GT-EXTRACTSEQ(1)

✨ NAME ✨

gt-extractseq — the lil icon that extracts sequences from your sequence file(s) or from a fastaindex. 💖

(it lives in the GenomeTools Manual, section 1 — yes bestie, that's the vibe 🦋)

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📜 SYNOPSIS 📜

gt extractseq [option ...] [sequence_file(s)] | fastaindex

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🌸 DESCRIPTION 🌸

Okay so before we get into the lore, here's the full option menu — no skips, no crumbs left behind: 👑

• -frompos [value] — extract the sequence starting from this position, and the counting starts at 1 (default: 0)
• -topos [value] — extract the sequence up to this position, again counting from 1 (default: 0)
• -match [string] — extract every sequence whose description matches the given pattern. Heads up bestie, the pattern has to be a valid extended regular expression. (default: undefined)
• -keys [filename] — extract substrings for the keys in the specified file (default: undefined)
• -width [value] — set the output width for FASTA sequence printing (0 disables formatting) (default: 0)
• -o [filename] — redirect output to the specified file (default: undefined)
• -gzip [yes|no] — write a gzip compressed output file (default: no)
• -bzip2 [yes|no] — write a bzip2 compressed output file (default: no)
• -force [yes|no] — force writing to the output file (default: no)
• -help — display help and exit 💅
• -version — display version information and exit

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🔑 the -keys situation (iykyk)

The option -keys lets you extract substrings or sequences from the given sequence file, or from a fasta index. The substrings you want get specified in a key file, which you hand over as the argument to this option. That key file must contain lines of the form

k

or

k i j

where k is a string (the key) and the optional i and j are positive integers such that i⇐j. So k is the key, and the optional numbers i and j specify the first position of the substring and the last position of the substring to be extracted. Those positions are counted from 1. If k is identical to the string between the first and second occurrence of the symbol | in a fasta header, then the fasta header and the corresponding sequence is output. Like, for example, in the fasta header

>tr|A0AQI4|A0AQI4_9ARCH Putative ammonia monooxygenase (Fragment)

the fasta key is A0AQI4. 🎀 If i and j are both specified, then the corresponding substring is shown in fasta format. In that latter case, the header of the fasta formatted sequence in the output begins with

>k i j

followed by the original fasta header.

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🗂️ if your input is fasta files

If the sequence input are fasta files, then the following holds:

• duplicated lines in the input file lead to only one sequence in the output
• the sequences are output according to the order in the original sequence files
• the formatting of the output can be controlled by the options -width, -o, -gzip, and -bzip2

🧚 if your input comes from a fasta index

If the sequence input comes from a fasta index (see below), the following holds:

• option -width is required ⚠️
• option -o, -gzip and -bzip2 do not work 😭
• the sequences are output in the order the corresponding keys appear in the key file

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🌈 the fastaindex pipeline

If the end of the argument list only contains one filename, say fastaindex, then it is checked if there is a file fastaindex.kys. That makes up part of the fasta index, which is constructed by calling the suffixerator tool as follows:

gt suffixerator -protein -ssp -tis -des -sds -kys -indexname fastaindex \
  -db inputfile1 [inputfile2 ..]

This reads the protein sequence files given to the option -db and creates several files:

• a file fastaindex.esq representing the sequence.
• a file fastaindex.ssp specifying the sequence separator positions.
• a file fastaindex.des showing the fasta headers line by line.
• a file fastaindex.sds giving the sequence header delimiter positions.
• a file fastaindex.kys containing the keys in the fasta files.

For the suffixerator command to work, the keys of the form |key| in the fasta header must satisfy the following constraints:

• they all have to be of the same length, not longer than 128, and not shorter than 1
• they have to appear in lexicographic order

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🐛 REPORTING BUGS 🐛

Report bugs to https://github.com/genometools/genometools/issues. (be nice, the maintainers are doing their best 🫶)

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okay that's the whole page, you ate that fr fr 💅✨

This was GenomeTools 1.6.6, dated 11/09/2025 — periodt. 👑💖