Table of Contents
Perl Exercises
read_and_write
Read from an input file and write the content to an output file. Assume the two filenames are provided in the command line.
Hint: learn about filehandle before attempting this exercise.
$ cat input.txt George Washington John Adams Thomas Jefferson James Madison James Monroe $ perl read_and_write.pl input.txt output.txt $ cat output.txt George Washington John Adams Thomas Jefferson James Madison James Monroe
See a sample answer here.
parse_first_name
Read from an input file (containing a list of full names) and write the first names to an output file. Assume the two filenames are provided in the command line.
Hint: learn about filehandle and array (or regular expression) before attempting this exercise.
$ cat input.txt George Washington John Adams Thomas Jefferson James Madison James Monroe $ perl parse_first_name.pl input.txt first_name.txt $ cat first_name.txt George John Thomas James James
See a sample answer here.
count_first_name
Read an input file that contains several names (assuming one name in each line, the first name and the last name are separate by a space). Count how the number of times each first name appeared in the input. Print the result to STDOUT, sort the names alphabetically.
Hint: learn about filehandle, array, hash, and sorting before attempting this exercise.
$ cat input.txt George Washington John Adams Thomas Jefferson James Madison James Monroe $ perl count_first_name.pl input.txt George appeared 1 times James appeared 2 times John appeared 1 times Thomas appeared 1 times
See a sample answer here.
write_lines_to_files
Obtain an input file and an output directory from the command line. Produce one output file for each line in the input file, use the line number (i.e., 1, 2, 3, etc) as the filenames.
Hint: learn about filehandle and directory operation before attempting this exercise.
$ cat input.txt George Washington John Adams Thomas Jefferson James Madison James Monroe $ perl write_lines_to_files.pl input.txt output/ $ head output/* ==> output/1 <== George Washington ==> output/2 <== John Adams ==> output/3 <== Thomas Jefferson ==> output/4 <== James Madison ==> output/5 <== James Monroe
See a sample answer here.
combine_files
The opposite of write_lines_to_files; obtain an input directory and an output file from the command line, read the files in the input directory and write their content to one single output file. Note that we want to exclude hidden files in the input directory.
Hint: learn about filehandle, directory operation, and pattern matching before attempting this exercise.
$ head output/* ==> output/1 <== George Washington ==> output/2 <== John Adams ==> output/3 <== Thomas Jefferson ==> output/4 <== James Madison ==> output/5 <== James Monroe $ perl combine_files.pl output/ combined.txt $ cat combined.txt George Washington John Adams Thomas Jefferson James Madison James Monroe
See a sample answer here.
unwrap_fasta
Read a fasta file, unwrap the sequences (i.e., remove all extra line breaks), and save the result to an output file.
Hint: learn about the $/ variable (input record separator) before attempting this exercise.
$ cat coding.fasta >NP_414542 ATGAAACGCATTAGCACCACCATT accaccaccatcaccattaccacaggta ACGGTGCGGGCTGA >NP_414617 ATGACTCACATCGTTCGCTTTA TCGGTCTACTA ctactaaacgcatcttctttgcgcggta GACGAGTGAGCGGCATCCAGCATTAA $ perl unwrap_fasta.pl coding.fasta unwrap.fasta $ cat unwrap.fasta >NP_414542 ATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGA >NP_414617 ATGACTCACATCGTTCGCTTTATCGGTCTACTACTACTAAACGCATCTTCTTTGCGCGGTAGACGAGTGAGCGGCATCCAGCATTAA
See a sample answer here.
display_codon
Read a fasta file that contain protein-coding sequences. Re-format the sequences to show codons (10 codons per line) in the output file.
Hint: learn about the substr function or regular expression before attempting this exercise.
$ cat coding.fasta >NP_414542 ATGAAACGCATTAGCACCACCATT accaccaccatcaccattaccacaggta ACGGTGCGGGCTGA >NP_414617 ATGACTCACATCGTTCGCTTTA TCGGTCTACTA ctactaaacgcatcttctttgcgcggta GACGAGTGAGCGGCATCCAGCATTAA $ perl display_codon_1.pl coding.fasta codon.fasta $ cat codon.fasta >NP_414542 ATG AAA CGC ATT AGC ACC ACC ATT ACC ACC ACC ATC ACC ATT ACC ACA GGT AAC GGT GCG GGC TGA >NP_414617 ATG ACT CAC ATC GTT CGC TTT ATC GGT CTA CTA CTA CTA AAC GCA TCT TCT TTG CGC GGT AGA CGA GTG AGC GGC ATC CAG CAT TAA
count_EcoRI_site
Read a fasta file and count the number of EcoRI restriction sites in each sequence.
Hint: learn about the regular expression before attempting this exercise.
$ cat EcoRI.fasta >Seq_1 nnnGAA TTCnnnGAATTCnnnGaattCnnn >Seq_2 nnnGAATTCnnngAa TtCnnn $ perl count_EcoRI_site.pl EcoRI.fasta Seq_1 has 3 EcoRI sites Seq_2 has 2 EcoRI sites
See a sample answer here.