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 -~----------~----~----~----~------~----~------~--~---
