Perl Program To Access Information From Ucsc

Question

[kranthiv1889]

I have a set of SNP identifiers and I need to retrieve information from UCSC. I know I can use a table browser and choose from tracks and groups but I need to write a perl program where someone can input a set of identifiers and then get a required output. For eg, Suppose I have selected SNP/CNV array track and AFFY SNP 6.0 as the SQL table data I need to write a perl program where I can input a set of SNP identifiers and get an output file.Can I use Bioperl? I just need someone to give me a general idea on how to go forward.

Answer 1

[Pavel Senin]

It was Is There Such A Thing As A Ucsc Api?, I guess

[kranthiv1889]

I am not good in SQL and a perl script will be really helpful.I will try putting this question in another way. I need to access the ftp for hg19 database and read an SNParray txt file. Then I just need to find overlaps in my query and the text file. can we do this using perl?

[Pavel Senin]

Sorry, I don't have a script, and can't hack it starting from a scratch right now, because I never worked with this task and it will eat my time. From other hands, pretty much anything is feasible with the help from this community, start coding, ask questions once your code throws exception or gives erroneous results, whoever knows and available at times - will give you hints.