tigr-extract(1) [debian man page]
TIGR-GLIMMER(1) General Commands Manual TIGR-GLIMMER(1) NAME
tigr-glimmer -- Fine start/stop positions of genes in genome sequence SYNOPSIS
tigr-extract [genome-file options] DESCRIPTION
Program extract takes a FASTA format sequence file and a file with a list of start/stop positions in that file (e.g., as produced by the long-orfs program) and extracts and outputs the specified sequences. The first command-line argument is the name of the sequence file, which must be in FASTA format. The second command-line argument is the name of the coordinate file. It must contain a list of pairs of positions in the first file, one per line. The format of each entry is: <IDstring>> <start position> <stop position> This file should contain no other information, so if you're using the output of glimmer or long-orfs , you'll have to cut off header lines. The output of the program goes to the standard output and has one line for each line in the coordinate file. Each line contains the IDstring , followed by white space, followed by the substring of the sequence file specified by the coordinate pair. Specifically, the substring starts at the first position of the pair and ends at the second position (inclusive). If the first position is bigger than the second, then the DNA reverse complement of each position is generated. Start/stop pairs that "wrap around" the end of the genome are allowed. OPTIONS
-skip makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program. -l makes the output omit an sequences shorter than n characters. n includes the 3 skipped characters if the -skip switch is one. SEE ALSO
tigr-glimmer3 (1), tigr-long-orfs (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), tigr-check (1), tigr-codon-usage (1), tigr- compare-lists (1), tigr-extract (1), tigr-generate (1), tigr-get-len (1), tigr-get-putative (1), http://www.tigr.org/software/glimmer/ Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR
This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for the Debian system. TIGR-GLIMMER(1)
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Bio::Tools::Run::Glimmer(3pm) User Contributed Perl Documentation Bio::Tools::Run::Glimmer(3pm) NAME
Bio::Tools::Run::Glimmer - Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM. SYNOPSIS
# glimmer2 my $factory = Bio::Tools::Run::Glimmer->new('-program' => 'glimmer3', '-model' => 'model.icm'); # glimmer3 my $factory = Bio::Tools::Run::Glimmer->new('-program' => 'glimmer2', '-model' => 'model.icm'); # glimmerm my $factory = Bio::Tools::Run::Glimmer->new('-program' => 'glimmerm'); # glimmerHMM my $factory = Bio::Tools::Run::Glimmer->new('-program' => 'glimmerHMM'); # Pass the factory Bio::Seq objects # returns a Bio::Tools::Glimmer object my $glimmer = $factory->run($seq); or my $glimmer = $factor->run(@seq); DESCRIPTION
Wrapper module for the Glimmer family of programs. Should work with all currently available flavors: Glimmer, GlimmerM and GlimmerHMM. However, only Glimmer 2.X and 3.X have been tested. Glimmer is open source and available at <http://www.cbcb.umd.edu/software/glimmer/>. GlimmerM is open source and available at <http://www.tigr.org/software/glimmerm/>. GlimmerHMM is open source and available at <http://www.cbcb.umd.edu/software/GlimmerHMM/>. Note that Glimmer 2.X will only process the first sequence in a fasta file (if you run() more than one sequence at a time, only the first will be processed). Note that Glimmer 3.X produces two output files. This module only passes the .predict file to Bio::Tools::Glimmer. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://redmine.open-bio.org/projects/bioperl/ AUTHOR - Mark Johnson Email: mjohnson-at-watson-dot-wustl-dot-edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ program_name Title : program_name Usage : $factory>program_name() Function: gets/sets the program name Returns: string Args : string program_dir Title : program_dir Usage : $factory->program_dir() Function: gets/sets the program dir Returns: string Args : string model Title : model Usage : $factory>model() Function: gets/sets the name of the model (icm) file Returns: string Args : string new Title : new Usage : $glimmer->new(@params) Function: creates a new Glimmer factory Returns: Bio::Tools::Run::Glimmer Args : run Title : run Usage : $obj->run($seq_file) Function: Runs Glimmer/GlimmerM/GlimmerHMM Returns : A Bio::Tools::Glimmer object Args : An array of Bio::PrimarySeqI objects _run Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An instance of Bio::Tools::Glimmer Args : file name, sequence identifier (optional) _write_seq_file Title : _write_seq_file Usage : obj->_write_seq_file($seq) or obj->_write_seq_file(@seq) Function: Internal(not to be used directly) Returns : Name of a temp file containing program output Args : One or more Bio::PrimarySeqI objects perl v5.12.3 2011-06-18 Bio::Tools::Run::Glimmer(3pm)