How to write a perl script to grab the first 100 sequences to a 227,000 sequence file?

Comment on How to write a perl script to grab the first 100 sequences to a 227,000 sequence file?
Re: How to write a perl script to grab the first 100 sequences to a 227,000 sequence file? by Anonymous Monk on Jul 26, 2012 at 21:39 UTC
Any pointers will help. Thank you. site:perlmonks.org FASTA Generic bioperl advice, RFC: Bioinformatics Tutorial, Perl and Bioinformatics, Bio::SeqIO/http://doc.bioperl.org/releases/bioperl-1.0.1/Bio/SeqIO.html/http://www.bioperl.org/wiki/Main_Page	[reply]
Re: How to write a perl script to grab the first 100 sequences to a 227,000 sequence file? by BrowserUk (Pope) on Jul 26, 2012 at 21:39 UTC
change the 99 to 1 less than the number of sequences you want: `perl -e"BEGIN{$/=qq[\n>]}" -ple"$. == 99 && last;" yourfile.fasta >new +file.fasta` [download] With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice. The start of some sanity?	[reply] [d/l]
Re^2: How to write a perl script to grab the first 100 sequences to a 227,000 sequence file? by Anonymous Monk on Apr 11, 2013 at 13:18 UTC
That's nice, but all > except the first one are missing...	[reply]
Re^3: How to write a perl script to grab the first 100 sequences to a 227,000 sequence file? by Anonymous Monk on Apr 11, 2013 at 13:24 UTC
I meant that all sequences are starting with a > inside a fasta file. The code above works perfectly, but somehow it doesn't put the > back, except the first one...	[reply]
Re^4: How to write a perl script to grab the first 100 sequences to a 227,000 sequence file? by educated_foo (Vicar) on Apr 11, 2013 at 13:59 UTC
Re: How to write a perl script to grab the first 100 sequences to a 227,000 sequence file? by pvaldes (Hermit) on Jul 26, 2012 at 21:44 UTC
to grab the first 200 lines (each sequence having at least two lines) its a simple "head -n 200 myfile" problem or, if you want to be more perlish, while $my_file print if $. <= 200, but I suggest you to take a look to bioperl in any case	[reply]
Re: How to write a perl script to grab the first 100 sequences to a 227,000 sequence file? by rnaeye (Monk) on Jul 29, 2012 at 03:31 UTC
Here is one liner: `perl -ne 'print if $. <= 100' inputfile` [download]	[reply] [d/l]


laziness, impatience, and hubris
	PerlMonks

How to write a perl script to grab the first 100 sequences to a 227,000 sequence file?

The best material for plates (tableware) is: