TRACKS(1) OGMP SEQUENCE UTILITY TRACKS(1) NAME tracks - A track comparison utility used in the end phase of a sequencing project SYNOPSIS tracks [-b] [-p] [-c] [-C] [-M] [-l length] [-t trackfile] [-m file_of_masterfiles] [-w width] DESCRIPTION tracks manages a list of tracks and a list of masterfiles, and allows the user to compare the tracks with the masterfiles. The program's initial environment requires that the user sets his/her current directory to a known sequencing project directory (e.g. /users/unit/NGRUB, as listed in /share/supported/apps/ogmp/lib/genome_name.lst, column PATH) before starting tracks, so that tracks will correctly set some internal parameters specific to the project. The user can also set his current directory to a subdirectory of a known project directory (e.g /users/unit/SOBLI/diane). tracks uses a global configuration file (/share/supported/apps/ogmp/lib/genome_name.lst) that describes each project. tracks keeps the list of tracks in a "trackfile" (usually called "tracks.tracks" in the project's directory, and the list of masterfiles in a "masterlist" (usually called "{project_name}.{user}, also see option -m) in a specially installed directory (usually "/share/supported/apps/ogmp/lib/tracks"). The first thing tracks does is to read the trackfile (if it exists) and the masterlist (if it exists). If both are read correctly, tracks enters "batch" mode: the user is asked to select which of the files in the masterlist are to be examined and then for each track in the trackfile a search is performed on the selected masterfiles. When all the tracks have been processed by the program and either accepted or rejected by the user, "interactive" mode is started: the user is repetitively asked to 1- select a subset of the files in the masterlist (again) and 2- enter a new track which is compared to the files selected in step 1. SELECTING LIBRARIES tracks allows the user to edit the masterlist by adding to it or removing files from it. Standard masterfiles are expected to be found in "/research/Seqbanks". Local masterfiles (any user supplied filenames, specified relative to the project directory or with an absolute path) can also be added for the session, but they are not saved back in the masterlist. RESULTS All matches between tracks and sequences in masterfiles that are confirmed by the user are saved in a "resultfile" in the project's directory. The default name for this file is "tracks.res", but if this file exists, a longer name will be used, built by adding the date in ".YYMMDD" format and possibly another increasing integer ".n". Each of the tracks.tracks and tracks.res files have a corresponding list of clones file (ending with a .clonelist extension) that contain the clones names (prepended with the organism code), one per line. The user can also put some match results in a separate file, for later analysis. The name of this file will be the same as the one used for the resultfile, but with the extension ".maybe" appended. If there is already a file with that name, a backup is created first. When the user exits tracks, tracks asks whether the mfmain(1) program should be run on the produced resultfile. The user can do so, which afterwards erase that resultfile, or can decide not to run it and kept the resultfile. It is also possible at that point to discard the resultfiles or to edit it (change certain properties of a given set of tracks). Note that tracks will not allow the user to run mfmain on a resultfile that contains more than one track associated with the same clone (a warning will be issued if such a situation occurs). OPTIONS -b Do not skip batchmode, ask whether or not to proceed with it. By default, tracks is run in interactive mode. -m file_of_masterfiles Specify an additional masterlist. The argument to this switch must be a file that contains names of files to search tracks in. The default is to use /share/supported/apps/ogmp/lib/tracks/PROJECT.USER. If this switch is used, the files in the default masterlist *and* the files in file_of_masterfiles are searched. -t specify an alternate name for the trackfile. -c Do not prompt the user for a comment each time a track is entered. -C disable the creation of the .clonelist files. -M disable the automatic execution of mfmain(1) at the end of the tracks session. This has the same effect as telling tracks to keep the resultfile when it asks whether mfmain(1) should be run (see previous section). -p The chosen project will be one of the directories underneath the current one (where tracks was started) or the current one itself. -l length Give length nucleotides of context downstream of the matched track during user interaction. If this switch is not used, tracks will display roughly 80 characters of context (with the matched track appearing right in the middle of this context). -w width Use lines of width characters when displaying a matched track. The default is 80. The maximum width you can specify is 200 characters. FILES /share/supported/apps/ogmp/lib/genome_name.lst A description of the OGMP projects; accessed mainly to find out and verify what is the organism code for the current project and the project's root directory. $PERLLIB/ogmp/ProjPak.pl $PERLLIB is the standard perl library path. A perl library to read and parse the genome_name.lst file. /share/supported/apps/ogmp/lib/vectors.lst List of basenames of cloning vectors files. /research/Seqbanks Directory where masterfile are taken for track analysis. . (The current working directory where tracks was started) From its name, the project is identified by accessing genome_name.lst. Also a place to put more masterfiles used for track analysis. ./tracks.tracks[.DATE.NUM] Where unmatched tracks are saved between sessions. ./tracks.res[.DATE.NUM] Where information about matching tracks are saved. This file is read in by mfmain(1). /tracks.res[.DATE.NUM].maybe File that contains the tracks that the user wants to keep for later analysis ./tracks.res.[.DATE.NUM].clonelist A list of clone names for the tracks in tracks.res. /share/supported/apps/ogmp/lib/tracks/{PROJECT}.{USER} Where the current list of masterfiles to scan for each user/project pair is kept between invocations. /share/supported/apps/ogmp/lib/tracks/failures/{PROJECT}.{USER} Where information about tracks producing no sequences are kept for each user/project pair. Used for statistical evaluation of the projects' progress. SEE ALSO mfmain(1), projpack(3), chkogmp(1). AUTHOR Pierre Rioux, Tim Littlejohn (Project Management), Organelle Genome Megasequencing Project, Jun. 1994.