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gnu_utils_04.md

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Redirecting and Piping Output

Now that you can view and filter files, it would be good to save that information without copying and pasting the text from your terminal. Luckily, Linux employs redirection for communication between processes and writing to files. In this section, we will explore the following commands

  • > - stdout
  • >> - append
  • < - stdin
  • | - pipe

We will again be using the data you generated for viewing files. If you no longer have these files, plese go back and regenerate them.

Redirecting Output

When the > character is placed at the end of a command, it instructs the shell to write the ouput into a file instead of printing it to your terminal.

$ head -n 8 SRR2014925_1.fastq > two_reads.fastq

You can then use cat or head to see the output of the new file two_reads.fastq.

$ ls *fastq
$ cat two_reads.fastq

This is especially useful when dealing with large outputs

$ head -n 400000 SRR2014925_1.fastq > 100k_reads.fastq

Explore

  • Write all exons from ecoli.gff3 to a file
  • Write all SRR2014925 reads to a single file

Appending Output

The >> command will do everything that > does, but instead of writing to the beginning of a file, it will append the text to an existing file.

$ cat fileA.bed > one.bed
$ cat fileB.bed > one.bed
$ cat one.bed

$ cat fileA.bed >> two.bed
$ cat fileB.bed >> two.bed
$ cat two.bed

This command is useful when you want to combine the output from multiple commands into a single file. Just remember that >> will append to any existing files, so you may have to delete your output file between runs.

$ head -n 4 SRR2014925_1.fastq >> one.bed
$ cat one.bed

Your scripts should either delete the old file

$ rm one.bed
$ head -n 4 SRR2014925_1.fastq >> one.bed

or not use append the first time.

$ head -n 4 SRR2014925_1.fastq > one.bed
$ head -n 4 SRR2014925_1.fastq >> one.bed

Explore

  • Write the first two reads from both SRR2014925 fastq files to a single file
  • Write all exons and gene records from ecoli.gff3 to a single file

Redirecting Input

If your program reads from stdin, you can also redirect a file to it on the command line.

$ head < fileA.bed

While turning a simple file into an input may not seem useful, taking a command and using it like a file is much more useful.

$ tail -n 1 <( head fileA.bed )

Gives you the 10th line of fileA.bed. You can also chain multiple input redirections together to process complex workflows.

$ head <( uniq <( cut -f 3 ecoli.gff3 ) )

Some commands also accept multiple inputs, and redirection also works in this case.

$ head <( cat fileA.bed ) <( cat fileB.bed )

Piping Output

Everyone that has interacted with bioinformatics has probably heard the term "pipeline" when referring to scripts. This term originates from creating scripts that chain multiple commands together with the | character. The pipe is a form of redirection, but instead of writing the output to a file, it uses it as input to another program. Right now, you can make a pipeline with temporary files.

$ grep "NZ_CP013024.1" ecoli.gff3 > NZ_CP013024.1.gff3
$ grep "exon" NZ_CP013024.1.gff3 > NZ_CP013024.1_exons.gff3

But pipes allow you to simplify your workflow down to

$ grep "NZ_CP013024.1" ecoli.gff3 | grep "exon" NZ_CP013024.1.gff3 > NZ_CP013024.1_exons.gff3

while also producing the same output. You can even simplify our nested input example.

$ cut -f 3 ecoli.gff3 | uniq | head

Counting lines

While not a redirection command, wc is an extremely useful command that counts characters or lines.

$ echo -n "1234" | wc -c

$ head fileA.bed | wc -l

Exercises

  • Print the first three exon records in ecoli.gff3 in a single command
  • For each record, only print the name value
    • Name=MJ49_RS00725; => MJ49_RS00725
  • Count how many sequences are in ecoli.fasta


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