This dir contains code to make and modify transcription graphs (txGraphs).
These are graphs with a node for each start, end, or splice site, and
an edge for each exon or intron. They represent a fair approximation 
to a gene with possible multiple transcripts.

The pipeline for generating these is
    txPslToBed | txBedToTgx | txOrtho | txgAddEvidence | txgWalk
where txgAddEvidence may be run several times to add different
evidence.  Here's a bit more info on each program:

txPslToBed - Transforms alignments to putative exons by projecting
    alignment onto genomic axis only.  It also merges together 
    blocks separated by only a small amount into exons.  It will
    extend or trim an exon by one base on either side to get
    gt/ag ends. It breaks up alignments with longer gaps that
    are not introns into separate bed records on either side of the
    gap.  Finally it trims small isolated bed records.
input: psl file, corresponding target dna
output: bed file
status: done.  It'd be good to add some logic to flip the psl strand
    if there's good evidence in the introns.

txBedToTgx - Clusters together overlapping exons (on same strand)
    and creates a transcript graph.  Associates evidence with each
    edge in the form of type, weight, name of item in bed file.
input: list of bed files, types, and weights.  Bed files are bed12
    (multiple block).
output: txg file
status: done.   Need to add option to take tgx.name root from command
    line.

txOrtho - Looks for orthologous edges in two graphs from two species.
input: txg files from both species, chains & nets between species
output: bed file for introns, bed file for exons
status: Seems to be working for the most part. 

txgAddEvidence - Adds evidence from a bed file to existing transcript
     graph.  
input: txg file, bed file, type, and weight. 
output: txg file with additional evidence.
status: done. Could use more testing for sure though.

txgTrim - Trims a graph to the subset with sufficient evidence.
input: txg file, weight threshold
output: trimmed txg file
status: done.  Could remove unused vertices and other nicenesses, but 
        works as is.

txgWalk - Walks graph producing transcripts. Does threaded walk
     following connected mRNA evidence (in current species) so
     as to avoid combinatorical explosions in alt-splice situations.
    input: txg file
output: bed 12 file (bed in exons)
status: planning. Will be hopefully minor changes to exonWalk.  Might
        in fact just keep exonWalk as is, and rely on txgToAgx to
	convert it to exonWalk format.

txgToXml - Converts txGraph to easier to read XML format.

txgToAgx - Converts from txGraph format to the altGraphX that exonWalk uses.

agxToTxg - Converts from altGraphX to txGraph.
