Adding work done looking for CRISPRS

There are a few prelim files here, just getting the data stage set.

get_NC_Ecoli_names.pl :
I only want NC type names that refer to E coli.

pick_E_coli_repeats_from_CRISPRdb_file.pl :
uses the E coli NC names (from above) to pull only E coli spacers from the set of all spacers.

simplify_reps_fa_file.pl :
might not be needed, but some CRISPRdb FA headers break bowtie. This swaps out the headers for an int, and makes a mapper file.

index_bowtie_contigs.pl :
generates bowtie indexes of the various samples of all of the sample sets (refered to as tps (timepoints)).

lookup_repeats.pl :
using the known E coli repeats, I just trawl through the bowtie indexes of each of the sample sets, looking occurences.
I am using bowtie to give me matches, or matches within maximally three bps away.

get_contig_with_rep_and_loc.pl
run through the output of the bowtie alignments, make sure that the repeats that are overlapping are ignored and ensuring some sanity allowing the creation of spacers. This file does simplifying of bowtie output to make spacer creation simple

make_spacers.pl
this takes the above output, and makes concrete spacers, per sample

make_spacers_uniq.pl
I want to look at the spacers now in blast. This takes all of the guys that were in each of the various samples, and aggregates them into time point wide sets. (No need to blast same spacer multiple times.)

parse_blast_results.pl
Once I've pulled the blast reports back from NCBI, this script goes through them and throws away the hits with crappy scores, examines what the spacer is likely to be, and classes them as EXISTING_COLI_CRISPR, EXISTING_OTHER_CRISPR, NOT_A_CRISPR_IS_SOMETHING_ELSE and NOTHING.

parse_blast_summaries.pl
this just goes through the summaries (above) and makes sure there are no samples that have vanished / bugs, output is sane.