ranges

Explanation of ranges

Ranges in st are used by commands like trim and mask, and returned by the find command.

They look like this: <start>..<end>. Open ranges are possible: <start>.. (trims only at the start, including the end of the sequence) and ..<end> (trims only at the end, including the start of the sequence to <end>). The coordinates are 1-based, meaning that 1 denotes the first character (unless -0 is used). It is also possible to use negative numbers, which will tell the tool to count from the end of the sequence:

sequence:    A   T  G   C   A   T   G   C
from start:  1   2  3   4   5   6   7   8
from end:   -8  -7 -6  -5  -4  -3  -2  -1
0-based:     0   1  2   3   4   5   6   7

All of the following commands will trim to the range shown in bold:

# 1-based positive
st trim "3..6" seqs.fa

# 1-based negative
# space before range and quote necessary
st trim " -6..-3" seqs.fa.

# 0-based
st trim 2..6 seqs.fa

Note: There is a problem with ranges starting with a negative number being interpreted as command line arguments. However, insertion of a space before the minus sign will work.

Empty ranges

Note that ranges of zero length are only possible if the start is greater than the end, e.g.: 5..4.