mestato/lab_code

Added primer3 parameter to utilize masking.

Removed a swp file left from a vi session

Added a readme and another rename to findSSRS_fastq_rawreads.pl to be… …

… super clear on usage.

Renamed files …

findSSRs_fastq.pl - This is an older script used to identify SSRs prior to an assembly.
findSSRs_fasta.pl - This is the new and improved script that should be used in all other circumstances.

Last little bug - now correctly calculating number of repeats

Everything working including excel data sheets.

Lots of fixes, excel summary sheet being produced.

fixed lots of errors and bugs in stats and output files. excel not wo… …

…rking yet.

Statistics being calculated and output.

cleaned up main method a bit

Added number of repeats to ssr flat file

Printing fasta files and other flat files done. Collapsing compound s… …

…srs into one entry now works correctly.

Fasta file output done.

parse primer3 output working again

primer3 input file being generated now

Collapse compound ssrs and flag multi ssrs are now done.

Back to basics. Control flow …

main
-> process_file
	-> process_seq
		-> process_ssr
->collapse_compound_ssrs (not yet written)
->flag_multiSSRs
Rest commented out for now

Rethinking things... changed output file description (not yet changed… …

… in code), removed constraint about SSRs being a certain length from end, changed default parameter values.

Moved flag_multiSSRs above output_primer_flat_files b/c the latter de… …

…pends on knowing which ssrs are multi

Subroutine flag_multi_SSRs now also prints fasta files.

New subroutine create_output_files now prints flat files

New subroutine flag_multiSSRs, to identify SSRs that are in contigs w… …

…ith other SSRs.

Separating out three types of output: fasta/flat files, statistics an… …

…d excel. (everything still broken)

New subroutine, initiate_workbooks (mostly code from original parseP3… …

…_output).

The method parseP3_output now deals solely with parsing primer3 outpu… …

…t (and not with initiating Excel worksheets and outputting lines of Excel and fasta files). Excel functionality is currently broken.

Changed name of function getContigHash to process_file. This makes mo… …

…re sense in the workflow (process_file -> process_seq -> process_ssr)

Rewrote process_seq method, now is broken into process_seq, which cal… …

…ls quality_check_ssr and process_ssr. Much cleaner to follow.

Changed hash name from CONTIG_SSRS to CONTIG_SSR_STARTS to clarify it… …

…s purpose

Fixing spaces.

Added output fasta files with sequences in fasta format.

The usage instructions now make it clear that masked file is required… …

…. Paths to primer3 changed to new UTK location.

Addition of warning to usage instructions.

adding post assembly script

adding comments

hwg gssr scripts