query using mysql on ucsc table browser

Question

[bioguy24]

I have a folder of 57 text files each with 1000 locations in them. I was going to use the mySQL browser at

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A

but I am getting a connection error using ubuntu 14.04

cmccabe@DTV-A5211QLM:~$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A
ERROR 2003 (HY000): Can't connect to MySQL server on 'genome-mysql.cse.ucsc.edu' (110)

Basically, I am trying to run a query in refGene that will use each of the locations in all 57 files and return the sequences of the CDS plus 10 bases at either end.

Example output:

>hg19_refGene_NM_001305275_0 range=chr1:955543-955763 5'pad=10 3'pad=10 strand=+ repeatMasking=none
cgcctgcgccATGGCCGGCCGGTCCCACCCGGGCCCGCTGCGGCCGCTGC
TGCCGCTCCTTGTGGTGGCCGCGTGCGTCCTGCCCGGAGCCGGCGGGACA
TGCCCGGAGCGCGCGCTGGAGCGGCGCGAGGAGGAGGCGAACGTGGTGCT
CACCGGGACGGTGGAGGAGATCCTCAACGTGGACCCGGTGCAGCACACGT
ACTCCTGCAAGgtgcgcccac
>hg19_refGene_NM_001305275_1 range=chr1:957571-957852 5'pad=10 3'pad=10 strand=+ repeatMasking=none
tccaccccagGTTCGGGTCTGGCGGTACTTGAAGGGCAAAGACCTGGTGG
CCCGGGAGAGCCTGCTGGACGGCGGCAACAAGGTGGTGATCAGCGGCTTT
GGAGACCCCCTCATCTGTGACAACCAGGTGTCCACTGGGGACACCAGGAT
CTTCTTTGTGAACCCTGCACCCCCATACCTGTGGCCAGCCCACAAGAACG
AGCTGATGCTCAACTCCAGCCTCATGCGGATCACCCTGCGGAACCTGGAG
GAGGTGGAGTTCTGTGTGGAAGgtgcgtggtg

I am not sure what is wrong or what query to use as AI have never used this tool. Thank you :).

[Pierre Lindenbaum]

works for me.

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg38 -e 'select now();
+---------------------+
| now()               |
+---------------------+
| 2016-01-19 09:29:40 |
+---------------------+

check your proxy settings?!!

[Pierre Lindenbaum]

to get the fasta sequence: you're looking for tabix , or twoBitToFa see How To Get The Sequence Of A Genomic Region From Ucsc?

[bioguy24]

Looks like it is the proxy settings... thank you :).