Hi Perumal,
There isn't a simple fasta extraction tool on the public Main Galaxy
server, but the extraction is possible and could be grouped into a
workflow for re-use once completed. This is simpler that it first looks,
really just 4 steps:
1. Convert the fasta file to tabular:
'FASTA manipulation' -> <javascript:void(0)>FASTA-to-Tabular
Settings: For the option "How many columns to divide title string
into?:" use "2" if there is "identifier" and "description" text. See the
next step for more details.
2. Load your list of identifiers as tabular
This mean "tabular" text format. Adjust the datatype to be "tabular
as needed, and any other formatting so that the "identifiers" are
exactly the same in both files. I am not sure if this is what you meant
by "fasta headers". To be clear, in the fasta file (#1) any characters
after the leading ">" but before the first whitespace (tab, space, etc)
are considered the "identifier" and everything else on the line is
considered the "description". This file (#2) should only contain the
"identifier", not the "description. Here is a link to FASTA format in
case you run into problems here (the IDs not being exact will almost
certainly be the root cause of any issues):
http://wiki.galaxyproject.org/Learn/Datatypes#Fasta
3. Compare the two files together, subsetting out the entries in #1 that
are present in #2.
' Join, Subtract and Group' -> Compare two Datasets
Settings: Compare file #1, column 1 (c1), against file #1, column 2
(c1), 'To find' = Matching rows of 1st dataset.
4. Transform the results back to tabular format.
'FASTA manipulation' -> Tabular-to-FASTA
Settings: Be sure to account for any description fields, if they
are included in your data. At this point you can either put them into
the final fasta output or omit the row/data altogether and just pull out
identifiers/sequence.
Hopefully this helps -
Jen
Galaxy team
On 11/30/12 7:55 AM, Perumal Vijayan wrote:
I have successfully uploaded a large fasta file (2.5 million genomic
sequence contigs) onto Galaxy server. I wish to extract a subset of
sequences from this file. I have a list of the fasta headers. Is
there a way I can accomplish this on Galaxy?
--
Perumal Vijayan
Saskatoon
Canada
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--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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please use the interface at:
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