Strange... Correct URL will be http://biodb.bioinformatics.ucla.edu/GENOMES/ponAbe2/ponAbe2.gz The URL you used does not exist, thus it give 404 error (HTML doc). Hmm... I never downloaded and built the hg18_multiz44way via XMLRPC. I will try that...
Thanks, Namshin Kim On Thu, Sep 3, 2009 at 6:54 AM, Paul Rigor (gmail) <paulri...@gmail.com>wrote: > Hi Namshim, > Downloading the 44way alignment was successful. However, the persistend > data (.pygrdata) seems to be unworkable. The metabase lists Bio.MSA, etc, > but it cannot be loaded. > > Also, I've attempted to download the genomes from the UCLA metabase, but a > genome might be corrupt. Specifically, > > http://biodb.bioinformatics.ucla.edu/GENOMES/ponAbe2/chromFa.tar.gz > > which gives the error message below. In fact, checking the file that is > downloaded (ponAbe2.tar.gz), is an HTML document! > > $ file ponAbe2.tar.gz > ponAbe2.tar.gz: HTML document text > > > ....[error trace below] > .... > /home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/python2.6/site-packages/pygr-0.8.0.beta1-py2.6-linux-x86_64.egg/pygr/downloader.pyc > in do_untar(filepath, mode, newpath, singleFile, **kwargs) > 105 newpath = filepath + '.out' > 106 import tarfile > --> 107 t = tarfile.open(filepath, mode) > 108 try: > 109 if singleFile: # extract to a single file > > /home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/python2.6/tarfile.pyc > in open(cls, name, mode, fileobj, bufsize, **kwargs) > 1662 else: > 1663 raise CompressionError("unknown compression type > %r" % comptype) > -> 1664 return func(name, filemode, fileobj, **kwargs) > 1665 > 1666 elif "|" in mode: > > /home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/python2.6/tarfile.pyc > in gzopen(cls, name, mode, fileobj, compresslevel, **kwargs) > 1713 **kwargs) > 1714 except IOError: > -> 1715 raise ReadError("not a gzip file") > 1716 t._extfileobj = False > 1717 return t > > ReadError: not a gzip file > > > > > On Tue, Sep 1, 2009 at 9:55 PM, Paul Rigor (gmail) <paulri...@gmail.com>wrote: > >> Well, we have time, storage and bandwidth =) >> I'll let you know how it goes? Maybe we can host an XMLRPC mirror someday >> too. >> >> Thanks, >> Paul >> >> >> On Tue, Sep 1, 2009 at 9:41 PM, Namshin Kim <deepr...@gmail.com> wrote: >> >>> Hi Paul, >>> I just checked the size of hg18_multiz44way and it is 167GB for just >>> NLMSA. If we consider genome assemblies you may not have, it would be ~ >>> 250GB. I think it would take a long time to download all files. >>> >>> -- >>> Namshin Kim >>> >>> >>> >>> On Wed, Sep 2, 2009 at 1:33 PM, Paul Rigor (gmail) >>> <paulri...@gmail.com>wrote: >>> >>>> >>>> Hi Namshin, >>>> I'm running this over night =) Has anyone successfully pulled and used >>>> this alignment? >>>> >>>> Thanks, >>>> Paul >>>> >>>> On Sun, Aug 2, 2009 at 4:40 PM, Namshin Kim <deepr...@gmail.com> wrote: >>>> >>>>> Now the downloadable resources are available on biodb2 XMLRPC server. >>>>> >>>>> Two ways to build NLMSA. >>>>> >>>>> 1. metabase >>>>> >>>>> >>> import os >>>>> >>> os.environ['WORLDBASEPATH'] = '., >>>>> http://biodb2.bioinformatics.ucla.edu:5000' >>>>> >>> from pygr import metabase >>>>> >>> mdb = metabase.MetabaseList() >>>>> >>> hg18 = mdb('Bio.MSA.UCSC.hg18_multiz44way',download=True) >>>>> >>>>> 2. from text files >>>>> >>>>> download text files from >>>>> http://biodb.bioinformatics.ucla.edu/PYGRDATA/ >>>>> use cnestedlist.textfile_to_binaries('hg18_multiz44way') function to >>>>> convert from text to binaries >>>>> >>>>> If you want to see the script used to add these resources, visit this >>>>> URL. >>>>> >>>>> >>>>> http://github.com/deepreds/pygr/tree/d7ab9247dcd39b7d474029cb8749a53eb8582968/tests/biodb2_update >>>>> >>>>> >>>> >>>> >>> >>> >>> >> >> >> -- >> Paul Rigor >> Graduate Student >> Institute for Genomics and Bioinformatics >> Donald Bren School of Information and Computer Sciences >> University of California, Irvine >> http://www.paulrigor.net/ >> http://www.ics.uci.edu/~prigor >> > > > > -- > Paul Rigor > Graduate Student > Institute for Genomics and Bioinformatics > Donald Bren School of Information and Computer Sciences > University of California, Irvine > http://www.paulrigor.net/ > http://www.ics.uci.edu/~prigor > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
