Hi guys, I'm very new to pygr and to python but after reading through the specs I think pygr will greatly simplify my work once I learn how to use it properly.. I've done this with just python but wanted to learn this framework and improve on my current work.
I have a couple of tasks I'm trying to accomplish for preparation of some wetlab work.. *Data I will be using:* 1. Disease specific TCGA SSM data (single mutations much like SNP) 2. 3'UTR libraries 3. miRNA target SNP datasets (mostly from PolymiRTS) 4. SNPdb disease specific data. *Actions that will be performed:* 1. map TCGA SSM mutations to 3UTRs 2. map TCGA SSM to PolymiRTS SNP datasets (all different formats) 3. ..... to SNPdb disease specific data. When looking through the documentation I came across literature on annotations and came up with a sample TCGA ssm class * class tcga_ssm(object):* * def __init__(self, chromosome_start, chromosome_end, chromosome_strand, gene_name, ensembl_gene_id):* * (self.id, self.start, self.stop, self.orientation) = \* * ( "%s|%s|%s" % (chromosome_start, gene_name, ensembl_gene_id), chromosome_start, chromosome_end, chromosome_strand) * the problem is this doesn't account for the 40+ other fields that I may need later once I match.. Also few of of the datasets include much sequence information and the example I saw requires a DNA db to create an annoDB annodb = annotation.AnnotationDB(slice_db, dna_db I will have to overlay coordinates, grab seed sequences and provide reports for mixing and matching of the above data.. what is the best approach.. a nudge in the right direction would be awesome. -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to pygr-dev+unsubscr...@googlegroups.com. To post to this group, send email to pygr-dev@googlegroups.com. Visit this group at http://groups.google.com/group/pygr-dev. For more options, visit https://groups.google.com/groups/opt_out.
