support for gzipped file: NLMSABuilder, textfile_to_binaries, and dump_textfile

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Text dump files from pre-built NLMSAs (available at 
http://biodb.bioinformagtics.ucla.edu/PYGRDATA) are extremely large. In 
total, if we uncompress them, it would be about 900GB.

I propose gzipped file support for three classes, NLMSABuilder, 
textfile_to_binaries, and dump_textfile. In that way, we can save disk 
space. Maybe we could give one option, compressed = True (or False) to 
work with gzipped archives.

Original issue reported on code.google.com by deepr...@gmail.com on 1 Jun 2008 at 12:14

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Any SourceURL downloaded by pygr.Data (using download_unpickler()), will be
automatically uncompressed, for a variety of formats based on suffix:
- .tgz, .tar.gz: gunzip and untar
- .tar.bz2: uncompress bz2 and untar
- .gz: gunzip
- .zip: unzip
- .tar: untar

This is handled in a modular way by SourceURL; classes like NLMSABuilder that 
use the
product of SourceURL do not need to be modified in any way to work with 
compressed
files.  There is no need for NLMSA-specific functions like 
textfile_to_binaries() or
dump_textfile() to incorporate (un)compression capabilities, unless we think 
that
users will not have enough disk space to even store the uncompressed file!

Original comment by cjlee...@gmail.com on 22 Aug 2008 at 8:34

• Changed state: Fixed

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Original comment by mare...@gmail.com on 21 Feb 2009 at 1:30

• Changed state: FixedNeedsReview

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Hi Namshin,
please verify the fix to this bug that you reported, and then change its status 
to
Closed.  We are now requiring that each fix be verified by someone other than 
the
developer who made the fix.

Thanks!

Chris

Original comment by cjlee...@gmail.com on 4 Mar 2009 at 8:55

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Original comment by mare...@gmail.com on 13 Mar 2009 at 12:54

• Added labels: reviewby-deepreds

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Original comment by deepr...@gmail.com on 22 Mar 2009 at 10:14

• Changed state: Closed