tag:blogger.com,1999:blog-14688252.post748067545529309283..comments2024-02-16T10:17:12.310+01:00Comments on YOKOFAKUN: CouchDB for Bioinformatics: Storing SNPs - My NotebookPierre Lindenbaumhttp://www.blogger.com/profile/13765837643388003852noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-14688252.post-23479377750988156902014-11-11T13:04:29.960+01:002014-11-11T13:04:29.960+01:00Hi, I rewrote your Java Code to Python http://t.co...Hi, I rewrote your Java Code to Python http://t.co/xHFTk0Lwwp .Anonymoushttps://www.blogger.com/profile/13834100362815820631noreply@blogger.comtag:blogger.com,1999:blog-14688252.post-10252251078172022862013-02-20T05:08:34.519+01:002013-02-20T05:08:34.519+01:00Could you please post the whole project on GitHub?...Could you please post the whole project on GitHub? Anonymoushttps://www.blogger.com/profile/13834100362815820631noreply@blogger.comtag:blogger.com,1999:blog-14688252.post-61825888724320500262009-05-13T10:38:00.000+02:002009-05-13T10:38:00.000+02:00ok, very interesting then.
I think I will stick wi...ok, very interesting then.<br />I think I will stick with sqlalchemy and mysql for the moment, but for the next project I will look at it.<br />I was also looking at hdf5, a binary format which is similar to a hierarchical database.dalloliogmhttps://www.blogger.com/profile/11230528124875348719noreply@blogger.comtag:blogger.com,1999:blog-14688252.post-24276226131263418602009-05-12T18:36:00.000+02:002009-05-12T18:36:00.000+02:00@dalloliogm I don't think you can do things li...@dalloliogm I don't think you can do things like that (join,...) with a *single* query. But I would store the start positions of the genes just like I stored the snp , I would query each gene for each snp and store the result in a temporary database before digesting the result.<br /><br />There is no SQL for this kind of key/value databases because you can store anything in the entries. You Pierre Lindenbaumhttps://www.blogger.com/profile/13765837643388003852noreply@blogger.comtag:blogger.com,1999:blog-14688252.post-8258920074795247052009-05-12T17:40:00.000+02:002009-05-12T17:40:00.000+02:00for example, let's say you want to collect all the...for example, let's say you want to collect all the snps within 40,000 bp of any gene in a list of genes.<br /><br />How would you do that with couchdb? Will it be simpler with respect to a relational database?<br /><br />Or another example may be representing a graph into couchdb. Do you think it would be easier to navigate it with this solutions?dalloliogmhttps://www.blogger.com/profile/11230528124875348719noreply@blogger.comtag:blogger.com,1999:blog-14688252.post-44218445855779433682009-05-12T17:38:00.000+02:002009-05-12T17:38:00.000+02:00The idea is good, and thank you for the post.
Howe...The idea is good, and thank you for the post.<br />However, I am not sure on which are the advantages of couchdb over a relational database, for bioinformatics...dalloliogmhttps://www.blogger.com/profile/11230528124875348719noreply@blogger.com