NAME

       gt-extractseq - Extract sequences from given sequence file(s) or fastaindex.

SYNOPSIS

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

OPTIONS

       -frompos
           extract sequence from this position counting from 1 on (default: 0)

       -topos
           extract sequence up to this position counting from 1 on (default: 0)

       -match
           extract all sequences whose description matches the given pattern. The given pattern must be a valid
           extended regular expression. (default: undefined)

       -keys
           extract substrings for keys in specified file (default: undefined)

       -width
           set output width for FASTA sequence printing (0 disables formatting) (default: 0)

       -o
           redirect output to specified file (default: undefined)

       -gzip
           write gzip compressed output file (default: no)

       -bzip2
           write bzip2 compressed output file (default: no)

       -force
           force writing to output file (default: no)

       -help
           display help and exit

       -version
           display version information and exit

DESCRIPTION

       The option -keys allows one to extract substrings or sequences from the given sequence file or from a
       fasta index. The substrings to be extracted are specified in a key file given as argument to this option.
       The 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. 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. The positions are counted from 1. If k is identical to the string between the
       first first and second occurrence of the symbol | in a fasta header, then the fasta header and the
       corresponding sequence is output. For example in the fasta header

       >tr|A0AQI4|A0AQI4_9ARCH Putative ammonia monooxygenase (Fragment) OS=uncultured archaeon GN=amoA PE=4
       SV=1

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

       >k i j

       followed by the original original fasta header. 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 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

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

       gt suffixerator -protein -ssp -tis -des -sds -kys -indexname fastaindex -db inp utfile1 [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 shorte r than 1

       •   they have to appear in lexicographic order

AUTHOR

       Report bugs to <gt-users@genometools.org>.

                                                   10/07/2012                                   GT-EXTRACTSEQ(1)