Comments on: Short Bioinformatics Hacks, ch. 1 http://bytesizebio.net/index.php/2009/05/25/short-bioinformatics-hacks-ch-1/ The musings and ravings of a computational biologist about science, computers, music and, you know, stuff Sat, 05 May 2012 18:13:49 +0000 hourly 1 http://wordpress.org/?v=3.3.2 By: Iddo http://bytesizebio.net/index.php/2009/05/25/short-bioinformatics-hacks-ch-1/comment-page-1/#comment-475 Iddo Tue, 23 Jun 2009 20:41:24 +0000 http://bytesizebio.net/?p=1337#comment-475 <a href="#comment-474" rel="nofollow">@Zee</a> Why not indeed.... :) @Zee
Why not indeed…. :)

]]> By: Zee http://bytesizebio.net/index.php/2009/05/25/short-bioinformatics-hacks-ch-1/comment-page-1/#comment-474 Zee Tue, 23 Jun 2009 19:41:48 +0000 http://bytesizebio.net/?p=1337#comment-474 Why not just use EMBOSS infoseq e.g. $ infoseq -auto -stdout -only -length mysequences.fa > dist.csv # And for GC $ infoseq -auto -stdout -only -pgc mysequences.fa And it should be a whole lot faster than gawk Why not just use EMBOSS infoseq e.g.

$ infoseq -auto -stdout -only -length mysequences.fa > dist.csv

# And for GC

$ infoseq -auto -stdout -only -pgc mysequences.fa

And it should be a whole lot faster than gawk

]]> By: riju aikkal http://bytesizebio.net/index.php/2009/05/25/short-bioinformatics-hacks-ch-1/comment-page-1/#comment-473 riju aikkal Fri, 19 Jun 2009 04:47:43 +0000 http://bytesizebio.net/?p=1337#comment-473 HI, Nice to see the code, I have been using the same trick. I wish to share another one to find the number of sequences in a fasta file. Open the file using microsoft word or other word processing application. Use 'find and replace' option there. Find > and replace all with >. then it will show how many replacement it did. Chears.. riju aikkal Bioinformatics centre, Indian Institute of Spices Research, India HI, Nice to see the code, I have been using the same trick. I wish to share another one to find the number of sequences in a fasta file. Open the file using microsoft word or other word processing application. Use ‘find and replace’ option there. Find > and replace all with >. then it will show how many replacement it did.

Chears..
riju aikkal
Bioinformatics centre, Indian Institute of Spices Research, India

]]> By: Iddo http://bytesizebio.net/index.php/2009/05/25/short-bioinformatics-hacks-ch-1/comment-page-1/#comment-447 Iddo Tue, 26 May 2009 02:43:07 +0000 http://bytesizebio.net/?p=1337#comment-447 <a href="#comment-445" rel="nofollow">@Neil</a> Good idea. You want to get on it? You can start with the stuff from here, I'll publicise it at the next posting. <a href="#comment-446" rel="nofollow">@PN</a> D'oh! thanks. I've been using an alias to my more cumbersome version since i don't know when... I updated the post with your more elegant version. @Neil

Good idea. You want to get on it? You can start with the stuff from here, I’ll publicise it at the next posting.

@PN

D’oh! thanks. I’ve been using an alias to my more cumbersome version since i don’t know when… I updated the post with your more elegant version.

]]> By: PN http://bytesizebio.net/index.php/2009/05/25/short-bioinformatics-hacks-ch-1/comment-page-1/#comment-446 PN Tue, 26 May 2009 01:33:52 +0000 http://bytesizebio.net/?p=1337#comment-446 grep ">" mysequences.fa | wc -l can be rewritten as grep -c "^>" mysequences.fa Using ^ and not tells you if the fasta format is valid. grep “>” mysequences.fa | wc -l

can be rewritten as

grep -c “^>” mysequences.fa

Using ^ and not tells you if the fasta format is valid.

]]> By: Neil http://bytesizebio.net/index.php/2009/05/25/short-bioinformatics-hacks-ch-1/comment-page-1/#comment-445 Neil Mon, 25 May 2009 23:32:12 +0000 http://bytesizebio.net/?p=1337#comment-445 Thanks for sharing - I know most bioinformaticians have many small hacks just like these. It would be nice if they were shared more widely. Perhaps <a href="http://gist.github.com/gists" rel="nofollow">gists</a> at Github is a good way to do this? Thanks for sharing – I know most bioinformaticians have many small hacks just like these. It would be nice if they were shared more widely. Perhaps gists at Github is a good way to do this?

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