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cat, tac, head, and tail

Lesson Navigation

  1. Introduction
  2. cat, tac, head, and tail
  3. wc and nl
  4. sort, uniq, and cut
  5. split and shuf
  6. paste and join
  7. tr and sed
  8. grep
  9. diff and comm

cat

One way to quickly view text files is to print the contents to standard output (your terminal window) using cat. Let's take a look at the subsetA_CID_51351709_similar.txt file located in the /Udata2/View folder. First, use cd to change your directory to the folder:

user@computer:~$ cd /home/user/Desktop/Udata2/View

We can then use the cat utility to print the contents of a file to standard output:

user@computer:~$ cat subsetA_CID_5135709_similar.txt 
CC.CC1CCC2CC(=C(CC2C1)C=C)C=C	154673141	232.400
CC1CCCCC1C2=CC=CCC2	154546688	176.300
CC1CCCC2C1=CC=C3C2C=CC=C3	154307178	198.300
CCC1=CC=C2C(C1)C(CCC2(C)C)(C)C	154280750	218.380
CC1C(=C)CCC2C1=CC=CC2	154236167	160.250

A common use of cat is also to concatenate files. For example, let's say we wanted to combine the three subset*.txt files and redirect, >, the output to a new file named combined_test.txt:

user@computer:~$ cat subset*.txt > combined_test.txt

tac

We can display the contents of files in reverse using tac. Compare tac to our example above with cat:

user@computer:~$ tac subsetA_CID_5135709_similar.txt
CC1C(=C)CCC2C1=CC=CC2	154236167	160.250
CCC1=CC=C2C(C1)C(CCC2(C)C)(C)C	154280750	218.380
CC1CCCC2C1=CC=C3C2C=CC=C3	154307178	198.300
CC1CCCCC1C2=CC=CCC2	154546688	176.300
CC.CC1CCC2CC(=C(CC2C1)C=C)C=C	154673141	232.400

head

Instead of using cat or tac first, it is usually a good idea to look at a preview of the file, so we don't unnecessarily print 100s or 1000s of lines to the standard output. For example, the file CID_51351709_similar.txt has ~500 lines. We can use head to print the first 10 lines of the file:

user@computer:~$ head CID_51351709_similar.txt
CC.CC1CCC2CC(=C(CC2C1)C=C)C=C	154673141	232.400
CC1CCCCC1C2=CC=CCC2	154546688	176.300
CC1CCCC2C1=CC=C3C2C=CC=C3	154307178	198.300
CCC1=CC=C2C(C1)C(CCC2(C)C)(C)C	154280750	218.380
CC1C(=C)CCC2C1=CC=CC2	154236167	160.250
CC(=C)C1CCC2CCC=CC2C1	153974464	176.300
CC1CCC(C2C1C(C=CC2C)C)C	153940528	192.340
[2H]C1C=CC2=CC=C3C(C(C(C(C3(C2(C1([2H])[2H])[2H])[2H])([2H])[2H])([2H])C)([2H])[2H])([2H])[2H]	153707997	212.390
[2H]C1C=C2C(C(C(C(C2(C(C1([2H])[2H])([2H])[2H])[2H])([2H])[2H])([2H])[2H])([2H])C)([2H])C	153707996	176.360
CC1CCC(CC1)C2=CC(C(C=C2)C)C	153688226	204.350

Further, we can specify the number of lines printed to standard output with head by adding the -n option followed by a digit. For example, the first 4 lines:

user@computer:~$ head -n4 CID_51351709_similar.txt
CC.CC1CCC2CC(=C(CC2C1)C=C)C=C	154673141	232.400
CC1CCCCC1C2=CC=CCC2	154546688	176.300
CC1CCCC2C1=CC=C3C2C=CC=C3	154307178	198.300
CCC1=CC=C2C(C1)C(CCC2(C)C)(C)C	154280750	218.380

tail

The tail program is similar to head, but it prints the last lines of files. For example, print the last 5 lines of CID_51351709_similar.txt:

user@computer:~$ tail -n5 CID_51351709_similar.txt 
CC1CCC(C2C1=CCC(=C2)C)C(C)C	519298	204.350
CCCC1C(C(CC2C1=CC=CC2)C)C	186376	204.350
CC1=C[C@H]2[C@H](CC1)C(=C)CC[C@@H]2C(C)C	92313	204.350
CC1=CC2C(CC1)C(=C)CCC2C(C)C	15094	204.350
CC1=CCCC2(C1CC(CC2)C(=C)C)C	10123	204.350

Note that the original order in the file is maintained with tail, so the last 5 lines are not reversed. If we want to reverse the output, one way to to do this is to pipe the tail results to tac:

user@computer:~$ tail -n5 CID_51351709_similar.txt | tac
CC1=CCCC2(C1CC(CC2)C(=C)C)C	10123	204.350
CC1=CC2C(CC1)C(=C)CCC2C(C)C	15094	204.350
CC1=C[C@H]2[C@H](CC1)C(=C)CC[C@@H]2C(C)C	92313	204.350
CCCC1C(C(CC2C1=CC=CC2)C)C	186376	204.350
CC1CCC(C2C1=CCC(=C2)C)C(C)C	519298	204.350

References and Further Reading

Attribution

Some content in this workshop have been adapted and derive from the Software Carpentry The Unix Shell lesson (CC BY 4.0 license for Instructional Materials and MIT License for programs and code examples). We reused a few parts of their lesson including some descriptions and command examples, but included our own specific datasets and use-case workflows. We have maintained the MIT license for program and code examples. Molecular and bibliographic dataset examples were retrieved from NCBI via their EDirect utility and is credited to NCBI and NLM. Please see the NCBI Website and Data Usage Policies and Disclaimers for more information regarding the data.