Hi Namshin, Thank you for the prompt reply on this. I eventually gave up trying to understand the error and, as you suggested, downloaded the pre- built NLMSA file. Regardless of how I do this (automatic download or using NLMSABuilder on a manually downloaded file), it always throws this error:
pygr.metabase.WorldbaseNotFoundError: 'unable to find Bio.MSA.UCSC.hg19_multiz46way in WORLDBASEPATH' Using worldbase.dir(), Bio.MSA.UCSC.hg19_multiz46way shows up along with local copies of the genomes that I've downloaded. I can access and use the genomes just fine, but the MSA throws this error. Yet, all of these files reside in the same folder! Any suggestions? Chris On Sep 16, 6:28 pm, Namshin Kim <n...@rna.kr> wrote: > Hi Chris, > > I think what you should check SequenceFileDB whether the the given > chromosome is in it. > > i.e. call the given chromosome, > > >>> hg19['chr6_qbl_hap6'] > >>> ponAbe2['chr6'] > > I don't see any problems with your NLMSA building script. > > If you want to build NLMSA from MULTIZ alignments from UCSC genome browser > not custom ones, I suggest another solution. You can download all genomes > and pre-built NLMSA files available > athttp://biodb.bioinformatics.ucla.edu/PYGRDATA/andhttp://biodb.bioinformatics.ucla.edu/GENOMES/ > > Or, you can give download=True option for automatic downloading and building > SequenceFileDB and NLMSA from biodb2.bioinformatics.ucla.edu > > WORLDBASEPATH = '.,http://biodb2.bioinformatics.ucla.edu:5000'# save your > resources in '.' current directory, and connect biodb2 pygr resources > viahttp://biodb2.bioinformatics.ucla.edu:5000 > > from pygr import worldbase > worldbase('Bio.MSA.UCSC.hg19_multiz46way', download=True) > > -- > Namshin Kim > > On Fri, Sep 17, 2010 at 6:29 AM, Chris Fuller <chriskful...@gmail.com>wrote: > > > Hello Pygr-dev, > > > It seems that others have previously run into warnings like: > > > *** WARNING: Unknown sequence hg19.chr6_qbl_hap6 ignored... > > *** WARNING: Unknown sequence panTro2.chr6 ignored... > > *** WARNING: Unknown sequence ponAbe2.chr6 ignored... > > > when building an NLMSA using MAF files. I'm running into thousands of > > these when using multiz46way and six corresponding genomes, all > > downloaded from UCSC. With grep I can verify that, for instance, > > ponAbe2.chr6 references exist in chr6.maf and that my ponAbe2 fasta > > file really contains a >chr6 header. > > > How can I determine if these errors originate in my files or my pygr > > code? Any suggestions? > > > Thank you, > > > Chris > > > Chris Fuller > > ch...@genome.ucsf.edu > > > The code I'm using (in Eclipse) is: > > > import os, glob > > from pygr import cnestedlist,seqdb > > > # Create list of full paths to all MAF files involved > > maf_path_string = '/home/chris/Storage/Data/Public/Human/hg19_MAF' > > maf_files_list = glob.glob(maf_path_string + '/*.maf') > > > # Create list of full paths to each Genome in single FASTA format > > genomes ={} > > seqlist = ['hg19','panTro2', 'ponAbe2', 'rheMac2', 'mm9', 'rn4'] > > genomes_path_string = '/home/chris/Storage/Data/Public/Genomes/ > > single_file' > > seqlist_path = [] > > for i in range(len(seqlist)): > > seqlist_path.append(genomes_path_string + '/' + seqlist[i]) > > > for orgstr in seqlist_path: > > genomes[orgstr] = seqdb.SequenceFileDB(orgstr) > > genomeUnion = seqdb.PrefixUnionDict(genomes) > > > # Now build it: > > NLMSA_path = '/home/chris/Storage/Data/Public/Human/hg19_MAF/NLMSA' > > msa = cnestedlist.NLMSA(pathstem=NLMSA_path, mode='w', > > seqDict=genomeUnion, mafFiles=maf_files_list, bidirectional=False) > > msa.build(saveSeqDict=True) > > > -- > > You received this message because you are subscribed to the Google Groups > > "pygr-dev" group. > > To post to this group, send email to pygr-...@googlegroups.com. > > To unsubscribe from this group, send email to > > pygr-dev+unsubscr...@googlegroups.com<pygr-dev%2bunsubscr...@googlegroups.com> > > . > > For more options, visit this group at > >http://groups.google.com/group/pygr-dev?hl=en. -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-...@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.
