**This is an old revision of the document!** ----
====== pluck_scripts ====== This is a set of Python scripts written by Kevin Karplus, originally created in /projects/lowelab/users/course/karplus (hence the acronym "pluck"). The scripts perform a variety of useful tasks. Each one has minimal internal documentation, invoked by running with the --help option. ===== Scripts ===== * check-hypotheses-with-solid given a set of hypotheses about possible changes to a scaffold, checks to see whether the SOLiD mate-pair reads provide more support for the original scaffold or the modified one. The hypotheses are in the form "AGT:contig00001 345:AGTA", that is, a string in the scaffold, where the string is located, and what the string is replaced with. Either string can be "-" to represent an insertion or deletion. The insertion "-:contig00001 345:AA" would mean the insertion of two As before position 345 of contig00001, with numbering starting at 1 in the contig. * check-inversions FIXME * classify-blast-reads FIXME * extract-fragments FIXME * filter-blat FIXME * find-dna-differences FIXME * find-frequent-color-kmers FIXME * kstitcher FIXME * make-contig-lengths FIXME * make-inversion-hypotheses FIXME * make-pseudoreads FIXME * make-scaffold-from-blat FIXME * map-colorspace FIXME * pair-contigs FIXME * select-by-color-kmers FIXME * tsv2gnuplot FIXME ===== Python modules ===== * aligner.py for doing local or global alignment. This is a rather slow way to align things and should only be used for short sequences (like showing a small indel in context). * compress.py This was an attempt to merge color-space and flow space, by reducing all runs of 0s to a single 0. It turned out not to be as useful as I'd hoped, and further exploration was abandoned. --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/15 22:19// * fasta.py Input/Output module for fasta files, together with alphabet definitions and utility functions like reverse complement. * subst_matrix.py for creating DNA substitution matrices from a small number of parameters.
