This means that there were no results. My fault - the Filter tool is
the wrong choice. The Select tool, as you were starting with, is
better for this case. The issues you had originally were most likely
with format or the regular expression. So, be sure to do the
following this time:
1. Converting to tabular format (choose "1" for the identifier on
this tool's form, to keep the output in a simple two column format)
2. Use a regular expression in the Select tool, "Matching", like
this:
\tATGC
Where the "\t" indicates tab (the tab between the two columns),
anchoring the matching text to the start of the sequence string. You
could be more specific with the regular expression if you need to,
following the guidelines on the tool help, but it probably isn't
necessary if the rest of your sequences are formatted like the
examples below.
These sequences in your example are seperated by an empty line - but
I am assuming that was just the way the data was pasted into the
email. In a properly formatted fasta file, there should be no empty
lines. To remove empty spaces in a fasta file, you can also use the
Select tool (directly on the fasta format file), with a "NOT
Matching" and this regular expression:
^$
Where ^ means the start of a line, and $ means the end. Together,
they indicate a blank line. "NOT Matching" selects all lines that
are not a blank line, e.g. have content.
Please give this a try and let us know how it works.
Jen
Galaxy team
On 12/17/12 8:53 AM, D. A. Cowart
wrote:
Hi Jennifer,
Thank you for your reply.
I tried used the options you gave me to split files.
The second option, which would filter by basepair identity
executes, however, the resulting job is green but empty and says
"no peek" in the columns when I go to view. Do you know what this
means?
Thank you,
Dominique
On Mon, Dec 17, 2012 at 7:57 AM, Jennifer
Jackson <jen@bx.psu.edu>
wrote:
Hello Dominique,
Would the tool 'NGS: QC and manipulation -> Barcode
Splitter' meet your needs? Please see the tool's help for
usage.
Another option is to first covert the file to tabular with
'FASTA manipulation ->FASTA-to-Tabular', then use the
'Filter and Sort -> Filter' tool. The match criteria
would look something like: c2=='ATGC' . Once done, convert
back to fasta with 'FASTA manipulation ->
Tabular-to-FASTA'.
Hopefully one of these methods will work out for you,
Jen
Galaxy team
On 12/14/12 11:10 AM, D. A. Cowart wrote:
Hello,
I would like to use Galaxy to divide a very large
Ilumnia fasta file (~3GB) into separate fasta files.
Is this possible on Galaxy? Here is an example of the
reads:
I have tried the "Filter and Sort" option to try and
select sequences just by a beginning sequence (ATGC,
for example) to separate these sequences into a
specific file, but I have been unsuccessful in this.
Thank you,
Dominique
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