169 lines
7.0 KiB
Plaintext
169 lines
7.0 KiB
Plaintext
Trace Editor Help
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-----------------
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The ted trace editor is a prototype to allow the display and editing
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of traces from sequencing machines, and the simple editing of plain
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sequences. It runs under the X window system. It provides simultaneous
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display of traces and bases. The editing allows individual bases to be
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removed and new ones added, and also a range of bases at either end to
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be cutoff. Currently, only ABI result files and plain sequences are
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accepted.
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Only one trace can be edited at a time.
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Invocation
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----------
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ted can be run from the command line by simply typing:
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ted
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It will come up with no sequence initially displayed. If provided with
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any arguments it does not understand, or invalid combinations of
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arguments, ted will exit with a message indicating its intended usage.
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ted accepts the standard X arguments allowing, for example, background
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colour or geometry to be specified. ted can accept an argument
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specifying an initial file to display. The key for this is the format
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of the file, for example:
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ted -ABI {ABI format filename}
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ted -plain {plain format filename}
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The file is then displayed at 50% magnification, with the caret
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initially positioned at the first base.
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When an initial file is given, a base number of interest and/or a
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magnification can also be given, for example:
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ted -ABI {ABI format file} -baseNum 280 -mag 30
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or the bottom strand may be specified:
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ted -ABI {ABI format file} -baseNum 280 -mag 30 -bottom 1
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or
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ted -ABI {ABI format file} -bottom 1
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or a string of nucleotides on which the center the window:
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ted -ABI {ABI format file} -astring 1
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or
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ted -ABI {ABI format file} -astring 1 -mag 30 -bottom 1
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Options can be specified in any order.
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An output filename can be specified in a similar manner:
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ted -ABI inputfilename -output outputfilename
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The default output filename is inputfilename.seq
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If you are running the program on a remote machine, you must
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specify a display parameter:
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ted -display machine_name:0.2
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You can also specify the size of the opening window or
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other screen parameters by the following:
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ted -geometry [{width}][x{height}][{+-}{xoff}[{+-}{yoff}]]
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[-fg {color}] [-bg {color}] [-bd {color}] [-bw {pixels}]
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Displays
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--------
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When running, ted displays the name of the file it is currently
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operating on (if any) and the original number of bases.
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A so-called viewport presents four different synchronised views of
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part of the trace. The top one indicates the sequence indices - the
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first digit of the number if positioned over the base to which that
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number corresponds. Below this is a list of the bases as originally
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found in the file (this is the interpretation of the trace as made by
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the sequencing machine). Below this is the list of bases as edited by
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the user --- initially, if this file has not been edited in the past,
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this is identical to the list of original bases. However, if in a
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previous session the user has edited this sequence, the edited
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version of the sequence will appear in the edit window.
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The final display is of the traces produced by the sequencing
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machine for the four respective bases.
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Two controls allow the view presented to be adjusted: both are
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horizontal sliders or scrollbars. The first affects the magnification
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at which the trace is viewed. The minimum magnification is such that
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the whole of the trace is visible within the viewport; when a trace is
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first input, this is the magnification used. The maximum magnification
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is such that bases are spaced out with several characters of space
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between them --- this should allow more than enough room for base
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insertions to be clearly visible. The second scrollbar is immediately
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above the viewport and allows the user to select which part of the
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trace is viewed. Both the sliders work in a similar way: the middle
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mouse button can be used to drag the thumb to any desired position,
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the left and right mouse buttons can be clicked within the scrollbar
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to indicate that paging up or down is desired. In the case of the
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viewport scrollbar, the amount of paging is determined by how far up
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the scrollbar the pointer is.
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The whole ted window can be expanded and contracted (to an extent) by
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dragging the "grow-region" provided by whatever window manager is
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running. The viewport takes up all of this change in size.
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Controls
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--------
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ted has four buttons. "Quit" exits the program after first checking
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whether there is a sequence which has been edited and not saved.
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"Help" pops up this window which has a scrollbar on the left allowing
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all the text to be viewed.
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"Input" presents a dialogue which asks for the format and name of a
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file to be processed. The bases and (if this is not a plain format
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file) traces are read in and displayed for editing. The only
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conversion performed on bases is from 'N' to '-'.
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"Output" presents a dialogue which asks for a filename into which the
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edited and clipped bases can be saved. The default value can be set
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on the command line using the "-output" keyword. No conversion of bases
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is performed on output.
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ted operates in one of three editing modes, one of which is selected
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from three "radio buttons". The currently selected mode is
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highlighted.
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Editing
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-------
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In "Edit sequence" mode, the (lower) list of editable bases can be
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edited in much the same way as a text editor operates. A "caret" which
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is visible in the display of edited bases can be moved left and right
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with the cursor keys (these are sometimes called arrow keys and often
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appear on numeric keypads). It can also be positioned by clicking any
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button while the pointer is pointing into either of the list of bases
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or the traces. The DELETE key deletes the base immediately to the left
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of the caret. Any printing character can be inserted to the right of
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the caret by simply typing it. Inserted characters are placed halfway
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between their neighbours, or if a space is left by the deletion of a
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base originally there, its position is used. A base can thus be
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changed by deleting it and entering the new base.
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Note that in the current version of ted the caret is not constrained
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to remain within the viewed part of the display and that editing can
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still continue while it is thus invisible. Such editing would probably
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only occur by accident.
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ted provides a facility to define a cutoff at either end of the trace.
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A number of the leftmost bases (corresponding to the vector) and the
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rightmost bases (corresponding to the point where the data become
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unreliable) can be defined by setting the editor into "Adjust left
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cutoff" or "Adjust right cutoff" mode. In either of these modes, the
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pointer and mouse buttons can be used to indicate the cutoff point,
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and the cursor keys can be used to adjust this leftwards or
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rightwards. Initially, the cutoff regions are both empty. The cutoff
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regions are clearly indicated on the list of edited bases display and
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on the traces display by being drawn with a dimmed background.
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When the sequence is written out, the list of edited bases, with both
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cutoff regions removed, is written. The output contains newlines
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for convenient formatting and always ends with one.
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