pslMap

Reference Code backup Executable files

Map PSLs alignments to new targets using alignments ofthe old target to the new target. Given inPsl and mapPsl, wherethe target of inPsl is the query of mapPsl, create a new PSLwith the query of inPsl aligned to all the targets of mapPsl.If inPsl is a protein to nucleotide alignment and mapPsl is anucleotide to nucleotide alignment, the resulting alignment isnucleotide to nucleotide alignment of a hypothetical mRNA thatwould code for the protein. This is useful as it gives basealignments of spliced codons. A chain file may be used insteadmapPsl.

Category

Generic

Usage

pslMap [options] inPsl mapFile outPsl

Manual

This tool is part of UCSC Genome Browser's utilities.


Options:
-chainMapFile - mapFile is a chain file instead of a psl file
-swapMap - swap query and target sides of map file.
-swapIn - swap query and target sides of inPsl file.
-suffix=str - append str to the query ids in the output
alignment. Useful with protein alignments, where the result
is not actually and alignment of the protein.
-keepTranslated - if either psl is translated, the output psl
will be translated (both strands explicted). Normally an
untranslated psl will always be created
-mapInfo=file - output a file with information about each mapping.
The file has the following columns:
o srcQName, srcQStart, srcQEnd, srcQSize - qName, etc of
psl being mapped (source alignment)
o srcTName, srcTStart, srcTEnd - tName, etc of psl being
mapped
o srcStrand - strand of psl being mapped
o srcAligned - number of aligned based in psl being mapped
o mappingQName, mappingQStart, mappingQEnd - qName, etc of
mapping psl used to map alignment
o mappingTName, mappingTStart, mappingTEnd - tName, etc of
mapping psl
o mappingStrand - strand of mapping psl
o mappingId - chain id, or psl file row
o mappedQName mappedQStart, mappedQEnd - qName, etc of
mapped psl
o mappedTName, mappedTStart, mappedTEnd - tName, etc of
mapped psl
o mappedStrand - strand of mapped psl
o mappedAligned - number of aligned bases that were mapped
o qStartTrunc - aligned bases at qStart not mapped due to
mapping psl/chain not covering the entire soruce psl.
This is from the start of the query in the positive
direction.
o qEndTrunc - similary for qEnd
If the psl count not be mapped, the mapping* and mapped* columns are empty.
-mappingPsls=pslFile - write mapping alignments that were used in
PSL format to this file. Transformations that were done, such as
-swapMap, will be reflected in this file. There will be a one-to-one
correspondence of rows of this file to rows of the outPsl file.
-simplifyMappingIds - simplifying mapping ids (inPsl target
name and mapFile query name) before matching them. This
first drops everything after the last `-', and then drops
everything after the last remaining `.'.

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