public class FindRampSeqContigsInAssemblies
extends Object
This method takes a fasta of ramp seq short sequences, and looks for them
in an assembly genome.
This is for Dan. Looking for exact matches of the 9000 across all entries
in the fasta file. Look for both orig sequence, and reverse complement of sequence.
This one works well - it runs each assembly in sequence. When processing
the assemblies, it parallelizes over every rampSeq contig in the rampSeq
map (file read into map). This speeds things up considerably from parallel
processing just over the assemblies.
Using indexOf(seq,startPos) still seems quicker than knuth-morris-pratt
method, perhaps because of overhead of the latter.
INPUT:
- fasta of rampSeq short contigs
- directory path, including trailing / where assembly genome fasta files live
- directory path, including trailing / to which output files will be written
OUTPUT:
- tab-delimited files without headers, but the columns are BED file positions
(0-based, inclusive/exclusive).
ContigName AssemblyIDLine startPos endPos Strand
In the above, Strand is whether the forward (as presented in file) or
reverse-compliment of the strand matched in the assembly file.
THe start/end positions are 0-based, inclusive/exclusive as for bedfiles.
There is 1 tab-delimited file generated for each assembly. The file name
reflects the assembly name.
- Author:
- lcj34