Sort lines in a file

To use a script, cut and paste the code from the light green or blue box into a terminal window, change the bold, red text as needed, and hit Enter.

See More Information for notes on using these tools.

Sort a file alphabetically

See General Sorting Notes for details on sorting order.

Sort alphabetically, in ASCENDING order (sort_alpha_asc)

Sort the lines in the file in ascending alphabetical order.

Input file(s)
Output file

perl -e ' while(<>) { push @lines, $_; } warn "\nSorted $. lines in ascending alphabetical order\n\n"; print sort @lines ' unsorted > sorted_asc

Example: Sort a gene list. Run the above script on a file called unsorted to get a file called sorted:

Original file (unsorted)	Output file (sorted_asc)	Screen Output
ap23 7 ap23 30 CG2500 3 cxb7 2 CG12345 9 CG2500 3	CG12345 9 CG2500 3 CG2500 3 ap23 30 ap23 7 cxb7 2	Sorted 6 lines in ascending alphabetical order

Sort alphabetically, in DESCENDING order (sort_alpha_desc)

Sort the lines in the file in descending alphabetical order.

Input file(s)
Output file

perl -e ' while(<>) { push @lines, $_; } warn "\nSorted $. lines in descending alphabetical order\n\n"; print sort { $b cmp $a } @lines ' unsorted > sorted_desc

Example: Sort a gene list. Run the above script on a file called unsorted to get a file called sorted_desc:

Original file (unsorted)	Output file (sorted_desc)	Screen Output
ap23 7 ap23 30 CG2500 3 cxb7 2 CG12345 9 CG2500 3	cxb7 2 ap23 7 ap23 30 CG2500 3 CG2500 3 CG12345 9	Sorted 6 lines in descending alphabetical order

Sort alphabetically, ignoring case

Z and z will count as the same letter in these sorts. See General Sorting Notes for more details on sorting order.

Sort alphabetically, ignoring case, in ASCENDING order (sort_nocase_asc)

Sort the lines in the file in ascending alphabetical order, counting z and Z as the same.

Input file(s)
Output file

perl -e ' while(<>) { push @lines, $_; } warn "\nSorted $. lines in ascending alphabetical order, ignoring case\n\n"; print sort { lc($a) cmp lc($b) } @lines ' unsorted > sorted_nc_asc

Example: Sort a gene list. Run the above script on a file called unsorted to get a file called sorted_nc_asc:

Original file (unsorted)	Output file (sorted_nc_asc)	Screen Output
ap23 7 ap23 30 CG2500 3 cxb7 2 CG12345 9 CG2500 3	ap23 30 ap23 7 CG12345 9 CG2500 3 CG2500 3 cxb7 2	Sorted 6 lines in ascending alphabetical order, ignoring case

Sort alphabetically, ignoring case, in DESCENDING order (sort_nocase_desc)

Sort the lines in the file in descending alphabetical order, counting z and Z as the same.

Input file(s)
Output file

perl -e ' while(<>) { push @lines, $_; } warn "\nSorted $. lines in descending alphabetical order, ignoring case\n\n"; print sort { lc($b) cmp lc($a) } @lines ' unsorted > sorted_nc_desc

Example: Sort a gene list. Run the above script on a file called unsorted to get a file called sorted_nc_desc:

Original file (unsorted)	Output file (sorted_nc_desc)	Screen Output
ap23 7 ap23 30 CG2500 3 cxb7 2 CG12345 9 CG2500 3	cxb7 2 CG2500 3 CG2500 3 CG12345 9 ap23 7 ap23 30	Sorted 6 lines in descending alphabetical order, ignoring case

Sort numerically

See General Sorting Notes for more details on sorting order.

Sort numerically, in ASCENDING order (sort_num_asc)

Sort a simple list numerically.

Input file(s)
Output file

perl -e ' while(<>) { push @lines, $_; } warn "\nSorted $. lines in ascending numerical order\n\n"; print sort { $a <=> $b } @lines ' unsorted > sorted_num_asc

Example: Sort a list of numbers. Run the above script on a file called unsorted to get a file called sorted_num_asc:

Original file (unsorted)	Output file (sorted_num_asc)	Screen Output
3 12 78.5 -10 1e5 1e-3	-10 1e-3 3 12 78.5 1e5	Sorted 6 lines in ascending numerical order

Sort numerically, in DESCENDING order (sort_num_desc)

Input file(s)
Output file

perl -e ' while(<>) { push @lines, $_; } warn "\nSorted $. lines in ascending numerical order\n\n"; print sort { $b <=> $a } @lines ' unsorted > sorted_num_desc

Example: Sort a list of numbers. Run the above script on a file called unsorted to get a file called sorted_num_desc:

Original file (unsorted)	Output file (sorted_num_desc)	Screen Output
3 12 78.5 -10 1e5 1e-3	1e5 78.5 12 3 1e-3 -10	Sorted 6 lines in ascending numerical order

Sort tabular data, based on the values in a given column

Sort numerically (ascending order) based on a given column (sort_on_column_num)

Sort lines in a tab-separated file in ascending order, based on the numerical value in a given column.

$column		Numerical column to sort by
Input file(s)
Output file

perl -e ' $column=1; while(<>) { s/\r?\n//; @F=split /\t/, $_; push @sort_col, $F[$column]; push @lines, "$_\n"; } warn "\nSorted $. lines in ascending order, based on numerical values in column $column\n\n"; print @lines[sort { $sort_col[$a] <=> $sort_col[$b] } 0..$#sort_col] ' unsorted > sorted_col

Example: Sort a gene list based on the score in the first column. Run the above script on a file called unsorted to get a file called sorted_col:

Original file (unsorted)	Output file (sorted_col)	Screen Output
ap23 7 ap23 30 CG2500 3 cxb7 2 CG12345 9 CG2500 3	cxb7 2 CG2500 3 CG2500 3 ap23 7 CG12345 9 ap23 30	Sorted 6 lines in ascending order, based on numerical values in column 1

Sort numerically (descending order) based on a given column (sort_on_column_num_desc)

Sort lines in a tab-separated file in descending order, based on the numerical values in a given column.

$column		Numerical column to sort by
Input file(s)
Output file

perl -e ' $column=1; while(<>) { s/\r?\n//; @F=split /\t/, $_; push @sort_col, $F[$column]; push @lines, "$_\n"; } warn "\nSorted $. lines in descending order, based on numerical values in column 1\n\n"; print @lines[sort { $sort_col[$b] <=> $sort_col[$a] } 0..$#sort_col] ' unsorted > sorted_col

Example: Sort a gene list based on the score in the second, tab-separated column. Run the above script on a file called unsorted to get a file called sorted_col:

Original file (unsorted)	Output file (sorted_col)	Screen Output
ap23 7 ap23 30 CG2500 3 cxb7 2 CG12345 9 CG2500 3	ap23 30 CG12345 9 ap23 7 CG2500 3 CG2500 3 cxb7 2	Sorted 6 lines in descending order, based on numerical values in column 1

Sort alphabetically (ascending order) based on a given column (sort_on_column_alpha)

Sort lines in a tab-separated file in ascending order, based on the text strings in a given column.

$column		Text column to sort by
Input file(s)
Output file

perl -e ' $column=1; while(<>) { s/\r?\n//; @F=split /\t/, $_; push @sort_col, $F[$column]; push @lines, "$_\n"; } warn "\nSorted $. lines in ascending order, based on text strings in column 1\n\n"; print @lines[sort { $sort_col[$a] cmp $sort_col[$b] } 0..$#sort_col] ' unsorted > sorted_col

Example: Sort a gene list based on the gene name in the second, tab-separated column. Run the above script on a file called unsorted to get a file called sorted_col:

Original file (unsorted)	Output file (sorted_col)	Screen Output
1 ap23 7 2 ap23 30 3 CG2500 3 4 cxb7 2 5 CG12345 9 6 CG2500 3	5 CG12345 9 3 CG2500 3 6 CG2500 3 1 ap23 7 2 ap23 30 4 cxb7 2	Sorted 6 lines in ascending order, based on text strings in column 1

Sort alphabetically (descending order) based on a given column (sort_on_column_alpha_desc)

Sort lines in a tab-separated file in descending order, based on the text strings in a given column.

$column		Text column to sort by
Input file(s)
Output file

perl -e ' $column=1; ; while(<>) { s/\r?\n//; @F=split /\t/, $_; push @sort_col, $F[$column]; push @lines, "$_\n"; } warn "\nSorted $. lines in descending order, based on text strings in column 1\n\n"; print @lines[sort { $sort_col[$b] cmp $sort_col[$a] } 0..$#sort_col] ' unsorted > sorted_col

Example: Sort a gene list based on the gene name in the second, tab-separated column. Run the above script on a file called unsorted to get a file called sorted_col:

Original file (unsorted)	Output file (sorted_col)	Screen Output
1 ap23 7 2 ap23 30 3 CG2500 3 4 cxb7 2 5 CG12345 9 6 CG2500 3	4 cxb7 2 1 ap23 7 2 ap23 30 3 CG2500 3 6 CG2500 3 5 CG12345 9