[med-svn] [psipred] 13/15: New upstream version 4.01
Andreas Tille
tille at debian.org
Mon Dec 18 20:32:29 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository psipred.
commit f8b77b68e8da50989795180e6356543124209221
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 18 21:28:19 2017 +0100
New upstream version 4.01
---
BLAST+/README | 34 +
BLAST+/runpsipredplus | 77 +
LICENSE | 89 +
README | 157 +
VERSION | 2 +
bin/chkparse | Bin 0 -> 13866 bytes
bin/psipass2 | Bin 0 -> 18373 bytes
bin/psipred | Bin 0 -> 13872 bytes
bin/seq2mtx | Bin 0 -> 13593 bytes
data/weights.dat | 498313 +++++++++++++++++++++++++++++++++
data/weights.dat2 | 498313 +++++++++++++++++++++++++++++++++
data/weights.dat3 | 498313 +++++++++++++++++++++++++++++++++
data/weights_p2.dat | 1703 +
data/weights_s.dat | 498313 +++++++++++++++++++++++++++++++++
data/weights_s.dat2 | 498313 +++++++++++++++++++++++++++++++++
data/weights_s.dat3 | 498313 +++++++++++++++++++++++++++++++++
debian/README.Debian | 8 -
debian/README.source | 14 -
debian/changelog | 6 -
debian/compat | 1 -
debian/control | 32 -
debian/copyright | 116 -
debian/patches/Makefile.patch | 42 -
debian/patches/error_messages.patch | 230 -
debian/patches/runpsipred.patch | 122 -
debian/patches/series | 3 -
debian/psipred-data.install | 1 -
debian/psipred-data.links | 2 -
debian/psipred.docs | 3 -
debian/psipred.examples | 4 -
debian/psipred.install | 4 -
debian/rules | 10 -
debian/source/format | 1 -
debian/upstream/metadata | 11 -
debian/watch | 2 -
example/example.fasta | 2 +
example/example.horiz | 19 +
example/example.ss2 | 149 +
runpsipred | 80 +
runpsipred_single | 61 +
src/Makefile | 32 +
src/chkparse.c | 255 +
src/seq2mtx.c | 237 +
src/ssdefs.h | 16 +
src/sspred_avpred.c | 293 +
src/sspred_hmulti.c | 351 +
src/sspred_net.h | 14 +
src/sspred_net2.h | 10 +
48 files changed, 2993459 insertions(+), 612 deletions(-)
diff --git a/BLAST+/README b/BLAST+/README
new file mode 100644
index 0000000..191c372
--- /dev/null
+++ b/BLAST+/README
@@ -0,0 +1,34 @@
+Running PSIPRED with BLAST+
+===========================
+
+NCBI are now encouraging users to switch over from the classic BLAST
+package to the new BLAST+ package. On the one hand this is a cleaner
+and nicer version of BLAST, but on the other hand, it omits some
+useful features. In particular, BLAST+ no longer offers the facility
+to extract more precise PSSM scores from checkpoint files in a
+"supported" way (previously we used the makemat utility to get this
+information).
+
+Unfortunate, BLAST+ saves PSSM data after scaling by 10 and rounding,
+which loses too much precision.
+
+One solution would be to patch BLAST+ to offer more precision on the
+PSSM file output. This is not a very convenient option - most users
+prefer to avoid building BLAST from source. Another solution would be
+to generate PSSM data from alignments, but this would entail
+generating and reading very large files and would be error prone.
+
+The compromise solution we are trialling is to extract PSSM information
+directly from the ASN.1 checkpoint files. This seems to work very well
+indeed - though the results are not exactly identical to those from
+classic BLAST makemat, as we have to recover the original internal scaling
+factor used by BLAST+ with a bit of a hack. The differences appear to
+be trivial, however.
+
+Eventually, we will probably switch over to this method as the preferred
+way of running PSIPRED, but for the time being the interface to BLAST+
+is considered experimental.
+
+If you wish to use PSIPRED with BLAST+, then use the runpsipredplus script
+here, rather than the normal runpsipred script. Please do let us know if
+you run into insurmountable problems using this script.
diff --git a/BLAST+/runpsipredplus b/BLAST+/runpsipredplus
new file mode 100755
index 0000000..e1a5e88
--- /dev/null
+++ b/BLAST+/runpsipredplus
@@ -0,0 +1,77 @@
+#!/bin/tcsh
+
+# This is a simple script which will carry out all of the basic steps
+# required to make a PSIPRED V3 prediction using BLAST+. Note that it
+# assumes that the following programs are in the appropriate directories:
+# psiblast - PSIBLAST executable (from NCBI BLAST+)
+# psipred - PSIPRED V4 program
+# psipass2 - PSIPRED V4 program
+# chkparse - PSIPRED V4 program
+
+# NOTE: Experimental PSIPRED script with BLAST+ compatability (DTJ May 2010)
+
+# The name of the BLAST+ data bank
+set dbname = uniref90filt
+
+# Where the NCBI BLAST+ programs have been installed
+set ncbidir = /usr/local/bin
+
+# Where the PSIPRED V3 programs have been installed
+set execdir = ../bin
+
+# Where the PSIPRED V3 data files have been installed
+set datadir = ../data
+
+set basename = $1:r
+set rootname = $basename:t
+
+# Generate a "unique" temporary filename root
+set hostid = `hostid`
+set tmproot = psitmp$$$hostid
+
+\cp -f $1 $tmproot.fasta
+
+echo "Running PSI-BLAST with sequence" $1 "..."
+
+$ncbidir/psiblast -db $dbname -query $tmproot.fasta -inclusion_ethresh 0.001 -out_pssm $tmproot.chk -num_iterations 3 -num_alignments 0 -num_descriptions 5000 >& $tmproot.blast
+
+if ($status != 0) then
+ tail $tmproot.blast
+ echo "FATAL: Error whilst running blastpgp - script terminated!"
+ exit $status
+endif
+
+echo "Predicting secondary structure..."
+
+$execdir/chkparse $tmproot.chk > $tmproot.mtx
+
+if ($status != 0) then
+ echo "FATAL: Error whilst running chkparse - script terminated!"
+ exit $status
+endif
+
+echo Pass1 ...
+
+$execdir/psipred $tmproot.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 > $rootname.ss
+
+if ($status != 0) then
+ echo "FATAL: Error whilst running psipred - script terminated!"
+ exit $status
+endif
+
+echo Pass2 ...
+
+$execdir/psipass2 $datadir/weights_p2.dat 1 1.0 1.0 $rootname.ss2 $rootname.ss > $rootname.horiz
+
+if ($status != 0) then
+ echo "FATAL: Error whilst running psipass2 - script terminated!"
+ exit $status
+endif
+
+# Remove temporary files
+
+echo Cleaning up ...
+\rm -f $tmproot.* error.log
+
+echo "Final output files:" $rootname.ss2 $rootname.horiz
+echo "Finished."
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..64806ab
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,89 @@
+PLEASE READ THE FOLLOWING LICENSE AGREEMENT. BY USING THE PROGRAM YOU ARE
+ACKNOWLEDGING THE FACT THAT YOU AGREE TO THE TERMS OUTLINED IN THIS
+AGREEMENT. USERS WISHING TO USE THE SOFTWARE FOR COMMERCIAL ACTIVITIES
+NOT COVERED BY THIS AGREEMENT SHOULD SEND E-MAIL TO: dtj at cs.ucl.ac.uk
+
+* NOTE RECENT CHANGES TO PARAGRAPH 8 *
+
+
+
+ PSIPRED3 - PROTEIN SECONDARY STRUCTURE PREDICTION PROGRAM BY D.T.JONES
+ ----------------------------------------------------------------------
+
+ GENERAL LICENSE &
+ -----------------
+
+ CONFIDENTIALITY AGREEMENT
+ -------------------------
+
+
+
+In regard to the protein structure prediction program (PSIPRED3)
+herewith (the Software) the copyright and other intellectual property
+rights to which belong to the Author(s).
+
+Any user (the User) of the program undertakes to the Copyright holder that he
+or she shall be bound by the following terms and conditions:-
+
+1. The User will receive the Software and any related documentation in
+confidence and will not use the same except for the purpose of their own
+research. The Software will be used only by such of the User's officers or
+employees to whom it must reasonably be communicated to enable them to
+undertake their research and who agree to be bound by the same confidence.
+The User shall procure and enforce such agreement from his or her staff for
+the benefit of the Copyright holder.
+
+2. The publication of research using the Software must include an
+appropriate citation to the method:
+
+Jones, D.T. (1999) Protein secondary structure prediction based on
+position-specific scoring matrices. J. Mol. Biol. 292:195-202.
+
+3. All forms of the Software will be kept in a reasonably secure place to
+prevent unauthorised access.
+
+4. Each copy of the Software or, if not practicable then, any package
+associated therewith shall be suitably marked (and such marking maintained)
+with the following copyright notice: "Copyright 2000 D.T.Jones. All Rights
+Reserved.".
+
+5. The Software may be modified, but any changes made shall be communicated
+to the Author(s) and made freely available.
+
+6. The Software may not be sold as a standalone package, or incorporated into
+a commercial software package without the written permission of the Copyright
+holder. The Software may be used freely for individual academic or commercial
+research. The Software may also be made freely available for training or
+teaching purposes.
+
+7. The results produced by the Software may not be incorporated into any
+data banks or databases which are subject to the payment of access or
+license fees without the written permission of the Copyright holder.
+
+8. The Software may be made available to users over a local network or
+wide area network (including the Internet), but only if access is granted
+free of charge to all authorised users. Incorporation of the Software into
+a commercial Web site or other fee paying service is not allowed without
+the written permission of the Copyright holder. If PSIPRED results are
+returned to the user via such a network service, then a suitable
+acknowledgement of the PSIPRED method must be returned somewhere in the
+output text.
+
+9. The confidentiality obligation in paragraph one shall not apply:
+
+ (i) to information and data known to the User at the time of
+ receipt hereunder (as evidenced by its written records);
+
+ (ii) to information and data which was at the time of receipt in the
+ public domain or thereafter becomes so through no wrongful act of
+ the User;
+
+ (iii) to information and data which the User receives from a third
+ party not in breach of any obligation of confidentiality owed to
+ the Author(s).
+
+10. The User understands that the Software is supplied "as is". No warranty
+ as to its fitness or suitability for any purpose whatsoever is made or
+ implied. In no event shall the Author(s) or Copyright holder be held
+ responsible for any direct or indirect damages arising through the use
+ of the Software.
diff --git a/README b/README
new file mode 100644
index 0000000..6a1ecd8
--- /dev/null
+++ b/README
@@ -0,0 +1,157 @@
+PSIPRED RELEASE NOTES
+=====================
+
+PSIPRED Version 4.01
+
+By David Jones, October 2016
+
+*** IMPORTANT *****************************************************
+NCBI are now trying to move users to the new BLAST+ package. Please
+see the README file in the BLAST+ subdirectory for more information
+on PSIPRED's support for BLAST+. For now the preferred option is
+to stick with the classic BLAST package as the default. If the tar
+or rpm file you are downloading from NCBI has "+" in the filename,
+then you are downloading BLAST+ rather than BLAST.
+*******************************************************************
+
+Here are some very brief notes on using the PSIPRED V4 software.
+
+PSIPRED is supplied in source code form - it must be compiled before
+it can be used. The code should compile on any ANSI C compiler e.g.
+the GNU C compiler.
+
+Please see the LICENSE file for the license terms for the software.
+Basically it's free to anyone (including commercial users) as long as
+you don't want to sell the software or, for example, store the results
+obtained with it in a database and then try to sell the database.
+If you do wish to sell the software or use it in a commercial product,
+then please contact UCL Business (http://www.uclb.com).
+
+PSIPRED is run via a tcsh shell script called "runpsipred" - this is a
+very simple script which you should be able to convert to Perl or whatever
+scripting language you like.
+
+If your sequence does not have any homologues in the current data banks,
+then it is possible to run PSIPRED on a single sequence. In this case,
+PSIPRED is run via a tcsh shell script called "runpsipred_single". Unfortunately,
+like every other secondary structure prediction method, PSIPRED does not
+perform as well on single sequences. Any secondary structure prediction based on
+a single sequence should be considered as unreliable.
+
+Before running PSIPRED, please check the runpsipred and runpsipred_single scripts
+to see if the path variables are set to wherever you have installed the
+program and data files. The default is to assume that the program is
+installed in the current directory - this is probably NOT what you want!
+
+INSTALLATION
+============
+
+Firstly compile the software:
+
+tcsh% cd to-wherever-you-untarred-PSIPRED
+
+tcsh% cd src
+
+tcsh% make
+
+tcsh% make install
+
+The executables will be placed in the PSIPRED bin directory.
+
+You must also install the PSI-BLAST and Impala software from the
+NCBI toolkit, and also install appropriate sequence data banks.
+
+The NCBI toolkit can be obtained from URL ftp://ftp.ncbi.nih.gov
+
+PSI-BLAST executables can be obtained from ftp://ftp.ncbi.nih.gov/blast
+
+
+EXAMPLE USAGE
+=============
+
+In this example the target sequence is called "example.fasta":
+
+tcsh% runpsipred example.fasta
+
+Running PSI-BLAST with sequence example.fasta ...
+Predicting secondary structure...
+Pass1 ...
+Pass2 ...
+Cleaning up ...
+Final output file: example.horiz
+Finished.
+
+That's it - you can then look at the output:
+
+tcsh% more example.horiz
+
+
+SPECIAL OPTIONS
+===============
+
+The psipass2 program has several special options which you can use if you wish.
+
+For example, the default command is as follows:
+
+psipass2 weights_p2.dat 1 1.0 1.0 output.ss2 input.ss > output.horiz
+
+Arguments 2,3 & 4 are as follows:
+
+Argument 2: No of filter iterations
+This controls the amount of "smoothing" that is carried out on the final
+prediction. The recommended setting is 1, but it may be worth trying
+higher values to increase the level of smoothing.
+
+Argument 3&4: Helix/Strand Decision constants
+These options control the bias for helix (Arg3) and strand (Arg4) predictions.
+The default values are equal to 1.0, but if you know your protein is, for
+example, mostly comprised of beta strands then you can increase the bias
+towards beta strand prediction. For example:
+
+psipass2 weights_p2.dat 1 1.0 1.3 output.ss2 input.ss > output.horiz
+
+increases the bias towards beta strand prediction by approximately 30%.
+
+
+
+SEQUENCE DATA BANK
+==================
+
+As of PSIPRED V4.0 onwards, we no longer believe it is necessary for the sequence
+data banks used with PSI-BLAST to be filtered to remove low-complexity regions,
+transmembrane regions, and coiled-coil segments. The search data bank can
+therefore be any large non-redundant protein sequence data bank, with
+UNIREF90 (http://www.uniprot.org/help/uniref