following commands do?

  1. ls *
  2. ls MiSeq/F3D*
  3. ls MiSeq/*fasta
  1. ls * lists files in the working directory and 1 level down.
  2. ls MiSeq/F3D* lists files in the data/MiSeq directory that start with "F3D".
  3. ls MiSeq/*fasta lists files in the data/MiSeq directory that end with "fasta".

grep

A lot of the time we want to know if a file contains what we expect. A useful thing to do is search the contents of files for a particular string of characters you would like to find. We can use the file pattern searcher grep to find things.

The MiSeq/ directory contains many of the sequence files ending in.fastq. We expect these files to contain information in a particular format throughout the file with four lines of information for each sequence string. Looking through a million-line file using less would take a long time. Rather than manually looking at the whole file, we can print only a portion of the file's contents to standard output.

Let's say you would like to find the sequence CATTAG in your MiSeq files. We can use the function grep to search for CATTAG in one or all of the fastq files located in our current working directory.

grep CATTAG F3D0_S188_L001_R2_001.fastq
grep CATTAG *.fastq

What line does CATTAG occur on in F3D141_S207_L001_R1_001.fastq?

Use grep --help to search for grep options related to line number. grep -n [filename] will print the line number.

In addition to searching for nucleotide sequences, you may want to search for information in the first line of a .fastq or .fasta file. The ^ (shift + 6) can be used to specify "the beginning of the line".

grep "^>" *fasta

This will print the name associated with a given sequence in the searched files. In this case, there is only one fasta file, so the name is not printed.

>A.baumannii.1
>A.odontolyticus.1
>B.cereus.1
...
>S.agalactiae.1
>S.mutans.1
>S.pneumoniae.1

We can also print the line before or after the line that matches a pattern with -B 1 -A 1, respectively.

grep -A 1 "^>" *fasta

This will print the name and sequence for every entry. The first is shown here.

>A.baumannii.1
TGGGGAATATTGGACAATGGGGGGAACCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGCCTTATGGTTGTAAAGCACTTTAAGCGAGGAGGAGGCTACTTTAGTTAATACCTAGAGATAGTGGACGTTACTCGCAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGATGTCTACTAGCCGTTGGGGCCTTTGAGGCTTTAGTGGCGCAGCTAACGCGATAAGTAGACCGCCTGGGGAGTACGGTC

find

As you have seen, grep is very useful for finding things within files, and the * or wildcard is useful for listing files that match a partial pattern. But, how do we find files when we do not know their location? The find command.

Let's navigate back to our home directory and use the find command to look for .fasta files. Use the -name flag to specify that you are looking for a file with the name listed in double quotes. Use the * wildcard to only search for files with a specific extension.

cd ~
find . -name "*.fasta"

This reveals that .fasta files were found in both the books and the MiSeq directories.

./books/yeast.fasta
./MiSeq/HMP_MOCK.v35.fasta
  1. Which directories contain a README.md file?
  2. Which directories contain images?

Use the commands:

find . -name "README.md"
find . -name "*.png"
to show the following README.md files

./seattle/README.md
./books/README.md
./MiSeq/README.md
./README.md
./southpark/README.md

and the following images.

./images/rstudio-binder-setup.png
./images/MiSeq-readcount-Mothur.png
./rstudio-terminal.png
./CFDE-logo.png

Key points

Command Description
find [filename] finds files with specific properties that match patterns
grep [option] [filename] selects lines in files that match patterns
find [path] [conditions] finds files with specific properties that match patterns

Last update: June 23, 2022