couple of scripts to batch run phyml/modelgen, convert mase to fasta and a seqConveter script (not mine)
new version of database requires a new add script!
Merge branch 'master' of github.com:guyleonard/random_scripts
relevant database info
updated to include NCBI parsing - and to handle funky NCI headers - I should include this in REFGEN!!
added date-time and old group name lookup
updated to now handle NCBI data from multi-header fasta files
it is reading FASTA from NCBI but the files shouldn't be larger than
5GB or it crashes out... a few other changes, but there's lots of comments
this time. it is working.
to do - update jgi/other import, more graceful character removal before mysql breaks
a script to query the orchard database to donwload taxa info...
rudimentary - needs polish. works
a script to split a fasta into chunks - gives option to limit on sequence number per file yoinked from http://bioinfocodelets.blogspot.co.uk/2009/04/perl-script-for-splitting-fasta-file.html
a couple of changes to the mysql - notantly INSERT IGNORE (to ignore duplicate entries
I have also changed the regex matching on species name to be faster/specific
cleaning up, adding etc files
well, i haven't updated this in a bit! shocking.
i've no put in a quick mysql check to see if data is in the DB
already and to skip it if so...
I'm also extracting all info from GenBank rather than pesky pattern match
each taxon name - code is commented out for now
useful script to count+report colour pages in PDFs - useful so you know which pages to print in color or b/w - i.e. thesis printing!!
parse blast output counting hits, useful for EST comparison etc
a simple AGP (from newbler) to GFF3 format converter for GMOD
essentially this is for plotting supercontig/contigs against an
alignmnet...
A script to sift out unwanted sequences based on their "top-hit" from a blast report, uses ncbi taxonomy to return class/division with user based sifting of unwanted groups...
updated to output kept, sifted and no hits into separate files!
Update plant_seed_in_orchard.pl
Update plant_seed_in_orchard_v2.pl
Update getspecies_gr_v2.pl