batch rename multiple fasta

Pedro · 03-19-2012, 03:55 AM

Hi,
I've a fairly high amount of hybrid assembly tests and the headers of the multiple-fasta files have different strings which I would like to normalize. Could you suggest how can I do a (customized) batch header renaming in multiple fasta files. I.e. [input multiple fasta file] [custom string in the headers, only differentiated by numbering of the contig] [output prefix]? If possible to add qualifiers even better.

Thanx
P

maasha · 03-19-2012, 05:29 AM

You could have a look at Biopieces.

Especially read_fasta, write_fasta, add_ident and merge_vals.

maubp · 03-19-2012, 06:47 AM

Learning a scripting language would be a good idea for working in bioinformatics. This would be easy with Perl and BioPerl, Python and Biopython, or Ruby and BioRuby etc.

Pedro · 03-19-2012, 01:35 PM

Quote:

Originally Posted by maasha

You could have a look at Biopieces.

Especially read_fasta, write_fasta, add_ident and merge_vals.

Thank you, it solved the question

cheers
P

P.S.-maubp, thank you for the hint...

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
hello and BLAST batch question	SophieP	Introductions	10	02-18-2014 04:20 AM
Batch effect, SNPs	YKay	Genomic Resequencing	0	12-13-2011 06:42 AM
Align multiple sequences in tabular or fasta format	pchiang	Bioinformatics	7	07-01-2011 11:18 PM
help needed to retrieve fasta reads from fasta db	prashanthpnu	Bioinformatics	1	06-21-2011 06:59 AM
batch job manager?	Richard Finney	Bioinformatics	2	04-26-2011 02:10 PM

03-19-2012, 03:55 AM	#1
Pedro Junior Member Location: Portugal Join Date: Dec 2008 Posts: 6	batch rename multiple fasta Hi, I've a fairly high amount of hybrid assembly tests and the headers of the multiple-fasta files have different strings which I would like to normalize. Could you suggest how can I do a (customized) batch header renaming in multiple fasta files. I.e. [input multiple fasta file] [custom string in the headers, only differentiated by numbering of the contig] [output prefix]? If possible to add qualifiers even better. Thanx P

03-19-2012, 05:29 AM	#2
maasha Senior Member Location: Denmark Join Date: Apr 2009 Posts: 153	You could have a look at Biopieces. Especially read_fasta, write_fasta, add_ident and merge_vals.

03-19-2012, 06:47 AM	#3
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Learning a scripting language would be a good idea for working in bioinformatics. This would be easy with Perl and BioPerl, Python and Biopython, or Ruby and BioRuby etc.