seq-tools
A toolkit for DNA/RNA sequence conversion and processing. It's super-fast, uses constant RAM, and scales to huge data sizes.
| Branch | Status |
|---|---|
| master |   |
| develop |    |
Installing
Prerequisites: git, gcc, make, diff, perl (diff and perl are only used for test suite).
E.g., to install on Ubuntu: sudo apt install git gcc make diffutils perl.
On Mac OS you may have to install Xcode Command Line Tools.
Building from source:
git clone https://github.com/KirillKryukov/seq-tools.git
cd seq-tools && make && make test && sudo make install
Building from latest unreleased source (for testing purpose only):
git clone --branch develop https://github.com/KirillKryukov/seq-tools.git
cd seq-tools && make && make test && sudo make install
To install in alternative location, add "prefix=DIR" to the "make install" command. E.g., sudo make prefix=/usr/local/bio install
For a staged install, add "DESTDIR=DIR". E.g., make DESTDIR=/tmp/stage install
On Windows it can be installed using Cygwin,
and should be also possible with WSL.
In Cygwin drop sudo: cd seq-tools && make && make test && make install
Tools
seq-tools seq-t2u <in.seq >out.seq - Convert T to U.
seq-tools seq-u2t <in.seq >out.seq - Convert U to T.
seq-tools seq-change-case-to-upper <in.seq >out.seq - Converts sequence to uppercase.
Removes soft mask from sequence.
seq-tools seq-merge-lines <in.mseq >out.seq - Remove end-of-line characters.
seq-tools seq-split-to-lines --line-length 100 <in.seq >out.mseq - Split single-line sequence into lines.
seq-tools seq-soft-mask-extract --mask out.mask <in.seq >out.seq - Separates mask (positions of lower case characters) from sequence.
Outputs sequence without mask (all in upper case).
seq-tools seq-soft-mask-add --mask in.mask <in.seq >out.seq - Soft-masks sequence (changes to lowercase) according to in.mask.
seq-tools seq-hard-mask-extract --mask out.mask <in.seq >out.seq - Removes hard mask ("N") from sequence.
Stores mask in a file, outputs sequence without mask (shorter sequence).
Only capital "N" is recognized as hard mask.
seq-tools seq-hard-mask-add --mask in.mask <in.seq >out.seq - Adds hard mask (stretches of "N") according to in.mask.
Note: Don't use with untrusted mask file, as a malicious mask can cause the output to exceed your storage capacity.
seq-tools seq-iupac-extract --iupac out.iupac <in.seq >out.seq - Removes ambiguous IUPAC nucleotide codes from sequence.
Removes capital characters R, Y, S, W, K, M, B, D, H, V (not N), and stores their locations in the "out.iupac" file.
seq-tools seq-iupac-add --iupac in.iupac <in.seq >out.seq - Adds back IUPAC codes,
previously removed with "seq-tools seq-iupac-extract" command.
File formats
Sequence (.seq): A text file containing only ASCII characters a-z and A-Z.
Multi-line sequence (.mseq): A sequence file where additionally character 0x0A can be used for separating lines.
Mask (.mask): A binary file storing 64-bit unsigned integer numbers (in platform native endianness). Each number is the length of a continuous sequence interval with the same mask. The first interval is always non-masked. If the sequence starts masked, then the first interval length is 0. Examples: sequence "AaaNAA" has soft mask intervals 1,2,3, and hard mask intervals 3,1,2.
IUPAC (.iupac): A binary file that stores locations of ambiguous IUPAC codes (except N). The file stores a sequence of 9 byte records. Each records consists of a number (64-bit unsigned, platform-native endianness) and a character. The meaning is: Skip this many bytes in the input, then add this character.
Other tools
Naturally, please be aware of numerous other toolkits that may or may not better suit your needs: Seqtk, FASTX-Toolkit, SeqKit, seqmagick, Fasta Utilities.