[Debian-med-packaging] Installation of binary tools inside MEME
James Johnson
j.johnson at imb.uq.edu.au
Thu Feb 14 04:41:28 UTC 2013
Hi Andreas,
On 13/02/13 16:36, Andreas Tille wrote:
> Hi James,
>
> On Wed, Feb 13, 2013 at 10:18:58AM +1000, James Johnson wrote:
>> ...
>>> Any hint would be welcome.
>> I'll work on a list of what each of the programs is used for and get
>> back to you. Even discounting the fossils there are probably quite a
>> few scripts and programs only relevant to installing the MEME Suite
>> on a webserver. For example a local user would almost never want to
>> use the update_db script as it's a very clumsy way to get sequence
>> data for specific tasks.
> This sounds great - so we stay in idle mode until we hear some news from
> your side.
>
> Thanks for your quick and helpful response
I've attached an annotated list of the things that the MEME Suite
currently installs to the bin directory in our main development branch
(there may be minor differences to the current distribution). There's
quite a few things that shouldn't be in there like Python libraries
(there are 4) and a few Perl libraries (there are 2). There are 6
programs which have no good reason to be there anymore annotated as
"Fossil".
Aside from that there's programs which have been obsoleted because
there's a newer better version (see most of the mhmm related things) and
a few scripts which are only used by us developers. There's also a few
scripts that would only be useful to someone running a webserver.
After that the decisions get a lot harder. There are programs which are
generally only called by other programs in the suite, however if they're
not in the bin directory they won't be found. I'm not sure how you're
going to work around the restriction on installing only programs "a user
should execute" with those ones (like meme.bin called by the meme script
or mast2txt called by mast). There's also quite a lot of programs that
might be conceivably useful to someone somewhere so I'm not sure how you
decide with those.
~James
>
> Andreas.
>
-------------- next part --------------
alphtype Webserver determines if a alphabet string is DNA or PROTEIN, I will probably reimplement as part of a Perl module
ama Useful calculates average/maximum motif score for sequences, first step in gomo analysis
ama-qvalues Useful calculates q-values for ama output
ame Useful calculates motif enrichment in sequences
beadstring Obsolete Obsoleted by MCAST
beeml2meme Useful converts motifs to MEME format from BEEML format
cat_max Fossil ...
centrimo Useful calculates areas of localised motif enrichment
ceqlogo Rarely Useful generates a single motif logo, it's not very user friendly and mostly called through the c interface
changetoweb Fossil ...
chen2meme Useful converts motifs to MEME format from Chen format
clustalw2fasta Possibly Useful converts sequences in clustalw format to fasta format
clustalw2phylip Possibly Useful converts sequences in clustalw format to phylip format
clustalw-io Not Useful allows testing of the clustalw parser
compare_dates Fossil another script used by the "download" script
compute-prior-dist Possibly Useful computes the distribution of priors in a MEME PSP file
compute-uniform-priors Possibly Useful computes a uniform prior psp file equal to the mean of all input priors in another psp file (missing doc)
create-priors Useful allows running MEME in discriminative mode by creating a position specific prior file
download Fossil old code for downloading sequence databases
draw-mhmm Possibly Useful produces a graphvis representation of a MHMM model
dreme Useful Discover short DNA motifs
dust Useful filters low complexity regions from sequences
fasta-center Possibly Useful filters a set of sequences to only leave the central region
fasta-dinucleotide-shuffle Useful shuffles a sequence while maintaining di-nucleotide frequencies
fasta-dinucleotide-shuffle.py Python Library I'll get this moved into the libs directory like with the Perl modules.
fasta-fetch Possibly Useful Seems to use an index generated by fasta-make-index to fetch sequences out of a fasta file
fasta-get-markov Useful generates a Markov model of letter frequencies used as backgrounds by many MEME Suite programs
fasta-hamming-enrich Possibly Useful compute the Hamming distance from a word to each sequence in two sets, apply Fisher Exact test
fasta-hamming-enrich.py Python Library ...
fasta-io Not Useful just allows testing of the fasta file reading
fasta-make-index Possibly Useful makes an index of a fasta file
fasta-most Useful finds the length of sequence that occurs most, used by MEME-ChIP
fasta-shuffle-letters Possibly Useful shuffles letters of a sequence, though fasta-dinucleotide-shuffle is better
fasta-subsample Useful selects a subset of the sequences
fasta-unique-names Possibly Useful makes sequence names unique, replaces U+0001 with space
fimo Useful searches for motif sites
fisher_exact Possibly Useful computes the result of the Fisher Exact test with the given numbers
fitevd Possibly Useful fits an extreme value distribution to a set of score-length pairs.
gendb Possibly Useful generates a synthetic fasta database from a background model
get_db_csv Webserver queries an online sequence repository for its databases and creates a csv file for update_db to use
getsize Useful measures statistics about a fasta file
glam2 Useful Discover gapped motifs
glam2format Possibly Useful converts GLAM2 output to FASTA (with gaps) or MSF
glam2html Useful converts GLAM2 output to HTML, called by glam2 but not often by users
glam2mask Useful used with GLAM2 to mask out found motifs and find weaker ones
glam2psfm Useful convert GLAM2 output to a MEME motif
glam2scan Useful scans a sequence with a GLAM2 motif
glam2scan2html Useful converts GLAM2SCAN output to HTML, called by glam2scan but not often by users
gomo Useful finds enriched GO terms associated with high ranking genes
gomo_highlight Useful post processes gomo XML output to include further information which makes the HTML better
hart2meme-bkg Possibly Useful Convert a Hartemink background to a MEME background
hartemink2psp Possibly Useful Convert a Hartemink PSP file into a MEME PSP file
hypergeometric.py Python Library ...
iupac2meme Useful Make a MEME motif from a IUPAC string
jaspar2meme Useful Convert motifs from JASPAR to MEME format
llr Possibly Useful Compute the probability distribution for the log-likelihood ratio (LLR) of N letters.
mast Useful Find sequences which best match a group of motifs
mast2txt Useful Convert mast XML output to mast text output. Called by mast
mcast Useful Find matches to a motif hidden markov model
meme Useful Discover motifs, this script calls meme.bin handling the details of parallelization
meme2images Useful Create motif logos for all motifs in a MEME motif file
meme2meme Useful Combine multiple MEME motif files into 1
meme.bin Useful Discover motifs, this is typically called by the meme script
meme-chip Useful Discover motifs, look for enriched motifs, calls MEME, DREME, CentriMo, TOMTOM, eventually FIMO and SpaMo
meme-get-motif Possibly Useful Extract motifs from a MEME text file.
meme-rename Possibly Useful Renames all the output HTML files from MEME-ChIP so they can be kept in one folder and emailed easily
meme-xml-html Possibly Useful Does an XML transformation to convert XML output to HTML output, not actually specific to MEME
metameme Fossil Used to handle web jobs for metameme
mhmm Obsolete Given MEME motif, write a motif-based HMM, obsoleted by MCAST
mhmm2html Obsolete Convert MHMM output to HTML, obsoleted by MCAST
mhmme Obsolete obsoleted by MCAST
mhmm-io Not Useful allows testing of reading/writing MHMM models
mhmms Obsolete obsoleted by MCAST
mhmmscan Obsolete obsoleted by MCAST
motiph Possibly Useful part of a publised paper so we want to keep it around
nmica2meme Useful converts motifs from NMICA format to MEME format
oldmeme2meme Fossil converts reallly really old MEME files into only really old MEME files...
plotgen Webserver used to generate usage plots from the logs
pmp_bf Possibly Useful calculates the statistical power of a phylogenetic motif model
priority2meme Useful converts motifs in priority format to MEME format
prior_utils.pl Perl library ...
psp-gen Useful calculates PSP files for MEME
purge Possibly Useful filters sequences to remove repeats
qvalue Possibly Useful computes q-values from a list of p-values
ramen Useful (bugs?) integration was never tested so it may have major bugs, does regression analysis of motif enrichment
ranksum_test Possibly Useful calculates the rank-sum test
read_fasta_file.pl Perl Library ...
readseq Useful converts sequence formats
reconcile-tree-alignment Possibly Useful identify the intersection of the sets of sequence IDs and leaf labels
reduce-alignment Possibly Useful Extract specified columns from a multiple alignment.
remove-alignment-gaps Possibly Useful Remove from an alignment all columns that correspond to a gap in a specified species.
rna2meme Useful convert an RNA sequence to it's binding motif in MEME format
scpd2meme Useful convert motifs in SCPD format to MEME format
sd Possibly Useful calcualtes mean and standard deviation of a list of numbers
sequence.py Python Library ...
shadow Not Useful related to the motiph program but never went anywhere, Perform phylogenetic shadowing
spamo Useful motif spacing enrichment analysis
taipale2meme Useful converts motifs from Taipale format to MEME format
tamo2meme Useful converts motifs from TAMO format to MEME format
tomtom Useful comparison of DNA motifs
transfac2meme Useful converts motifs from Transfac matrics to MEME format
tree Obsolete obsoleted by MCAST
uniprobe2meme Useful convert motifs from Uniprobe format to MEME format
update_db Webserver download sequences listed on the page get_db_list.cgi if there timestamp is newer
update_meme_tests Not Useful updates the MEME and MAST smoke tests (they must be run first), shouldn't be needed by end users
xsltproc_lite Rarely Useful used to generate the documentation from XML, the next version will not need it
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