[med-svn] r22218 - in trunk/packages/rostlab/libzerg/trunk/debian: . examples
Tatiana Malygina
latticetower-guest at moszumanska.debian.org
Mon Jun 27 10:07:12 UTC 2016
Author: latticetower-guest
Date: 2016-06-27 10:07:12 +0000 (Mon, 27 Jun 2016)
New Revision: 22218
Added:
trunk/packages/rostlab/libzerg/trunk/debian/examples/
trunk/packages/rostlab/libzerg/trunk/debian/examples/converged.ali
trunk/packages/rostlab/libzerg/trunk/debian/examples/example.cpp
Log:
add example files for testsuite
Added: trunk/packages/rostlab/libzerg/trunk/debian/examples/converged.ali
===================================================================
--- trunk/packages/rostlab/libzerg/trunk/debian/examples/converged.ali (rev 0)
+++ trunk/packages/rostlab/libzerg/trunk/debian/examples/converged.ali 2016-06-27 10:07:12 UTC (rev 22218)
@@ -0,0 +1,132 @@
+BLASTP 2.2.18 [Mar-02-2008]
+
+
+Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
+Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
+"Gapped BLAST and PSI-BLAST: a new generation of protein database search
+programs", Nucleic Acids Res. 25:3389-3402.
+
+
+Reference for compositional score matrix adjustment: Altschul, Stephen F.,
+John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
+Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
+using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
+
+
+Reference for composition-based statistics starting in round 2:
+Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
+Sergei Shavirin, John L. Spouge, Yuri I. Wolf,
+Eugene V. Koonin, and Stephen F. Altschul (2001),
+"Improving the accuracy of PSI-BLAST protein database searches with
+composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005.
+
+Query= query
+ (113 letters)
+
+Database: big_80
+ 7,170,017 sequences; 2,505,616,640 total letters
+
+Searching..................................................done
+
+
+Results from round 1
+
+
+ Score E
+Sequences producing significant alignments: (bits) Value
+
+pdb|pdb|2vh3_B 212 8e-54
+
+>pdb|pdb|2vh3_B
+ Length = 117
+
+ Score = 212 bits (539), Expect = 8e-54, Method: Compositional matrix adjust.
+ Identities = 109/113 (96%), Positives = 109/113 (96%)
+
+Query: 1 AXAXSFPPXEIPGSKECLAEALQKHQGFKKKSYALIXAYLNYKEDAENYERAAEDFDSAV 60
+ A A SFPP EIPGSKECLAEALQKHQGFKKKSYALI AYLNYKEDAENYERAAEDFDSAV
+Sbjct: 1 AXACSFPPXEIPGSKECLAEALQKHQGFKKKSYALICAYLNYKEDAENYERAAEDFDSAV 60
+
+Query: 61 KXTGXKEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSLXTLFQKLYAIPHN 113
+ K TG KEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSL TLFQKLYAIPHN
+Sbjct: 61 KCTGXKEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSLCTLFQKLYAIPHN 113
+
+
+Searching..................................................done
+
+
+Results from round 2
+
+
+ Score E
+Sequences producing significant alignments: (bits) Value
+Sequences used in model and found again:
+
+pdb|pdb|2vh3_B 226 5e-58
+
+Sequences not found previously or not previously below threshold:
+
+
+CONVERGED!
+>pdb|pdb|2vh3_B
+ Length = 117
+
+ Score = 226 bits (575), Expect = 5e-58, Method: Composition-based stats.
+ Identities = 109/113 (96%), Positives = 109/113 (96%)
+
+Query: 1 AXAXSFPPXEIPGSKECLAEALQKHQGFKKKSYALIXAYLNYKEDAENYERAAEDFDSAV 60
+ A A SFPP EIPGSKECLAEALQKHQGFKKKSYALI AYLNYKEDAENYERAAEDFDSAV
+Sbjct: 1 AXACSFPPXEIPGSKECLAEALQKHQGFKKKSYALICAYLNYKEDAENYERAAEDFDSAV 60
+
+Query: 61 KXTGXKEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSLXTLFQKLYAIPHN 113
+ K TG KEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSL TLFQKLYAIPHN
+Sbjct: 61 KCTGXKEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSLCTLFQKLYAIPHN 113
+
+
+ Database: big_80
+ Posted date: Feb 6, 2012 9:39 AM
+ Number of letters in database: 999,999,843
+ Number of sequences in database: 1,100,691
+
+ Database: /mnt/project/rost_db/data/big/big_80.01
+ Posted date: Feb 6, 2012 9:42 AM
+ Number of letters in database: 999,999,792
+ Number of sequences in database: 2,641,400
+
+ Database: /mnt/project/rost_db/data/big/big_80.02
+ Posted date: Feb 6, 2012 9:44 AM
+ Number of letters in database: 505,617,005
+ Number of sequences in database: 3,427,926
+
+Lambda K H
+ 0.313 0.133 0.375
+
+Lambda K H
+ 0.267 0.0413 0.140
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Hits to DB: 932,412,166
+Number of Sequences: 7170017
+Number of extensions: 30007572
+Number of successful extensions: 53414
+Number of sequences better than 1.0: 1
+Number of HSP's better than 1.0 without gapping: 2
+Number of HSP's successfully gapped in prelim test: 0
+Number of HSP's that attempted gapping in prelim test: 53412
+Number of HSP's gapped (non-prelim): 2
+length of query: 113
+length of database: 2,505,616,640
+effective HSP length: 81
+effective length of query: 32
+effective length of database: 1,924,845,263
+effective search space: 61595048416
+effective search space used: 61595048416
+T: 11
+A: 40
+X1: 16 ( 7.2 bits)
+X2: 38 (14.6 bits)
+X3: 64 (24.7 bits)
+S1: 42 (21.9 bits)
+S2: 82 (36.2 bits)
Added: trunk/packages/rostlab/libzerg/trunk/debian/examples/example.cpp
===================================================================
--- trunk/packages/rostlab/libzerg/trunk/debian/examples/example.cpp (rev 0)
+++ trunk/packages/rostlab/libzerg/trunk/debian/examples/example.cpp 2016-06-27 10:07:12 UTC (rev 22218)
@@ -0,0 +1,33 @@
+// Simple example file for autopkgtest:
+// Reads data from file and prints to output stream.
+// Author: Tatiana Malygina <merlettaia at gmail.com>
+
+#include <iostream>
+#include <zerg.h>
+
+
+int main(int argc, char *argv[]) {
+ if (argc < 2) {
+ std::cout << "Please, provide file name with BLAST results\n";
+ return 0;
+ }
+ zerg_open_file(argv[1]);
+ // This program doesn't check if given file is not .ali,
+ // it is made for testing `libzerg` library is correctly installed and
+ // supposes that provided file exists and there is a read permission.
+
+ int code = 0;
+ char* value = new char[1024]();
+ // I picked buffer size at a random -
+ // if you want to use libzerg in a real application, you probably should
+ // allocate more space.
+
+ while (zerg_get_token(&code, &value)) {
+ std::cout << "Parsed: " << code << ", value: " << value << std::endl;
+ }
+ zerg_close_file();;
+ return 0;
+}
+
+// Compile with:
+// g++ -Wall -lzerg example.cpp -o example
More information about the debian-med-commit
mailing list