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From: Robert C. <rw...@al...> - 2005-12-03 17:21:02
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Hello all, Here's my quick-and-dirty tar ball of both MyGenBank and dbtree: http://mgb.sourceforge.net/download/quick-and-dirty-beta/ Hopefully, I'll get a chance later tonight to clean it up and put it into SF's CVS. Regards, - Robert |
From: Robert C. <rw...@al...> - 2004-01-08 21:04:56
|
On Thursday, January 8, 2004, at 10:23 AM, Feng, Yucheng wrote: > Hi, Robert: > Thanks a lot. It seems to work fine now, That's good to hear. > except.... > > One little glitch still left in update. I got an error when try to > update: > > [yfeng:Bioinf/MyGenBank/bin] yuchengfeng% mygb_admin update > update :update > updating MyGenBank > ftp-ing 1222 > Bad file descriptor at .//mygb_admin line 193. > > gunzip: stdin: unexpected end of file > ... > Maybe in the subroutine ftpNCBI( ), we should exclude the files that > start with con_nc. Made these changes to the admin script: # next unless $file =~ /(\w+)\.flat\.gz$/; next unless $file =~ /(nc\w+)\.flat\.gz$/; Tested it with: mygb_admin -t update Now the script skips the con_nc files and only gets files beginning with nc. Again, thanks for the feedback. Hopefully, when I get back from PAG I can get all this stuff into the CVS server on SourceForge, especially because I created a bunch of little helper scripts to install and uninstall MyGenBank. This will allow you to easily create multiple instances of the data directories and the database. Regards, - Robert |
From: Robert C. <rw...@al...> - 2004-01-08 10:09:12
|
Hello Yucheng, > From: Feng, Yucheng > Subject: Question about MyGenBank > > I downloaded mygenbank from http://sourceforge.net/projects/mgb/ > Here is the problem: > > When I run > > mygb_admin ftp (or -t ftp), I got the following error message: > > gunzip: stdin: invalid compressed data--format violated > Caught a SIGPIPE at /Library/Perl/Net/FTP.pm line 503 > $ = Net::FTP::get('Net::FTP=GLOB(0x24a560)', 'gbbct1.seq.gz', > 'GLOB(0xc780c)') called > from file `.//mygb_admin' line 194 > $ = main::ftpNCBI('gbbct1') called from file `.//mygb_admin' line 180 > $ = main::ftp called from file `.//mygb_admin' line 94 > Abort After a bit of sleuthing, I discovered one needs to add $ftp->binary() after every ftp login: $ftp->login("anonymous", "$ENV{USER}\@$ENV{HOST}"); $ftp->binary(); My guess is that requiring to specify binary is a new "feature" of net::ftp. See below for details on how I determined this. I'll try to put a new MyGenBank package together during the PAG conference. > Although the first file is downloaded and correctly gunzipped into > $DATA/GenBank/, it stopped right there, and the 2nd file is not > processed. I would not trust any of the data you have downloaded thus far using MyGenBank. I would scrap what you have, make the changes to the mygb_admin script, and then start again. Regards, - Robert ----- Details: I suspected that there was a either a bug in the libnet library or some setting was not being set. To test this, I downloaded the gbbct1.seq.gz file using both ncftp and this minimal perl script: #!/usr/bin/perl -w use strict; use Net::FTP; my $file='gbbct1' ; my $ftp = new Net::FTP("ftp.ncbi.nih.gov") ; if (not defined $ftp) {warn "FTP error\n" ; die $! ; } $ftp->login("anonymous", "guest\@localhost") or die $!; $ftp->cwd("genbank"); open(GZIP, "> $file.seq.gz") or die $! ; $ftp->get("$file.seq.gz", \*GZIP) or die $! ; close GZIP; I then compared the two downloaded files: -rw-r--r-- 1 robertci staff 68560715 Jan 8 03:20 gbbct1.seq.gz # downloaded with perl script -rw-r--r-- 1 robertci staff 68561549 Jan 8 02:26 gz/gbbct1.seq.gz # downloaded with ncftp I then tried uncompressing each: $ zcat gz/gbbct1.seq.gz >/dev/null # file using ncftp had no errors $ zcat gbbct1.seq.gz >/dev/null # file using net::ftp had errors zcat: gbbct1.seq.gz: invalid compressed data--format violated It seems as though downloading using Net::FTP somehow corrupts the file. I read through 'perldoc net::ftp' and noticed that one of the modules was "binary" So, I added $ftp->binary(); to the ftp.pl script: $ftp->cwd("genbank"); $ftp->binary(); open(GZIP, "> $file.seq.gz") or die $! ; When I reran the script, everything worked just fine. I then added it to the mygb_admin script and now the 'mygb_admin -t ftp' works just fine. |
From: Robert C. <rw...@al...> - 2002-12-12 16:27:47
|
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