fasta-shuffle-letters doesn't work

[yusuke]

I want to make "shuffled control sequences" for AME (--control shuffled**.fa).

When I type the as follows, it didnt work.

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fasta-shuffle-letters sample.fa shuffled_sample.fa

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Message was as follows.

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  USAGE:

        fasta-shuffle-letters

-tod use time of day as seed for the random number generator

default: 0

Shuffle each sequence in a file of fasta sequences.

(Does not shuffle the order of the sequences.)

Reads file from standard input.

Writes to standard output.

##

My Input fasta format (sample.fa) is like this.

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>1

CCAGACACTATACATGTCATTTTTTTACCGTGGCTTTTTTTAAGTCACAATTCTCAAGGCCGTCGTCTTTTTAGTCGGTT

TTCATCAGCAGGCTAGATGGTTTGAATATCTGAGTCCAAGAGTGAGCCTCAGTGCTCATGCGCTTTAAGCCCTCGGCAAT

GCCTGTCCTGCGTCCCAGAGAACGCTCTGCCGGAGGGGTTTCGATGGAACTCGTAGCAACCTACCGCCTACTGCCTGATC

CCTCTGGCGTGAAAGCCGGACTCCGTCCAACTCCAGCTCGCCAGCAACGCGAGTCCGGATAGGGCCGGAAGTTCCAGACT

GCTGGGGGCGGGAATAGATTAAAAGAACAGCGCACGCCTGAGCGAGCCACTTCTACTTTCCAGTCTCCTGCGATCGATTC

G

>2

CTGTACTCAAGTTGGTTAGAAACCCTTGTTCTCCTGGTGTCATCCATCTCCTCTGGCTCTTACACTCCTGCCTTCTCTTC

CTCAGGGTCCTCTGAGCTCTGAGGGTAGGGATTTGATGGAGATATTCCATTTAGGGCTGAGTGTTCTCTCTCTCTCTCTC

TTCATAATGTCTAGTTGTGATCTTTGTACTTGTGCCCATTTGCTGCAGGAGCAAGCTTCACTGATGATGGCTCTATAAGG

CACTGATACATGAGGATAGCTGAATAGAATATCACTAGGAGTCATTTTAGCATGCTTTTTTATTTCAAAGACCAGTAGTA

TTTGGTTTTACCTTAGGTCTCTGGGCTATAGTTGGCACACAAGCAGTGTTTGGAATGAATCCTATCTTGTGTGCCTTAAG

C

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Following commands didnt work too.

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fasta-shuffle-letters -alph alphabet.txt -kmer 2 -tag -dinuc -seed 1 sample.fa shuffled_sample.fa

fasta-shuffle-letters -tod sample.fa shuffled_sample.fa

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alphabet.txt was follows

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ALPHABET "DNA" DNA-LIKE

A "Adenine" CC0000 ~ T "Thymine" 008000

C "Cytosine" 0000CC ~ G "Guanine" FFB300

N "Any base" = ACGT

X = ACGT

. = ACGT

V "Not T" = ACG

H "Not G" = ACT

D "Not C" = AGT

B "Not A" = CGT

M "Amino" = AC

R "Purine" = AG

W "Weak" = AT

S "Strong" = CG

Y "Pyrimidine" = CT

K "Keto" = GT

U = T

##

When I uploaded above fasta file for Web Service AME. It works.

Now I completely stacked with command line AME. What is the problem???

[CharlesEGrant]

It looks like your local installation is using an older version of the MEME Suite. You command line was correct for the current version of fasta-shuffle-letters, but not for the version you have installed locally.

Notice that the usage statement for your copy says:

Reads file from standard input.

Writes to standard output.

This means that you can't just specify the input and output file names, you have to use the standard UNIX IO redirection operators, > and <.

For example,

fasta-shuffle-letters < sample.fa > shuffled_sample.fa

The < operator directs the shell to use the file sample.fa as standard input, and the > operator directs the shell to use the file shuffled_sample.fa as standard output.

This has been simplified in the current version of fasta-shuffle-letters. The current version of the MEME Suite is 4.11.2 patch 1, and is available here.

The man page for the current version of fasta-shuffle-letters can be found here. For example, using your files, the command line for the current version would be:

fasta-shuffle-letters sample.fa shuffled_sample.fa

[yusuke]

Hi CharlesEGrant

Now I got ame results with shuffled control sequences using still old version of MEME.

The problem is lack of standard redirection, as you pointed out.

Best!