[EMBOSS] shuffleseq for multifasta?

[Peter Rice]

Hi Anand,

As we found when we wrote EMBOSS, "FASTA format" is actually hard to 
define. The problem is the many ways you can define the ID, and the 
other information on the first line (it is amazing how much information 
you can encode in a simple description).

Our solution was to define a set of formats that all read FASTA files, 
but parse the first line in different ways, for example "ncbi format" 
tries to read the NCBI database and id syntax.

We added a format to read the sequence ID as-is for really awkward 
cases, and in honour of the author of FASTA we called it "pearson"

So, if you add -sformat pearson it should read the full IDs up to the 
first space. If you re-read the output, you should use -sf pearson again 
(-sf is just short for -sformat)

Hope that helps.

Peter Rice
ricepeterm at yahoo.co.uk

On 09/11/2018 07:30, David Bauer wrote:
> Hi Anand,
> 
> if you run “shuffleseq –help” you will see the type of input and output 
> sequences.
> 
> Version: EMBOSS:6.5.7.0
> 
>     Standard (Mandatory) qualifiers:
> 
>    [-sequence]          seqall     Sequence(s) filename and optional 
> format, or
> 
>                                    reference (input USA)
> 
>    [-outseq]            seqoutall  [<sequence>.<format>] Sequence set(s)
> 
>                                    filename and optional format (output USA)
> 
> The “all” in seqall and seqoutall indicates that input and output can be 
> sequence files with multiple sequences.
> 
> This can be fasta format or any other sequence format supported by 
> EMBOSS (genbank, embl etc.)
> 
> The names of the sequences as they are in the original file, will be 
> preserved in the output file.
> 
> If I try to reproduce your example with the file downloaded from IPK:
> 
> shuffleseq Athaliana_167_TAIR9.fa test1.fa
> 
> the output file contains the sequences as named in the input file:
> 
> infoseq -only -name -desc test1.fa
> 
> Name           Description
> 
> Chr1           CHROMOSOME dumped from ADB: Feb/3/09 16:9; last updated: 
> 2007-12-20
> 
> Chr2           CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 
> 2007-12-20
> 
> Chr3           CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 
> 2007-12-20
> 
> Chr4           CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 
> 2007-12-20
> 
> Chr5           CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 
> 2007-12-20
> 
> ChrM           CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 
> 2005-06-03
> 
> ChrC           CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 
> 2005-06-03
> 
> Your input file contains in the name “shIDscleaned-up”. You may have 
> done some modifications to the sequence names which confuse EMBOSS.
> 
> You can test this by running the infoseq as above and check if you get 
> for “Name” what you expect.
> 
> Make sure you don’t have any “:” characters in the sequence names in 
> your fasta file. This character has a special meaning in EMBOSS sequence 
> names.
> 
> Hope this helps.
> 
> Sincerely,
> 
> David.
> 
> *Von:*EMBOSS <emboss-bounces+david.bauer=bayer.com at mailman.open-bio.org> 
> *Im Auftrag von *Anandkumar Surendrarao
> *Gesendet:* 09 November 2018 04:20
> *An:* emboss at mailman.open-bio.org
> *Betreff:* [EMBOSS] shuffleseq for multifasta?
> 
> Greetings!
> 
> I am new to EMBOSS, and trying to use shufflseq to randomly shuffle 
> entire genomes (one-by-one). My input genomic sequences are in 
> multifasta format. And I wish to retain the same multifasta format for 
> the output file as well, containing the shuffled DNA sequences.
> 
>  From the information at 
> http://emboss.sourceforge.net/apps/cvs/emboss/apps/shuffleseq.html, it 
> appears to me that FASTA format for neither input not output is 
> supported. Am I mistaken?
> 
> OR
> 
> Is there a way to specify (multi)FASTA as both input and output formats?
> 
> In one run that I completed with a genome assembly with 5 chromosmes - 
> Chr1 ... Chr5, the syntax I used was:
> 
> shuffleseq -sequence Athaliana_167_TAIR9.fa.shIDscleaned-up -outseq 
> Athaliana_167_TAIR9_EmbossShuffled.fas
> 
> Strangely, in the output file, the fasta headers were all repetitive Chr1.
> 
> Hence my confusion. Could someone please clarify what my input 
> formatting should be and the correct syntax?
> 
> Thanks, in advance, for your help.
> 
> Sincerely,
> 
> Anand
> 
> _____
> 
> *Anand**k*umar *S*urendra*rao*, PhD
> 
> +1.530.574.5134
> 
> +91.91760.70887
> 
> 
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