Convert FASTA file RNA to DNA using sed on the linux command line

sed '/^[^>]/ y/uU/tT/' uracil.fasta > thymine.fasta 

Piece of cake.

lftp mirror: best way to download an entire directory from a FTP server

As much as I hate FTP, there situations where one must use it.  I finally have settled on the best way to get an entire directory, with recursive file retrieval:

lftp -e "mirror dir1/subdir2/subdir3" -u username,password ftphost.domain.com

Of course, FTP must die, but until then, I am glad there is lftp.

GNU parallel -- the best thing since sliced bread

When I first found GNU parallel last fall, I thought it was the bee's knees. So well conceived, so well executed, so well documented... so generous to the user, and most of all, so darn handy.


I've been using it extensively with the ::: notation to feed data files into a pipeline in parallel, and it does exactly what I want it to do.

But today it goes to a whole new level, as I realize there is a whole other side to the tool: the ability to feed parts of a single input file into a pipeline in parallel.

For example, BLAST can be effectively (embarrassingly) parallelized as follows:

cat temp.fa | parallel -j 10 --block 100k --recstart '>' --pipe blastn -evalue 0.01 -outfmt 6 -db refseq_genomic -query - > result.txt

The magic is in the pipe option.  Of course, we've all written blast parallelizers, but I've never seen a solution as neat and simple as this one liner!

This is from Michael Kuhn's excellent post on the subject.  Thanks!

Of bash and streams and pipes - One Tee To Rule Them All

There is a great answer on stack overflow showing how to feed one output stream into multiple processes.  It is a little bit of a hack of the excellent tool tee, which I've been using for some time.  Normally, tee take stout and writes it to a file, while passing it along to stout.  This solution provided on s.o. shows how to hack this with the bash trick >(process)  -- so as far as tee knows, it is writing to 2 or more files, but the "files" are actually background processes.

This syntax is bash-dependent, so won't work in sh, and this will likely come up if you're using system() in, say,  perl.  There is another excellent answer on stack overflow on how to deal with this.

Side note:  Using the <(command) trick, my post from March 16 can now be written:

paste <(grep -v "#" hsa.gff | cut -f 1,4,5,9) <(grep -v "#" hsa.gff | cut -f 6,7) | sed s/^/chr/ >mirbase18.bed

 

mirbase gff annotations in bed format

The mirbase.org folks in Manchester are doing a great job, I think, but they only release their annotations in gff format.  I think the following will convert that into an acceptable bed-format file:

## get mirbase18 annotation and convert to a bed like format
 wget ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff
 grep -v "#" hsa.gff | cut -f 1,4,5,9 >mirbase18.temp1
 grep -v "#" hsa.gff | cut -f 6,7 >mirbase18.temp2
 paste mirbase18.temp1 mirbase18.temp2 | sed s/^/chr/ >mirbase18.bed

Extra credit: Is there a clever shell trick to piping two separate stdins into paste, thus avoiding the temp files?

2012 NAR Database Summary (Category List)

Bioinformatic databases grow like kudzu, so I'll no doubt be referring to this directory in the coming year.

http://www.oxfordjournals.org/nar/database/c/

 

How to get the entire recursive directory structure of an FTP site using wget

How can I use wget to get a recursive directory listing of an entire FTP site?

yes, wget --no-remove-listing ftp://myftpserver/ftpdirectory/ will get and retain a directory listing for a single directory (which was discussed here)

but, wget -r --no-remove-listing ftp://myftpserver/ftpdirectory/ will recurse and download an entire site

so, if you want to get the recursive directory structure, but not download the entire site, try wget -r --no-remove-listing --spider ftp://myftpserver/ftpdirectory/