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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> |
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<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"><title>Layout File Format</title></head> |
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<body> |
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<h3>Layout file format specification (proposal)<br> |
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</h3> |
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<b><br> |
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</b>Besides the usual ACE files, <b>clview </b>also recognizes a proprietary "layout" format (stored in file usually having the extension <tt>.lyt</tt>) |
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for representing multiple sequence alignment (MSA) layouts -- where |
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typically smaller "component"sequences (henceforth called "<b>reads</b>") are aligned to (or are making up) a larger sequence (henceforth called "the <b>contig</b>").<br> |
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<br> |
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These layout files are text files having a pseudo-FASTA format-- each |
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FASTA record representing one contig's "layout", like this:<br> |
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<br> |
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<big><b>></b></big><i><small><</small>contigName<small>></small></i> <small><</small><i>number_of_reads<small>></small> </i><small><</small><i>contig_start_coord<small>></small> </i><small><</small><i>contig_end_coord<small>></small> [<sequence></i><i>]<br> |
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</i><i><small><</small>readName<small>></small></i> <small><</small><i>orientation<small>></small> </i><small><</small><i>read_length<small>></small> </i><small><</small><i>read_start_coord<small>></small></i> <small><</small><i>clip_left<small>> </small></i><small><</small><i>clip_right<small>> </small></i><i>[ <extra_attributes...></i><i>]</i><i><br> |
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</i>.<br> |
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.<br> |
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All the fields on every line are space delimited (tab or plain space). Therefore no spaces are allowed <i>within</i> the fields (so contig and read names are not allowed to contain spaces).<br> |
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Each FASTA-like record in such multi-layout file represents one layout |
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definition (a multiple alignment space). Every such layout definition |
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must start with line beginning with the '<b>></b>' character and |
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containing some general contig/layout data (contig name, number of |
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component reads, the start/end coordinates for the layout space and |
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optionally the actual contig sequence, if any). This first |
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contig/layout general info line must be followed by exactly <small><</small><i>number_of_reads<small>></small></i> lines containing component/read information (one line per read). For each <i>read</i> line , that fields are as follows:<br> |
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<table bgcolor="#ccccff" border="0" cellpadding="2" cellspacing="2" width="100%"> |
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<tbody> |
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<tr> |
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<td bgcolor="#ffffff" valign="top">1.<br> |
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</td> |
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<td bgcolor="#ffffff" valign="top"><i><small><</small>readName<small>></small></i></td> |
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<td bgcolor="#ffffff" valign="top">a sequence identifier, unique within the current contig/layout</td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top">2.<br> |
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</td> |
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<td bgcolor="#ffffff" valign="top"><small><</small><i>orientation<small>></small> </i></td> |
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<td bgcolor="#ffffff" valign="top">one character: '+' or '-', representing the forward or reverse orientation of the read in the current layout<br> |
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</td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top">3.<br> |
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</td> |
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<td bgcolor="#ffffff" valign="top"><small><</small><i>read_length<small>></small> </i></td> |
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<td bgcolor="#ffffff" valign="top">the actual length of the read (including the clipped ends). If segmented (see the <b>G:</b> option of <i><extra_attributes></i>), the intra-segment gaps are not considered as part of read length in the layout. <br> |
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</td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top">4.<br> |
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</td> |
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<td bgcolor="#ffffff" valign="top"><small><</small><i>read_start_coord<small>></small></i></td> |
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<td bgcolor="#ffffff" valign="top">the leftmost (lowest) |
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coordinate of this read in the current layout. The position could be |
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"virtual" if the read is clipped at that left end. The orientation of |
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the read does not matter for this assessment.<br> |
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</td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top">5.<br> |
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</td> |
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<td bgcolor="#ffffff" valign="top"><small><</small><i>clip_left<small>> </small></i></td> |
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<td bgcolor="#ffffff" valign="top">the number of nucleotides trimmed at the left end. (Orientation doesn't matter)<br> |
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</td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top">6.<br> |
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</td> |
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<td bgcolor="#ffffff" valign="top"><i><small> </small></i><small><</small><i>clip_right<small>> </small></i></td> |
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<td bgcolor="#ffffff" valign="top">the number of nucleotides trimmed at the right end of this read.<br> |
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</td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top">7.-...<br> |
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</td> |
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<td bgcolor="#ffffff" valign="top"><i>[<extra_attributes...>]</i></td> |
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<td bgcolor="#ffffff" valign="top">One ore more space delimited<i> optional</i> |
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attributes for this read may follow. Their order is not enforced and |
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they should all start with a letter code followed by the ':' character |
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and then followed by attribute specific text data (spaces not allowed). |
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General format is: <small><</small><i>attr_code<small>></small></i><small><big><b>:</b></big></small><small><</small><i>attr_data<small>><br> |
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<br> |
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</small></i>Attributes recognized by the current specification:<br> |
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<table bgcolor="#cccccc" border="0" cellpadding="4" cellspacing="3" width="100%"> |
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<tbody> |
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<tr> |
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<td bgcolor="#ffffff" valign="top"><b>C:</b><small><</small><i>grp#<small>></small></i></td> |
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<td bgcolor="#ffffff" valign="top">group color for the current read. This instructs the viewer to |
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draw this read with a specific color uniquely associated to the given <small><</small><i>grp#<small>></small> |
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</td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top"><b>L:</b><small><</small><i>other_readName<small>,..></small></i></td> |
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<td bgcolor="#ffffff" valign="top">[clone] link to another |
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read in the layout. This instructs the viewer to place the other read |
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on the same vertical line in the layout display (if possible), with |
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perhaps a dotted line connecting such reads; a comma delimited list of |
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read names can be given if such links extend to more than one other |
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read. Only one read in such a linked list needs to have such a L: |
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entry in order to declare the linked list/group of reads (that is, the |
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other linked reads do not need to reciprocate by having the |
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corresponding, but redundant L: attribute).<br> |
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</td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top"><b>S:</b><small><</small><i>sequence<small>></small></i></td> |
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<td bgcolor="#ffffff" valign="top">The nucleotide sequence |
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of the read exactly as it is included in the alignment. It must include |
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the clipped ends and the small gaps (indels) introduced by the MSA |
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(represented as '-' or '*' in the<small> <</small><i>sequence<small>></small></i>) -- so the length of such <small><</small><i>sequence<small>></small></i> string must be equal to <small><</small><i>read_length<small>></small> </i></td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top"><b>G:</b><small><</small><i>seg1_end[</i><big><tt><b>c</b></tt></big><i><small><</small>seq1clipright<small>></small>]</i><i>[</i><big><tt><b>s</b><i>|</i><b>S</b></tt></big><i><small></small>]</i><tt><b>-</b></tt><i><br> |
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seg2_start</i><i>[</i><big><tt><b>c</b></tt></big><i><small><</small>seg2clipleft<small>></small>]</i><i>[</i><big><tt><b>s</b><i>|</i><b>S</b></tt></big><i>]</i><b>,</b><i>...></i></td> |
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<td bgcolor="#ffffff" valign="top">Segmented alignment |
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(e.g. EST to genome). This is an indication that the read contains |
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large internal gaps -- which should be displayed as <i>segments</i> |
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connected by lines. The data for this attribute consists of a comma |
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delimited list of coordinate pairs for the inter-segment gaps. |
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Coordinates in a pair are separated by the '-' character. For each pair |
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the first coordinate is the <i>end</i> position in the layout of the <i>previous</i> segment, while the second coordinate is the <i>start</i> position of the <i>next </i>segment in the layout.<br> |
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<br> |
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Example: say we have a "read" (e.g. a mRNA) called "MRNA244" which |
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aligns onto the "contig" (e.g. genomic sequence) of length 34000 as 3 |
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distinct segments (e.g. 3 exons), aligned at genomic coordinates: 300 |
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to 500 (first segment), 800 to 1100 (second segment) and 1500 to 1900 |
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(third segment) respectively. Assuming there is a 30nt clipping at the |
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left end and 20nt clipping at the right end, and that the alignment has |
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a "forward" orientation, the contig and the sequence line for MRNA244 |
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in the layout file would look like this (let's assume there are 281 |
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"reads" total in this imagined layout):<br> |
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<br> |
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<tt>>contig1 281 1 34000<br> |
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MRNA244 + 953 270 30 20 G:500-800,1100-1500<br> |
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</tt><br> |
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The actual length of the "read" accounts for the length of each segment |
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(201, 301 and 401 respectively) plus the clipping lengths at each end |
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(20 and 30), so the total is 201+301+401+20+30=953<br> |
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The left coordinate of the sequence in the alignment (270) is equal to |
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the position of the first (leftmost) segment (300) minus the left-end |
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clipping (30). <br> |
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<br> |
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There is a possibility to have clipping for each segment. This can be |
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specified for each segment's end by appending the character <big><b><tt>c</tt></b></big> |
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followed by the amount of clipping at that end. If in the example |
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segment alignment above we had the 1st exon clipped 10 nucleotides at |
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the right end, the 2nd exon clipped 5nt at the left end and 7nt at the |
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right end, with the 3rd exon having 9nt clipped at the left end, the |
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above read line may look like this:<br> |
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<br> |
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<tt> |
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MRNA244 + 953 270 30 20 G:490c10-805c5,1093c7-1509c9<br> |
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</tt><br> |
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Please note that in this last example the actual coordinates of the |
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alignment of the 3 segments (exons) to the genomic sequence are |
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300-490, 805-1093 and 1509-1900 respectively. The way the clipping is |
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specified in this G: attribute differs from the way the leftmost and |
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rightmost clipping of the whole read is given. The difference is that |
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the <big><b><tt>c</tt></b></big> |
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clipping lengths in the G: attribute lie OUTSIDE the coordinates given |
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for the segment ends in the same G: attibute, while the global leftmost |
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clipping (30 in the example above) is included in the offset coordinate |
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for the whole read (270 here).<br> |
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<br> |
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For EST to genome alignments, an optional 'S' (or 's') character may |
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follow the inter-segment ends, indicating that a splice consensus |
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(major or minor, respectively) was found on that side of the intron |
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corresponding to that inter-segment gap.<br> |
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<br> |
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</td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top"><b>D:</b><small><</small><i>se</i><i>q_diffs<small>..><br> |
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</small></i> or for segmented (G:) reads:<i><small><br> |
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</small></i><b>D:</b><small><</small><i>se</i><i>g1_diffs<small>..></small></i><big><b>/</b></big><small><</small><i>se</i><i>g2_diffs<small>..></small></i><i><small><br> |
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<br> |
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</small></i><br> |
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</td> |
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<td bgcolor="#ffffff" valign="top">If the contig sequence is given, this read attribute is the way to provide the display application with only a list of point-<i>differences</i> between this read's sequence and the contig sequence (so S: is not be needed). The <small><</small><i>seq_diffs<small>></small></i> is a concatenation of elements of this format:<br> |
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<small><</small><i>incremental_coordinate<small>></small></i><small><</small><i>character<small>></small></i><i><br> |
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<br> |
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</i>..where <small><</small><i>incremental_coordinate<small>></small></i> is the numeric position of such a difference <i>relative </i>to |
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the previous difference -- or if no such previous difference exists, relative to |
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the first (leftmost) non-clipped nucleotide of the read. This incremental |
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coordinate (which is always at least 1) must be followed by a <small><</small><i>character<small>></small></i> |
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code. This character can be either an actual DNA base letter ('A', 'G', 'C', 'T', 'N', etc.) -- which |
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indicates a nucleotide mismatch at that position, or the "dash" |
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character ('-') indicating a gap in the alignment or this read to the |
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contig sequence. <br> |
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<br> |
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Example: the following alignment is there between contig sequence and the read sequence:<br> |
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<br> |
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<tt>contig: ..A G T T G C T - C C T A - C T A C A G A C C N G...<br> |
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read: ..A G T <font color="#990000">-</font> <font color="#990000">C</font> C T <font color="#990000">T</font> C C <font color="#990000">A</font> A <font color="#990000">N</font> C T <font color="#990000">- -</font> A <font color="#990000">T</font> A C C <font color="#990000">A</font> G...<br> |
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(increments: 4 1 3 |
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3 2 3 1 2 |
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4 ... )<br> |
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</tt><br> |
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Assuming that the above alignment starts at position 200 in the contig |
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and that the read called RDAAA of length 620 has 20 bp clipping right |
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before this alignment (so the read left end coordinate in the layout is |
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181), the following line description would apply to this read in the |
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layout file (the ending ellipsis ... is not part of the actual text but |
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just e placeholder for possible other differences to report):<br> |
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<br> |
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<tt>RDAAA + 620 181 20 0 D:4-1C3T3A2N3-1-2T4A...<br> |
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</tt><br> |
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Note that in this compact MSA representation there is no information |
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provided about the nucleotide content of the clipped ends of the read. |
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The viewer application may choose to represent such clipped regions as |
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empty or gray boxes (rectangles), with the actual nucleotides only |
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displayed in the non-clipped regions.<br> |
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<br> |
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For segmented alignments (i.e. those reads having a <b>G:</b> |
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attribute), multiple such lists should be given (one for each segment), |
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separated by the '/' (slash) character. For each such |
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segment-differences list, the first incremental coordinate will be the |
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distance from the beginning of the first (leftmost) non-clipped |
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nucleotide of that segment.<br> |
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<br> |
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</td> |
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</tr><tr> |
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<td bgcolor="#ffffff" valign="top"><b>I:</b><small><</small><i>se</i><i>q_indels<small>..><br> |
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</small></i>or for segmented (G:) reads:<i><small><br> |
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</small></i><b>I:</b><small><</small><i>se</i><i>g1_indels<small>..></small></i><big><b>/</b></big><small><</small><i>se</i><i>g2_indels<small>..></small></i><br> |
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</td> |
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<td bgcolor="#ffffff" valign="top">Similar to the D: attribute, only that the <i>original</i> |
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sequence for the read is assumed known from other sources (e.g. an |
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indexed multi-FASTA file) and only gaps and deletions are reported as |
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the operations needed to make that sequence fit into the current MSA. <br> |
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The coordonate system is now entirely based on the <i>original</i>, raw |
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read sequence, but with the same adjustment of the start coordinate |
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based on the left clipping (i.e. all coordinates are relative to the |
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first (leftmost) base in the read that is not clipped but actually used |
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in the MSA).<br> |
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The <small><</small><i>seq_indels<small>></small></i> is a concatenation of elements of this format:<br> |
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<br> |
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<small><</small><i>incremental_coordinate<small>></small></i><small><</small><i>indel_char<small>></small></i> <br> |
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<br> |
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..where <small><</small><i>indel_char<small>> </small></i>can |
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be either '-' (gap) or 'd' (deletion) at the specific base |
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position in the original read sequence. The actual base position can be |
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obtained by this iterative formula:<br> |
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<br> |
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<i><base_position></i> = <i><incremental_coordinate></i> + <i><prev_base_position></i><br> |
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<br> |
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..where <i><prev_base_position></i> = <i><clip_left></i> for the first iteration (first element of <i><seq_indels></i>)<br> |
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<br> |
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<i><small></small></i></td> |
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</tr> |
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<tr> |
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<td bgcolor="#ffffff" valign="top"><b>R:</b><i><small><</small>gaplist<small>></small></i><b><big>/</big></b><i><small><</small>contig_gaplist<small>></small></i><br> |
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</td> |
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<td bgcolor="#ffffff" valign="top">a special attribute for |
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the Assembly-on-Reference procedure, providing all gap information for |
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the alignment of this read to the parent contig. The gapping |
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information (as produced by mgblast with -D5 option) is stored directly |
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in this attribute data: the gaps in the read are in the first list <i><small><</small>gaplist<small>></small></i> and the gaps in the contig (reference) sequence are stored in <i><small><</small>contig_gaplist<small>></small></i>. The two lists are separated by the '/' (slash) character. Just like |
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mgblast's -D5 output, the gap list has the format:<br> |
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<br> |
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<i><small><</small>gap1pos<small>></small>[+<small><</small>gap1length<small>></small>]</i><b>,</b><i><small><</small>gap2pos<small>></small>[+<small><</small>gap2length<small>></small>],...</i><br> |
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<br>The <i>nrcl</i> |
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(non-redundandification clustering) program automatically writes this |
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attribute in the layout file produced when the -y option is given (if |
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the gap information is available in the parsed mgblast hits).<br> |
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<br> |
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The <i>mblaor</i> (mgblast assembly-on-reference) program requires this |
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attribute to be present when parsing an input layout file in order to |
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generate a full MSA, transforming this info into indel operations |
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applied to the read.<br> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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