debian/0000755000000000000000000000000012231040320007151 5ustar debian/watch0000644000000000000000000000025411734563556010237 0ustar # Compulsory line, this is a version 3 file version=3 # Uncomment to find new files on sourceforge, for devscripts >= 2.9 http://sf.net/libzerg/libzerg-perl_(.*)\.tar\.gz debian/README.source0000644000000000000000000000071711636711335011360 0ustar libzerg-perl for Debian ----------------------- patches: debian-changes-1.0.4-1: * automatic patch, captures old Makefiles generated during building new_tokens: * added new tokens of libzerg-1.0.7-2 to perl module * extended Report.pm to handle blastpgp (iterated blast) results * corrected bug in Report.pm that prevented reporting the last blast result * added the alignments to the structure returned by Report.pm # vim:et:ts=2: debian/rules0000755000000000000000000000067411775572306010272 0ustar #!/usr/bin/make -f export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) %: dh $@ --parallel --sourcedirectory=Zerg .PHONY: override_dh_auto_configure override_dh_auto_configure: dh_auto_configure -- OPTIMIZE="$(CPPFLAGS) $(CFLAGS)" LD="$(shell perl -V::ld:) $(LDFLAGS)" debian/README.Debian0000644000000000000000000000053011634640261011230 0ustar libzerg-perl for Debian ----------------------- Reference ========= * Paquola, Apuã C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio: Zerg: a very fast BLAST parser library., Bioinformatics 19(8), volume 19, 1035–6, May 2003 -- Laszlo Kajan Fri, 16 Sep 2011 11:52:32 +0200 debian/copyright0000644000000000000000000000244311637620707011135 0ustar This work was packaged for Debian by: Laszlo Kajan on Fri, 16 Sep 2011 11:52:32 +0200 It was downloaded from: http://code.google.com/p/libzerg/ Upstream Author: Apuã Paquola Copyright: Copyright (C) 2002 Apuã Paquola - Instituto de Química - Universidade de São Paulo - Brasil License: This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version. This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. The Debian packaging is: Copyright (C) 2011 Laszlo Kajan and is licensed under the GPL version 3, see "/usr/share/common-licenses/GPL-3". debian/upstream0000644000000000000000000000111111752041017010741 0ustar Contact: Apuã Paquola Homepage: http://code.google.com/p/libzerg/ Name: libzerg-perl Reference: author: Paquola, Apuã C M and Machado, Abimael A and Reis, Eduardo M and Da Silva, Aline M and Verjovski-Almeida, Sergio title: "Zerg: a very fast BLAST parser library" journal: Bioinformatics volume: 19 number: 8 pages: 1035-6 year: 2003 URL: http://bioinformatics.oxfordjournals.org/content/19/8/1035.short eprint: http://bioinformatics.oxfordjournals.org/content/19/8/1035.full.pdf+html DOI: 10.1093/bioinformatics/btg122 PMID: 12761068 debian/source/0000755000000000000000000000000011775572313010501 5ustar debian/source/format0000644000000000000000000000001411634640261011677 0ustar 3.0 (quilt) debian/patches/0000755000000000000000000000000011775572313010630 5ustar debian/patches/debian-changes-1.0.4-10000644000000000000000000013436411636711335014205 0ustar Description: Upstream changes introduced in version 1.0.4-1 This patch has been created by dpkg-source during the package build. Here's the last changelog entry, hopefully it gives details on why those changes were made: . libzerg-perl (1.0.4-1) UNRELEASED; urgency=low . * Initial release (Closes: #641799) . The person named in the Author field signed this changelog entry. Author: Laszlo Kajan Bug-Debian: http://bugs.debian.org/641799 --- The information above should follow the Patch Tagging Guidelines, please checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here are templates for supplementary fields that you might want to add: Origin: , Bug: Bug-Debian: http://bugs.debian.org/ Bug-Ubuntu: https://launchpad.net/bugs/ Forwarded: Reviewed-By: Last-Update: --- /dev/null +++ libzerg-perl-1.0.4/Zerg/Makefile.old @@ -0,0 +1,950 @@ +# This Makefile is for the Zerg extension to perl. +# +# It was generated automatically by MakeMaker version +# 6.55_02 (Revision: 65502) from the contents of +# Makefile.PL. Don't edit this file, edit Makefile.PL instead. +# +# ANY CHANGES MADE HERE WILL BE LOST! +# +# MakeMaker ARGV: (q[INSTALLDIRS=vendor]) +# + +# MakeMaker Parameters: + +# ABSTRACT_FROM => q[Zerg.pm] +# AUTHOR => q[Apuã Paquola ] +# BUILD_REQUIRES => { } +# DEFINE => q[] +# INC => q[] +# LIBS => [q[-L/usr/local/lib -lzerg]] +# NAME => q[Zerg] +# PREREQ_PM => { } +# VERSION_FROM => q[Zerg.pm] + +# --- MakeMaker post_initialize section: + + +# --- MakeMaker const_config section: + +# These definitions are from config.sh (via /usr/lib/perl/5.10/Config.pm). +# They may have been overridden via Makefile.PL or on the command line. +AR = ar +CC = cc +CCCDLFLAGS = -fPIC +CCDLFLAGS = -Wl,-E +DLEXT = so +DLSRC = dl_dlopen.xs +EXE_EXT = +FULL_AR = /usr/bin/ar +LD = cc +LDDLFLAGS = -shared -O2 -g -L/usr/local/lib -fstack-protector +LDFLAGS = -fstack-protector -L/usr/local/lib +LIBC = /lib/libc-2.11.2.so +LIB_EXT = .a +OBJ_EXT = .o +OSNAME = linux +OSVERS = 2.6.32-5-amd64 +RANLIB = : +SITELIBEXP = /usr/local/share/perl/5.10.1 +SITEARCHEXP = /usr/local/lib/perl/5.10.1 +SO = so +VENDORARCHEXP = /usr/lib/perl5 +VENDORLIBEXP = /usr/share/perl5 + + +# --- MakeMaker constants section: +AR_STATIC_ARGS = cr +DIRFILESEP = / +DFSEP = $(DIRFILESEP) +NAME = Zerg +NAME_SYM = Zerg +VERSION = 1.0.4 +VERSION_MACRO = VERSION +VERSION_SYM = 1_0_4 +DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\" +XS_VERSION = 1.0.4 +XS_VERSION_MACRO = XS_VERSION +XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\" +INST_ARCHLIB = blib/arch +INST_SCRIPT = blib/script +INST_BIN = blib/bin +INST_LIB = blib/lib +INST_MAN1DIR = blib/man1 +INST_MAN3DIR = blib/man3 +MAN1EXT = 1p +MAN3EXT = 3pm +INSTALLDIRS = vendor +DESTDIR = +PREFIX = /usr +PERLPREFIX = $(PREFIX) +SITEPREFIX = $(PREFIX)/local +VENDORPREFIX = $(PREFIX) +INSTALLPRIVLIB = $(PERLPREFIX)/share/perl/5.10 +DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB) +INSTALLSITELIB = $(SITEPREFIX)/share/perl/5.10.1 +DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB) +INSTALLVENDORLIB = $(VENDORPREFIX)/share/perl5 +DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB) +INSTALLARCHLIB = $(PERLPREFIX)/lib/perl/5.10 +DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB) +INSTALLSITEARCH = $(SITEPREFIX)/lib/perl/5.10.1 +DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH) +INSTALLVENDORARCH = $(VENDORPREFIX)/lib/perl5 +DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH) +INSTALLBIN = $(PERLPREFIX)/bin +DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN) +INSTALLSITEBIN = $(SITEPREFIX)/bin +DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN) +INSTALLVENDORBIN = $(VENDORPREFIX)/bin +DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN) +INSTALLSCRIPT = $(PERLPREFIX)/bin +DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT) +INSTALLSITESCRIPT = $(SITEPREFIX)/bin +DESTINSTALLSITESCRIPT = $(DESTDIR)$(INSTALLSITESCRIPT) +INSTALLVENDORSCRIPT = $(VENDORPREFIX)/bin +DESTINSTALLVENDORSCRIPT = $(DESTDIR)$(INSTALLVENDORSCRIPT) +INSTALLMAN1DIR = $(PERLPREFIX)/share/man/man1 +DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR) +INSTALLSITEMAN1DIR = $(SITEPREFIX)/man/man1 +DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR) +INSTALLVENDORMAN1DIR = $(VENDORPREFIX)/share/man/man1 +DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR) +INSTALLMAN3DIR = $(PERLPREFIX)/share/man/man3 +DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR) +INSTALLSITEMAN3DIR = $(SITEPREFIX)/man/man3 +DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR) +INSTALLVENDORMAN3DIR = $(VENDORPREFIX)/share/man/man3 +DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR) +PERL_LIB = /usr/share/perl/5.10 +PERL_ARCHLIB = /usr/lib/perl/5.10 +LIBPERL_A = libperl.a +FIRST_MAKEFILE = Makefile +MAKEFILE_OLD = Makefile.old +MAKE_APERL_FILE = Makefile.aperl +PERLMAINCC = $(CC) +PERL_INC = /usr/lib/perl/5.10/CORE +PERL = /usr/bin/perl +FULLPERL = /usr/bin/perl +ABSPERL = $(PERL) +PERLRUN = $(PERL) +FULLPERLRUN = $(FULLPERL) +ABSPERLRUN = $(ABSPERL) +PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" +FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" +ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" +PERL_CORE = 0 +PERM_DIR = 755 +PERM_RW = 644 +PERM_RWX = 755 + +MAKEMAKER = /usr/share/perl/5.10/ExtUtils/MakeMaker.pm +MM_VERSION = 6.55_02 +MM_REVISION = 65502 + +# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle). +# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle) +# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar) +# DLBASE = Basename part of dynamic library. May be just equal BASEEXT. +MAKE = make +FULLEXT = Zerg +BASEEXT = Zerg +PARENT_NAME = +DLBASE = $(BASEEXT) +VERSION_FROM = Zerg.pm +INC = +DEFINE = +OBJECT = $(BASEEXT)$(OBJ_EXT) +LDFROM = $(OBJECT) +LINKTYPE = dynamic +BOOTDEP = + +# Handy lists of source code files: +XS_FILES = Zerg.xs +C_FILES = Zerg.c +O_FILES = Zerg.o +H_FILES = +MAN1PODS = +MAN3PODS = Zerg.pm + +# Where is the Config information that we are using/depend on +CONFIGDEP = $(PERL_ARCHLIB)$(DFSEP)Config.pm $(PERL_INC)$(DFSEP)config.h + +# Where to build things +INST_LIBDIR = $(INST_LIB) +INST_ARCHLIBDIR = $(INST_ARCHLIB) + +INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT) +INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT) + +INST_STATIC = $(INST_ARCHAUTODIR)/$(BASEEXT)$(LIB_EXT) +INST_DYNAMIC = $(INST_ARCHAUTODIR)/$(DLBASE).$(DLEXT) +INST_BOOT = $(INST_ARCHAUTODIR)/$(BASEEXT).bs + +# Extra linker info +EXPORT_LIST = +PERL_ARCHIVE = +PERL_ARCHIVE_AFTER = + + +TO_INST_PM = Zerg.pm + +PM_TO_BLIB = Zerg.pm \ + $(INST_LIB)/Zerg.pm + + +# --- MakeMaker platform_constants section: +MM_Unix_VERSION = 6.55_02 +PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc + + +# --- MakeMaker tool_autosplit section: +# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto +AUTOSPLITFILE = $(ABSPERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1)' -- + + + +# --- MakeMaker tool_xsubpp section: + +XSUBPPDIR = /usr/share/perl/5.10/ExtUtils +XSUBPP = $(XSUBPPDIR)$(DFSEP)xsubpp +XSUBPPRUN = $(PERLRUN) $(XSUBPP) +XSPROTOARG = +XSUBPPDEPS = /usr/share/perl/5.10/ExtUtils/typemap $(XSUBPP) +XSUBPPARGS = -typemap /usr/share/perl/5.10/ExtUtils/typemap +XSUBPP_EXTRA_ARGS = + + +# --- MakeMaker tools_other section: +SHELL = /bin/sh +CHMOD = chmod +CP = cp +MV = mv +NOOP = $(TRUE) +NOECHO = @ +RM_F = rm -f +RM_RF = rm -rf +TEST_F = test -f +TOUCH = touch +UMASK_NULL = umask 0 +DEV_NULL = > /dev/null 2>&1 +MKPATH = $(ABSPERLRUN) -MExtUtils::Command -e 'mkpath' -- +EQUALIZE_TIMESTAMP = $(ABSPERLRUN) -MExtUtils::Command -e 'eqtime' -- +FALSE = false +TRUE = true +ECHO = echo +ECHO_N = echo -n +UNINST = 0 +VERBINST = 0 +MOD_INSTALL = $(ABSPERLRUN) -MExtUtils::Install -e 'install([ from_to => {@ARGV}, verbose => '\''$(VERBINST)'\'', uninstall_shadows => '\''$(UNINST)'\'', dir_mode => '\''$(PERM_DIR)'\'' ]);' -- +DOC_INSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'perllocal_install' -- +UNINSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'uninstall' -- +WARN_IF_OLD_PACKLIST = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'warn_if_old_packlist' -- +MACROSTART = +MACROEND = +USEMAKEFILE = -f +FIXIN = $(ABSPERLRUN) -MExtUtils::MY -e 'MY->fixin(shift)' -- + + +# --- MakeMaker makemakerdflt section: +makemakerdflt : all + $(NOECHO) $(NOOP) + + +# --- MakeMaker dist section: +TAR = tar +TARFLAGS = cvf +ZIP = zip +ZIPFLAGS = -r +COMPRESS = gzip --best +SUFFIX = .gz +SHAR = shar +PREOP = $(NOECHO) $(NOOP) +POSTOP = $(NOECHO) $(NOOP) +TO_UNIX = $(NOECHO) $(NOOP) +CI = ci -u +RCS_LABEL = rcs -Nv$(VERSION_SYM): -q +DIST_CP = best +DIST_DEFAULT = tardist +DISTNAME = Zerg +DISTVNAME = Zerg-1.0.4 + + +# --- MakeMaker macro section: + + +# --- MakeMaker depend section: + + +# --- MakeMaker cflags section: + +CCFLAGS = -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 +OPTIMIZE = -O2 -g +PERLTYPE = +MPOLLUTE = + + +# --- MakeMaker const_loadlibs section: + +# Zerg might depend on some other libraries: +# See ExtUtils::Liblist for details +# +EXTRALIBS = -L/usr/local/lib -lzerg +LDLOADLIBS = -L/usr/local/lib -lzerg +BSLOADLIBS = + + +# --- MakeMaker const_cccmd section: +CCCMD = $(CC) -c $(PASTHRU_INC) $(INC) \ + $(CCFLAGS) $(OPTIMIZE) \ + $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \ + $(XS_DEFINE_VERSION) + +# --- MakeMaker post_constants section: + + +# --- MakeMaker pasthru section: + +PASTHRU = LIBPERL_A="$(LIBPERL_A)"\ + LINKTYPE="$(LINKTYPE)"\ + OPTIMIZE="$(OPTIMIZE)"\ + PREFIX="$(PREFIX)"\ + PASTHRU_DEFINE="$(PASTHRU_DEFINE)"\ + PASTHRU_INC="$(PASTHRU_INC)" + + +# --- MakeMaker special_targets section: +.SUFFIXES : .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT) + +.PHONY: all config static dynamic test linkext manifest blibdirs clean realclean disttest distdir + + + +# --- MakeMaker c_o section: + +.c.i: + cc -E -c $(PASTHRU_INC) $(INC) \ + $(CCFLAGS) $(OPTIMIZE) \ + $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \ + $(XS_DEFINE_VERSION) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c > $*.i + +.c.s: + $(CCCMD) -S $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c + +.c$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c + +.cpp$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cpp + +.cxx$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cxx + +.cc$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cc + +.C$(OBJ_EXT): + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.C + + +# --- MakeMaker xs_c section: + +.xs.c: + $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $(XSUBPP_EXTRA_ARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c + + +# --- MakeMaker xs_o section: + +.xs$(OBJ_EXT): + $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c + $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c + + +# --- MakeMaker top_targets section: +all :: pure_all manifypods + $(NOECHO) $(NOOP) + + +pure_all :: config pm_to_blib subdirs linkext + $(NOECHO) $(NOOP) + +subdirs :: $(MYEXTLIB) + $(NOECHO) $(NOOP) + +config :: $(FIRST_MAKEFILE) blibdirs + $(NOECHO) $(NOOP) + +help : + perldoc ExtUtils::MakeMaker + + +# --- MakeMaker blibdirs section: +blibdirs : $(INST_LIBDIR)$(DFSEP).exists $(INST_ARCHLIB)$(DFSEP).exists $(INST_AUTODIR)$(DFSEP).exists 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$(NOOP) + + +# --- MakeMaker dynamic_bs section: +BOOTSTRAP = $(BASEEXT).bs + +# As Mkbootstrap might not write a file (if none is required) +# we use touch to prevent make continually trying to remake it. +# The DynaLoader only reads a non-empty file. +$(BOOTSTRAP) : $(FIRST_MAKEFILE) $(BOOTDEP) $(INST_ARCHAUTODIR)$(DFSEP).exists + $(NOECHO) $(ECHO) "Running Mkbootstrap for $(NAME) ($(BSLOADLIBS))" + $(NOECHO) $(PERLRUN) \ + "-MExtUtils::Mkbootstrap" \ + -e "Mkbootstrap('$(BASEEXT)','$(BSLOADLIBS)');" + $(NOECHO) $(TOUCH) $@ + $(CHMOD) $(PERM_RW) $@ + +$(INST_BOOT) : $(BOOTSTRAP) $(INST_ARCHAUTODIR)$(DFSEP).exists + $(NOECHO) $(RM_RF) $@ + - $(CP) $(BOOTSTRAP) $@ + $(CHMOD) $(PERM_RW) $@ + + +# --- MakeMaker dynamic_lib section: + +# This section creates the dynamically loadable $(INST_DYNAMIC) +# from $(OBJECT) and possibly $(MYEXTLIB). +ARMAYBE = : +OTHERLDFLAGS = +INST_DYNAMIC_DEP = +INST_DYNAMIC_FIX = + +$(INST_DYNAMIC): $(OBJECT) $(MYEXTLIB) $(BOOTSTRAP) $(INST_ARCHAUTODIR)$(DFSEP).exists $(EXPORT_LIST) $(PERL_ARCHIVE) $(PERL_ARCHIVE_AFTER) $(INST_DYNAMIC_DEP) + $(RM_F) $@ + $(LD) $(LDDLFLAGS) $(LDFROM) $(OTHERLDFLAGS) -o $@ $(MYEXTLIB) \ + $(PERL_ARCHIVE) $(LDLOADLIBS) $(PERL_ARCHIVE_AFTER) $(EXPORT_LIST) \ + $(INST_DYNAMIC_FIX) + $(CHMOD) $(PERM_RWX) $@ + + +# --- MakeMaker static section: + +## $(INST_PM) has been moved to the all: target. +## It remains here for awhile to allow for old usage: "make static" +static :: $(FIRST_MAKEFILE) $(INST_STATIC) + $(NOECHO) $(NOOP) + + +# --- MakeMaker static_lib section: + +$(INST_STATIC) : $(OBJECT) $(MYEXTLIB) $(INST_ARCHAUTODIR)$(DFSEP).exists + $(RM_RF) $@ + $(FULL_AR) $(AR_STATIC_ARGS) $@ $(OBJECT) && $(RANLIB) $@ + $(CHMOD) $(PERM_RWX) $@ + $(NOECHO) $(ECHO) "$(EXTRALIBS)" > $(INST_ARCHAUTODIR)/extralibs.ld + + +# --- MakeMaker manifypods section: + +POD2MAN_EXE = $(PERLRUN) "-MExtUtils::Command::MM" -e pod2man "--" +POD2MAN = $(POD2MAN_EXE) + + +manifypods : pure_all \ + Zerg.pm + $(NOECHO) $(POD2MAN) --section=$(MAN3EXT) --perm_rw=$(PERM_RW) \ + Zerg.pm $(INST_MAN3DIR)/Zerg.$(MAN3EXT) + + + + +# --- MakeMaker processPL section: + + +# --- MakeMaker installbin section: + + +# --- MakeMaker subdirs section: + +# The default clean, realclean and test targets in this Makefile +# have automatically been given entries for each subdir. + + +subdirs :: + $(NOECHO) cd Report && $(MAKE) $(USEMAKEFILE) $(FIRST_MAKEFILE) all $(PASTHRU) + + +# --- MakeMaker clean_subdirs section: +clean_subdirs : + $(ABSPERLRUN) -e 'chdir '\''Report'\''; system '\''$(MAKE) clean'\'' if -f '\''$(FIRST_MAKEFILE)'\'';' -- + + +# --- MakeMaker clean section: + +# Delete temporary files but do not touch installed files. We don't delete +# the Makefile here so a later make realclean still has a makefile to use. + +clean :: clean_subdirs + - $(RM_F) \ + *$(LIB_EXT) core \ + core.[0-9] $(INST_ARCHAUTODIR)/extralibs.all \ + core.[0-9][0-9] $(BASEEXT).bso \ + pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \ + $(BASEEXT).x $(BOOTSTRAP) \ + perl$(EXE_EXT) tmon.out \ + Zerg.c *$(OBJ_EXT) \ + pm_to_blib $(INST_ARCHAUTODIR)/extralibs.ld \ + blibdirs.ts core.[0-9][0-9][0-9][0-9][0-9] \ + *perl.core core.*perl.*.? \ + $(MAKE_APERL_FILE) $(BASEEXT).def \ + perl core.[0-9][0-9][0-9] \ + mon.out lib$(BASEEXT).def \ + perl.exe perlmain.c \ + so_locations $(BASEEXT).exp + - $(RM_RF) \ + blib + - $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) $(DEV_NULL) + + +# --- MakeMaker realclean_subdirs section: +realclean_subdirs : + - $(ABSPERLRUN) -e 'chdir '\''Report'\''; system '\''$(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) realclean'\'' if -f '\''$(MAKEFILE_OLD)'\'';' -- + - $(ABSPERLRUN) -e 'chdir '\''Report'\''; system '\''$(MAKE) $(USEMAKEFILE) $(FIRST_MAKEFILE) realclean'\'' if -f '\''$(FIRST_MAKEFILE)'\'';' -- + + +# --- MakeMaker realclean section: +# Delete temporary files (via clean) and also delete dist files +realclean purge :: clean realclean_subdirs + - $(RM_F) \ + $(OBJECT) $(MAKEFILE_OLD) \ + $(FIRST_MAKEFILE) + - $(RM_RF) \ + $(DISTVNAME) + + +# --- MakeMaker metafile section: +metafile : create_distdir + $(NOECHO) $(ECHO) Generating META.yml + $(NOECHO) $(ECHO) '--- #YAML:1.0' > META_new.yml + $(NOECHO) $(ECHO) 'name: Zerg' >> META_new.yml + $(NOECHO) $(ECHO) 'version: 1.0.4' >> META_new.yml + $(NOECHO) $(ECHO) 'abstract: a lexical scanner for BLAST reports.' >> META_new.yml + $(NOECHO) $(ECHO) 'author:' >> META_new.yml + $(NOECHO) $(ECHO) ' - Apuã Paquola ' >> META_new.yml + $(NOECHO) $(ECHO) 'license: unknown' >> META_new.yml + $(NOECHO) $(ECHO) 'distribution_type: module' >> META_new.yml + $(NOECHO) $(ECHO) 'configure_requires:' >> META_new.yml + $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: 0' >> 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$(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{META.yml} => q{Module meta-data (added by MakeMaker)}}) } ' \ + -e ' or print "Could not add META.yml to MANIFEST: $${'\''@'\''}\n"' -- + + + +# --- MakeMaker distsignature section: +distsignature : create_distdir + $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{SIGNATURE} => q{Public-key signature (added by MakeMaker)}}) } ' \ + -e ' or print "Could not add SIGNATURE to MANIFEST: $${'\''@'\''}\n"' -- + $(NOECHO) cd $(DISTVNAME) && $(TOUCH) SIGNATURE + cd $(DISTVNAME) && cpansign -s + + + +# --- MakeMaker install section: + +install :: pure_install doc_install + $(NOECHO) $(NOOP) + +install_perl :: pure_perl_install doc_perl_install + $(NOECHO) $(NOOP) + +install_site :: pure_site_install doc_site_install + $(NOECHO) $(NOOP) + +install_vendor :: pure_vendor_install doc_vendor_install + $(NOECHO) $(NOOP) + +pure_install :: 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+doc_vendor_install :: all + + +uninstall :: uninstall_from_$(INSTALLDIRS)dirs + $(NOECHO) $(NOOP) + +uninstall_from_perldirs :: + +uninstall_from_sitedirs :: + $(NOECHO) $(UNINSTALL) $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist + +uninstall_from_vendordirs :: + + + +# --- MakeMaker force section: +# Phony target to force checking subdirectories. +FORCE : + $(NOECHO) $(NOOP) + + +# --- MakeMaker perldepend section: + +PERL_HDRS = \ + $(PERL_INC)/EXTERN.h \ + $(PERL_INC)/INTERN.h \ + $(PERL_INC)/XSUB.h \ + $(PERL_INC)/av.h \ + $(PERL_INC)/cc_runtime.h \ + $(PERL_INC)/config.h \ + $(PERL_INC)/cop.h \ + $(PERL_INC)/cv.h \ + $(PERL_INC)/dosish.h \ + $(PERL_INC)/embed.h \ + $(PERL_INC)/embedvar.h \ + $(PERL_INC)/fakethr.h \ + $(PERL_INC)/form.h \ + $(PERL_INC)/gv.h \ + $(PERL_INC)/handy.h \ + $(PERL_INC)/hv.h \ + $(PERL_INC)/intrpvar.h \ + $(PERL_INC)/iperlsys.h \ + $(PERL_INC)/keywords.h \ + $(PERL_INC)/mg.h \ + $(PERL_INC)/nostdio.h \ + $(PERL_INC)/op.h \ + $(PERL_INC)/opcode.h \ + 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$(USEMAKEFILE) $(MAKEFILE_OLD) clean $(DEV_NULL) + $(PERLRUN) Makefile.PL "INSTALLDIRS=vendor" + $(NOECHO) $(ECHO) "==> Your Makefile has been rebuilt. <==" + $(NOECHO) $(ECHO) "==> Please rerun the $(MAKE) command. <==" + $(FALSE) + + + +# --- MakeMaker staticmake section: + +# --- MakeMaker makeaperl section --- +MAP_TARGET = perl +FULLPERL = /usr/bin/perl + +$(MAP_TARGET) :: static $(MAKE_APERL_FILE) + $(MAKE) $(USEMAKEFILE) $(MAKE_APERL_FILE) $@ + +$(MAKE_APERL_FILE) : $(FIRST_MAKEFILE) pm_to_blib + $(NOECHO) $(ECHO) Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET) + $(NOECHO) $(PERLRUNINST) \ + Makefile.PL DIR=Report \ + MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \ + MAKEAPERL=1 NORECURS=1 CCCDLFLAGS= \ + INSTALLDIRS=vendor + + +# --- MakeMaker test section: + +TEST_VERBOSE=0 +TEST_TYPE=test_$(LINKTYPE) +TEST_FILE = test.pl +TEST_FILES = +TESTDB_SW = -d + +testdb :: testdb_$(LINKTYPE) + +test :: $(TEST_TYPE) subdirs-test + +subdirs-test :: + $(NOECHO) $(NOOP) + +subdirs-test :: + $(NOECHO) cd Report && $(MAKE) test $(PASTHRU) + + +test_dynamic :: pure_all + PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + +testdb_dynamic :: pure_all + PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + +test_ : test_dynamic + +test_static :: pure_all $(MAP_TARGET) + PERL_DL_NONLAZY=1 ./$(MAP_TARGET) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + +testdb_static :: pure_all $(MAP_TARGET) + PERL_DL_NONLAZY=1 ./$(MAP_TARGET) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + + + +# --- MakeMaker ppd section: +# Creates a PPD (Perl Package Description) for a binary distribution. +ppd : + $(NOECHO) $(ECHO) '' > $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' a lexical scanner for BLAST reports.' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' Apuã Paquola <apua@iq.usp.br>' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' ' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' ' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' ' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' ' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) '' >> $(DISTNAME).ppd + + +# --- MakeMaker pm_to_blib section: + +pm_to_blib : $(FIRST_MAKEFILE) $(TO_INST_PM) + $(NOECHO) $(ABSPERLRUN) -MExtUtils::Install -e 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', q[$(PM_FILTER)], '\''$(PERM_DIR)'\'')' -- \ + Zerg.pm $(INST_LIB)/Zerg.pm + $(NOECHO) $(TOUCH) pm_to_blib + + +# --- MakeMaker selfdocument section: + + +# --- MakeMaker postamble section: + + +# End. --- /dev/null +++ libzerg-perl-1.0.4/Zerg/Report/Makefile.old @@ -0,0 +1,602 @@ +# This Makefile is for the Zerg::Report extension to perl. +# +# It was generated automatically by MakeMaker version +# 6.55_02 (Revision: 65502) from the contents of +# Makefile.PL. Don't edit this file, edit Makefile.PL instead. +# +# ANY CHANGES MADE HERE WILL BE LOST! +# +# MakeMaker ARGV: (q[INSTALLDIRS=vendor]) +# + +# MakeMaker Parameters: + +# ABSTRACT_FROM => q[Report.pm] +# AUTHOR => q[Abimael A. Machado ] +# BUILD_REQUIRES => { } +# NAME => q[Zerg::Report] +# PREREQ_PM => { } +# VERSION_FROM => q[Report.pm] + +# --- MakeMaker post_initialize section: + + +# --- MakeMaker const_config section: + +# These definitions are from config.sh (via /usr/lib/perl/5.10/Config.pm). +# They may have been overridden via Makefile.PL or on the command line. +AR = ar +CC = cc +CCCDLFLAGS = -fPIC +CCDLFLAGS = -Wl,-E +DLEXT = so +DLSRC = dl_dlopen.xs +EXE_EXT = +FULL_AR = /usr/bin/ar +LD = cc +LDDLFLAGS = -shared -O2 -g -L/usr/local/lib -fstack-protector +LDFLAGS = -fstack-protector -L/usr/local/lib +LIBC = /lib/libc-2.11.2.so +LIB_EXT = .a +OBJ_EXT = .o +OSNAME = linux +OSVERS = 2.6.32-5-amd64 +RANLIB = : +SITELIBEXP = /usr/local/share/perl/5.10.1 +SITEARCHEXP = /usr/local/lib/perl/5.10.1 +SO = so +VENDORARCHEXP = /usr/lib/perl5 +VENDORLIBEXP = /usr/share/perl5 + + +# --- MakeMaker constants section: +AR_STATIC_ARGS = cr +DIRFILESEP = / +DFSEP = $(DIRFILESEP) +NAME = Zerg::Report +NAME_SYM = Zerg_Report +VERSION = 1.0.4 +VERSION_MACRO = VERSION +VERSION_SYM = 1_0_4 +DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\" +XS_VERSION = 1.0.4 +XS_VERSION_MACRO = XS_VERSION +XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\" +INST_ARCHLIB = ../blib/arch +INST_SCRIPT = ../blib/script +INST_BIN = ../blib/bin +INST_LIB = ../blib/lib +INST_MAN1DIR = ../blib/man1 +INST_MAN3DIR = ../blib/man3 +MAN1EXT = 1p +MAN3EXT = 3pm +INSTALLDIRS = site +DESTDIR = +PREFIX = /usr +PERLPREFIX = $(PREFIX) +SITEPREFIX = $(PREFIX)/local +VENDORPREFIX = $(PREFIX) +INSTALLPRIVLIB = $(PERLPREFIX)/share/perl/5.10 +DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB) +INSTALLSITELIB = $(SITEPREFIX)/share/perl/5.10.1 +DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB) +INSTALLVENDORLIB = $(VENDORPREFIX)/share/perl5 +DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB) +INSTALLARCHLIB = $(PERLPREFIX)/lib/perl/5.10 +DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB) +INSTALLSITEARCH = $(SITEPREFIX)/lib/perl/5.10.1 +DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH) +INSTALLVENDORARCH = $(VENDORPREFIX)/lib/perl5 +DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH) +INSTALLBIN = $(PERLPREFIX)/bin +DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN) +INSTALLSITEBIN = $(SITEPREFIX)/bin +DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN) +INSTALLVENDORBIN = $(VENDORPREFIX)/bin +DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN) +INSTALLSCRIPT = $(PERLPREFIX)/bin +DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT) +INSTALLSITESCRIPT = $(SITEPREFIX)/bin +DESTINSTALLSITESCRIPT = $(DESTDIR)$(INSTALLSITESCRIPT) +INSTALLVENDORSCRIPT = $(VENDORPREFIX)/bin +DESTINSTALLVENDORSCRIPT = $(DESTDIR)$(INSTALLVENDORSCRIPT) +INSTALLMAN1DIR = $(PERLPREFIX)/share/man/man1 +DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR) +INSTALLSITEMAN1DIR = $(SITEPREFIX)/man/man1 +DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR) +INSTALLVENDORMAN1DIR = $(VENDORPREFIX)/share/man/man1 +DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR) +INSTALLMAN3DIR = $(PERLPREFIX)/share/man/man3 +DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR) +INSTALLSITEMAN3DIR = $(SITEPREFIX)/man/man3 +DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR) +INSTALLVENDORMAN3DIR = $(VENDORPREFIX)/share/man/man3 +DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR) +PERL_LIB = /usr/share/perl/5.10 +PERL_ARCHLIB = /usr/lib/perl/5.10 +LIBPERL_A = libperl.a +FIRST_MAKEFILE = Makefile +MAKEFILE_OLD = Makefile.old +MAKE_APERL_FILE = Makefile.aperl +PERLMAINCC = $(CC) +PERL_INC = /usr/lib/perl/5.10/CORE +PERL = /usr/bin/perl +FULLPERL = /usr/bin/perl +ABSPERL = $(PERL) +PERLRUN = $(PERL) +FULLPERLRUN = $(FULLPERL) +ABSPERLRUN = $(ABSPERL) +PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" +FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" +ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" +PERL_CORE = 0 +PERM_DIR = 755 +PERM_RW = 644 +PERM_RWX = 755 + +MAKEMAKER = /usr/share/perl/5.10/ExtUtils/MakeMaker.pm +MM_VERSION = 6.55_02 +MM_REVISION = 65502 + +# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle). +# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle) +# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar) +# DLBASE = Basename part of dynamic library. May be just equal BASEEXT. +MAKE = make +FULLEXT = Zerg/Report +BASEEXT = Report +PARENT_NAME = Zerg +DLBASE = $(BASEEXT) +VERSION_FROM = Report.pm +OBJECT = +LDFROM = $(OBJECT) +LINKTYPE = dynamic +BOOTDEP = + +# Handy lists of source code files: +XS_FILES = +C_FILES = +O_FILES = +H_FILES = +MAN1PODS = +MAN3PODS = Report.pm + +# Where is the Config information that we are using/depend on +CONFIGDEP = $(PERL_ARCHLIB)$(DFSEP)Config.pm $(PERL_INC)$(DFSEP)config.h + +# Where to build things +INST_LIBDIR = $(INST_LIB)/Zerg +INST_ARCHLIBDIR = $(INST_ARCHLIB)/Zerg + +INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT) +INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT) + +INST_STATIC = +INST_DYNAMIC = +INST_BOOT = + +# Extra linker info +EXPORT_LIST = +PERL_ARCHIVE = +PERL_ARCHIVE_AFTER = + + +TO_INST_PM = Report.pm + +PM_TO_BLIB = Report.pm \ + $(INST_LIB)/Zerg/Report.pm + + +# --- MakeMaker platform_constants section: +MM_Unix_VERSION = 6.55_02 +PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc + + +# --- MakeMaker tool_autosplit section: +# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto +AUTOSPLITFILE = $(ABSPERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1)' -- + + + +# --- MakeMaker tool_xsubpp section: + + +# --- MakeMaker tools_other section: +SHELL = /bin/sh +CHMOD = chmod +CP = cp +MV = mv +NOOP = $(TRUE) +NOECHO = @ +RM_F = rm -f +RM_RF = rm -rf +TEST_F = test -f +TOUCH = touch +UMASK_NULL = umask 0 +DEV_NULL = > /dev/null 2>&1 +MKPATH = $(ABSPERLRUN) -MExtUtils::Command -e 'mkpath' -- +EQUALIZE_TIMESTAMP = $(ABSPERLRUN) -MExtUtils::Command -e 'eqtime' -- +FALSE = false +TRUE = true +ECHO = echo +ECHO_N = echo -n +UNINST = 0 +VERBINST = 0 +MOD_INSTALL = $(ABSPERLRUN) -MExtUtils::Install -e 'install([ from_to => {@ARGV}, verbose => '\''$(VERBINST)'\'', uninstall_shadows => '\''$(UNINST)'\'', dir_mode => '\''$(PERM_DIR)'\'' ]);' -- +DOC_INSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'perllocal_install' -- +UNINSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'uninstall' -- +WARN_IF_OLD_PACKLIST = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'warn_if_old_packlist' -- +MACROSTART = +MACROEND = +USEMAKEFILE = -f +FIXIN = $(ABSPERLRUN) -MExtUtils::MY -e 'MY->fixin(shift)' -- + + +# --- MakeMaker makemakerdflt section: +makemakerdflt : all + $(NOECHO) $(NOOP) + + +# --- MakeMaker dist section skipped. + +# --- MakeMaker macro section: + + +# --- MakeMaker depend section: + + +# --- MakeMaker cflags section: + + +# --- MakeMaker const_loadlibs section: + + +# --- MakeMaker const_cccmd section: + + +# --- MakeMaker post_constants section: + + +# --- MakeMaker pasthru section: + +PASTHRU = LIBPERL_A="$(LIBPERL_A)"\ + LINKTYPE="$(LINKTYPE)"\ + PREFIX="$(PREFIX)" + + +# --- MakeMaker special_targets section: +.SUFFIXES : .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT) + +.PHONY: all config static dynamic test linkext manifest blibdirs clean realclean disttest distdir + + + +# --- MakeMaker c_o section: + + +# --- MakeMaker xs_c section: + + +# --- MakeMaker xs_o section: + + +# --- MakeMaker top_targets section: +all :: pure_all manifypods + $(NOECHO) $(NOOP) + + +pure_all :: config pm_to_blib subdirs linkext + $(NOECHO) $(NOOP) + +subdirs :: $(MYEXTLIB) + $(NOECHO) $(NOOP) + +config :: $(FIRST_MAKEFILE) blibdirs + $(NOECHO) $(NOOP) + +help : + perldoc ExtUtils::MakeMaker + + +# --- MakeMaker blibdirs section: +blibdirs : $(INST_LIBDIR)$(DFSEP).exists $(INST_ARCHLIB)$(DFSEP).exists $(INST_AUTODIR)$(DFSEP).exists $(INST_ARCHAUTODIR)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists $(INST_SCRIPT)$(DFSEP).exists $(INST_MAN1DIR)$(DFSEP).exists $(INST_MAN3DIR)$(DFSEP).exists + $(NOECHO) $(NOOP) + +# Backwards compat with 6.18 through 6.25 +blibdirs.ts : blibdirs + $(NOECHO) $(NOOP) + +$(INST_LIBDIR)$(DFSEP).exists :: Makefile.PL + $(NOECHO) $(MKPATH) $(INST_LIBDIR) + $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_LIBDIR) + $(NOECHO) $(TOUCH) $(INST_LIBDIR)$(DFSEP).exists + +$(INST_ARCHLIB)$(DFSEP).exists :: Makefile.PL + $(NOECHO) $(MKPATH) $(INST_ARCHLIB) + $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHLIB) + $(NOECHO) $(TOUCH) $(INST_ARCHLIB)$(DFSEP).exists + +$(INST_AUTODIR)$(DFSEP).exists :: Makefile.PL + $(NOECHO) $(MKPATH) $(INST_AUTODIR) + $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_AUTODIR) + $(NOECHO) $(TOUCH) $(INST_AUTODIR)$(DFSEP).exists + +$(INST_ARCHAUTODIR)$(DFSEP).exists :: Makefile.PL + $(NOECHO) $(MKPATH) $(INST_ARCHAUTODIR) + $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHAUTODIR) + $(NOECHO) $(TOUCH) $(INST_ARCHAUTODIR)$(DFSEP).exists + +$(INST_BIN)$(DFSEP).exists :: Makefile.PL + $(NOECHO) $(MKPATH) $(INST_BIN) + $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_BIN) + $(NOECHO) $(TOUCH) $(INST_BIN)$(DFSEP).exists + +$(INST_SCRIPT)$(DFSEP).exists :: Makefile.PL + $(NOECHO) $(MKPATH) $(INST_SCRIPT) + $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_SCRIPT) + $(NOECHO) $(TOUCH) $(INST_SCRIPT)$(DFSEP).exists + +$(INST_MAN1DIR)$(DFSEP).exists :: Makefile.PL + $(NOECHO) $(MKPATH) $(INST_MAN1DIR) + $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN1DIR) + $(NOECHO) $(TOUCH) $(INST_MAN1DIR)$(DFSEP).exists + +$(INST_MAN3DIR)$(DFSEP).exists :: Makefile.PL + $(NOECHO) $(MKPATH) $(INST_MAN3DIR) + $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN3DIR) + $(NOECHO) $(TOUCH) $(INST_MAN3DIR)$(DFSEP).exists + + + +# --- MakeMaker linkext section: + +linkext :: $(LINKTYPE) + $(NOECHO) $(NOOP) + + +# --- MakeMaker dlsyms section: + + +# --- MakeMaker dynamic section: + +dynamic :: $(FIRST_MAKEFILE) $(INST_DYNAMIC) $(INST_BOOT) + $(NOECHO) $(NOOP) + + +# --- MakeMaker dynamic_bs section: + +BOOTSTRAP = + + +# --- MakeMaker dynamic_lib section: + + +# --- MakeMaker static section: + +## $(INST_PM) has been moved to the all: target. +## It remains here for awhile to allow for old usage: "make static" +static :: $(FIRST_MAKEFILE) $(INST_STATIC) + $(NOECHO) $(NOOP) + + +# --- MakeMaker static_lib section: + + +# --- MakeMaker manifypods section: + +POD2MAN_EXE = $(PERLRUN) "-MExtUtils::Command::MM" -e pod2man "--" +POD2MAN = $(POD2MAN_EXE) + + +manifypods : pure_all \ + Report.pm + $(NOECHO) $(POD2MAN) --section=$(MAN3EXT) --perm_rw=$(PERM_RW) \ + Report.pm $(INST_MAN3DIR)/Zerg::Report.$(MAN3EXT) + + + + +# --- MakeMaker processPL section: + + +# --- MakeMaker installbin section: + + +# --- MakeMaker subdirs section: + +# none + +# --- MakeMaker clean_subdirs section: +clean_subdirs : + $(NOECHO) $(NOOP) + + +# --- MakeMaker clean section: + +# Delete temporary files but do not touch installed files. We don't delete +# the Makefile here so a later make realclean still has a makefile to use. + +clean :: clean_subdirs + - $(RM_F) \ + *$(LIB_EXT) core \ + core.[0-9] $(INST_ARCHAUTODIR)/extralibs.all \ + core.[0-9][0-9] $(BASEEXT).bso \ + pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \ + $(BASEEXT).x $(BOOTSTRAP) \ + perl$(EXE_EXT) tmon.out \ + *$(OBJ_EXT) pm_to_blib \ + $(INST_ARCHAUTODIR)/extralibs.ld blibdirs.ts \ + core.[0-9][0-9][0-9][0-9][0-9] *perl.core \ + core.*perl.*.? $(MAKE_APERL_FILE) \ + perl $(BASEEXT).def \ + core.[0-9][0-9][0-9] mon.out \ + lib$(BASEEXT).def perlmain.c \ + perl.exe so_locations \ + $(BASEEXT).exp + - $(RM_RF) \ + blib + - $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) $(DEV_NULL) + + +# --- MakeMaker realclean_subdirs section: +realclean_subdirs : + $(NOECHO) $(NOOP) + + +# --- MakeMaker realclean section: +# Delete temporary files (via clean) and also delete dist files +realclean purge :: clean realclean_subdirs + - $(RM_F) \ + $(MAKEFILE_OLD) $(FIRST_MAKEFILE) + - $(RM_RF) \ + $(DISTVNAME) + + +# --- MakeMaker metafile section: +metafile : create_distdir + $(NOECHO) $(ECHO) Generating META.yml + $(NOECHO) $(ECHO) '--- #YAML:1.0' > META_new.yml + $(NOECHO) $(ECHO) 'name: Zerg-Report' >> META_new.yml + $(NOECHO) $(ECHO) 'version: 1.0.4' >> META_new.yml + $(NOECHO) $(ECHO) 'abstract: get attributes from a BLAST file in a data structure' >> META_new.yml + $(NOECHO) $(ECHO) 'author:' >> META_new.yml + $(NOECHO) $(ECHO) ' - Abimael A. Machado ' >> META_new.yml + $(NOECHO) $(ECHO) 'license: unknown' >> META_new.yml + $(NOECHO) $(ECHO) 'distribution_type: module' >> META_new.yml + $(NOECHO) $(ECHO) 'configure_requires:' >> META_new.yml + $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: 0' >> META_new.yml + $(NOECHO) $(ECHO) 'build_requires:' >> META_new.yml + $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: 0' >> META_new.yml + $(NOECHO) $(ECHO) 'requires: {}' >> META_new.yml + $(NOECHO) $(ECHO) 'no_index:' >> META_new.yml + $(NOECHO) $(ECHO) ' directory:' >> META_new.yml + $(NOECHO) $(ECHO) ' - t' >> META_new.yml + $(NOECHO) $(ECHO) ' - inc' >> META_new.yml + $(NOECHO) $(ECHO) 'generated_by: ExtUtils::MakeMaker version 6.55_02' >> META_new.yml + $(NOECHO) $(ECHO) 'meta-spec:' >> META_new.yml + $(NOECHO) $(ECHO) ' url: http://module-build.sourceforge.net/META-spec-v1.4.html' >> META_new.yml + $(NOECHO) $(ECHO) ' version: 1.4' >> META_new.yml + -$(NOECHO) $(MV) META_new.yml $(DISTVNAME)/META.yml + + +# --- MakeMaker signature section: +signature : + cpansign -s + + +# --- MakeMaker dist_basics section skipped. + +# --- MakeMaker dist_core section skipped. + +# --- MakeMaker distdir section skipped. + +# --- MakeMaker dist_test section skipped. + +# --- MakeMaker dist_ci section skipped. + +# --- MakeMaker distmeta section: +distmeta : create_distdir metafile + $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{META.yml} => q{Module meta-data (added by MakeMaker)}}) } ' \ + -e ' or print "Could not add META.yml to MANIFEST: $${'\''@'\''}\n"' -- + + + +# --- MakeMaker distsignature section: +distsignature : create_distdir + $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{SIGNATURE} => q{Public-key signature (added by MakeMaker)}}) } ' \ + -e ' or print "Could not add SIGNATURE to MANIFEST: $${'\''@'\''}\n"' -- + $(NOECHO) cd $(DISTVNAME) && $(TOUCH) SIGNATURE + cd $(DISTVNAME) && cpansign -s + + + +# --- MakeMaker install section skipped. + +# --- MakeMaker force section: +# Phony target to force checking subdirectories. +FORCE : + $(NOECHO) $(NOOP) + + +# --- MakeMaker perldepend section: + + +# --- MakeMaker makefile section: +# We take a very conservative approach here, but it's worth it. +# We move Makefile to Makefile.old here to avoid gnu make looping. +$(FIRST_MAKEFILE) : Makefile.PL $(CONFIGDEP) + $(NOECHO) $(ECHO) "Makefile out-of-date with respect to $?" + $(NOECHO) $(ECHO) "Cleaning current config before rebuilding Makefile..." + -$(NOECHO) $(RM_F) $(MAKEFILE_OLD) + -$(NOECHO) $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) + - $(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) clean $(DEV_NULL) + $(PERLRUN) Makefile.PL "INSTALLDIRS=vendor" + $(NOECHO) $(ECHO) "==> Your Makefile has been rebuilt. <==" + $(NOECHO) $(ECHO) "==> Please rerun the $(MAKE) command. <==" + $(FALSE) + + + +# --- MakeMaker staticmake section: + +# --- MakeMaker makeaperl section --- +MAP_TARGET = ../perl +FULLPERL = /usr/bin/perl + + +# --- MakeMaker test section: + +TEST_VERBOSE=0 +TEST_TYPE=test_$(LINKTYPE) +TEST_FILE = test.pl +TEST_FILES = +TESTDB_SW = -d + +testdb :: testdb_$(LINKTYPE) + +test :: $(TEST_TYPE) subdirs-test + +subdirs-test :: + $(NOECHO) $(NOOP) + + +test_dynamic :: pure_all + PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + +testdb_dynamic :: pure_all + PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE) + +test_ : test_dynamic + +test_static :: test_dynamic +testdb_static :: testdb_dynamic + + +# --- MakeMaker ppd section: +# Creates a PPD (Perl Package Description) for a binary distribution. +ppd : + $(NOECHO) $(ECHO) '' > $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' get attributes from a BLAST file in a data structure' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' Abimael A. Machado <abimael@iq.usp.br>' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' ' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' ' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' ' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) ' ' >> $(DISTNAME).ppd + $(NOECHO) $(ECHO) '' >> $(DISTNAME).ppd + + +# --- MakeMaker pm_to_blib section: + +pm_to_blib : $(FIRST_MAKEFILE) $(TO_INST_PM) + $(NOECHO) $(ABSPERLRUN) -MExtUtils::Install -e 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', q[$(PM_FILTER)], '\''$(PERM_DIR)'\'')' -- \ + Report.pm $(INST_LIB)/Zerg/Report.pm + $(NOECHO) $(TOUCH) pm_to_blib + + +# --- MakeMaker selfdocument section: + + +# --- MakeMaker postamble section: + + +# End. debian/patches/new_tokens0000644000000000000000000005056011775567743012750 0ustar Author: Laszlo Kajan Description: added new tags to handle iterated blast Forwarded: no Index: libzerg-perl-1.0.4/Zerg/Zerg.pm =================================================================== --- libzerg-perl-1.0.4.orig/Zerg/Zerg.pm 2006-03-07 18:00:37.000000000 +0100 +++ libzerg-perl-1.0.4/Zerg/Zerg.pm 2011-09-22 21:44:27.000000000 +0200 @@ -1,5 +1,5 @@ -# Copyright (C) 2002 Apuã Paquola - Instituto de Química - -# Universidade de São Paulo - Brasil +# Copyright (C) 2002 Apuã Paquola - Instituto de Química - +# Universidade de São Paulo - Brasil # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -37,73 +37,95 @@ # If you do not need this, moving things directly into @EXPORT or @EXPORT_OK # will save memory. our %EXPORT_TAGS = ( 'all' => [ qw( - ALIGNMENT_LENGTH - BLAST_VERSION - DESCRIPTION_ANNOTATION - DESCRIPTION_EVALUE - DESCRIPTION_HITNAME - DESCRIPTION_SCORE - END_OF_REPORT - EVALUE - GAPS - IDENTITIES - NOHITS - PERCENT_IDENTITIES - PERCENT_POSITIVES - POSITIVES - QUERY_ANNOTATION - QUERY_END - QUERY_FRAME - QUERY_LENGTH - QUERY_NAME - QUERY_ORIENTATION - QUERY_START - SCORE - SCORE_BITS - SUBJECT_ANNOTATION - SUBJECT_END - SUBJECT_FRAME - SUBJECT_LENGTH - SUBJECT_NAME - SUBJECT_ORIENTATION - SUBJECT_START - UNMATCHED + ALIGNMENT_LENGTH + BLAST_VERSION + CONVERGED + DATABASE + DESCRIPTION_ANNOTATION + DESCRIPTION_EVALUE + DESCRIPTION_HITNAME + DESCRIPTION_SCORE + END_OF_REPORT + EVALUE + GAPS + HSP_METHOD + IDENTITIES + NOHITS + PERCENT_IDENTITIES + PERCENT_POSITIVES + POSITIVES + QUERY_ALI + QUERY_ANNOTATION + QUERY_END + QUERY_FRAME + QUERY_LENGTH + QUERY_NAME + QUERY_ORIENTATION + QUERY_START + REFERENCE + ROUND_NUMBER + ROUND_SEQ_FOUND + ROUND_SEQ_NEW + SCORE + SCORE_BITS + SEARCHING + SUBJECT_ALI + SUBJECT_ANNOTATION + SUBJECT_END + SUBJECT_FRAME + SUBJECT_LENGTH + SUBJECT_NAME + SUBJECT_ORIENTATION + SUBJECT_START + TAIL_OF_REPORT + UNMATCHED ) ] ); our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } ); our @EXPORT = qw( - ALIGNMENT_LENGTH - BLAST_VERSION - DESCRIPTION_ANNOTATION - DESCRIPTION_EVALUE - DESCRIPTION_HITNAME - DESCRIPTION_SCORE - END_OF_REPORT - EVALUE - GAPS - IDENTITIES - NOHITS - PERCENT_IDENTITIES - PERCENT_POSITIVES - POSITIVES - QUERY_ANNOTATION - QUERY_END - QUERY_FRAME - QUERY_LENGTH - QUERY_NAME - QUERY_ORIENTATION - QUERY_START - SCORE - SCORE_BITS - SUBJECT_ANNOTATION - SUBJECT_END - SUBJECT_FRAME - SUBJECT_LENGTH - SUBJECT_NAME - SUBJECT_ORIENTATION - SUBJECT_START - UNMATCHED + ALIGNMENT_LENGTH + BLAST_VERSION + CONVERGED + DATABASE + DESCRIPTION_ANNOTATION + DESCRIPTION_EVALUE + DESCRIPTION_HITNAME + DESCRIPTION_SCORE + END_OF_REPORT + EVALUE + GAPS + HSP_METHOD + IDENTITIES + NOHITS + PERCENT_IDENTITIES + PERCENT_POSITIVES + POSITIVES + QUERY_ALI + QUERY_ANNOTATION + QUERY_END + QUERY_FRAME + QUERY_LENGTH + QUERY_NAME + QUERY_ORIENTATION + QUERY_START + REFERENCE + ROUND_NUMBER + ROUND_SEQ_FOUND + ROUND_SEQ_NEW + SCORE + SCORE_BITS + SEARCHING + SUBJECT_ALI + SUBJECT_ANNOTATION + SUBJECT_END + SUBJECT_FRAME + SUBJECT_LENGTH + SUBJECT_NAME + SUBJECT_ORIENTATION + SUBJECT_START + TAIL_OF_REPORT + UNMATCHED ); our $VERSION = '1.0.4'; @@ -209,37 +231,48 @@ =head2 EXPORTED CONSTANTS (TOKEN CODES) - ALIGNMENT_LENGTH - BLAST_VERSION - DESCRIPTION_ANNOTATION - DESCRIPTION_EVALUE - DESCRIPTION_HITNAME - DESCRIPTION_SCORE - END_OF_REPORT - EVALUE - GAPS - IDENTITIES - NOHITS - PERCENT_IDENTITIES - PERCENT_POSITIVES - POSITIVES - QUERY_ANNOTATION - QUERY_END - QUERY_FRAME - QUERY_LENGTH - QUERY_NAME - QUERY_ORIENTATION - QUERY_START - SCORE - SCORE_BITS - SUBJECT_ANNOTATION - SUBJECT_END - SUBJECT_FRAME - SUBJECT_LENGTH - SUBJECT_NAME - SUBJECT_ORIENTATION - SUBJECT_START - UNMATCHED + ALIGNMENT_LENGTH + BLAST_VERSION + CONVERGED + DATABASE + DESCRIPTION_ANNOTATION + DESCRIPTION_EVALUE + DESCRIPTION_HITNAME + DESCRIPTION_SCORE + END_OF_REPORT + EVALUE + GAPS + HSP_METHOD + IDENTITIES + NOHITS + PERCENT_IDENTITIES + PERCENT_POSITIVES + POSITIVES + QUERY_ALI + QUERY_ANNOTATION + QUERY_END + QUERY_FRAME + QUERY_LENGTH + QUERY_NAME + QUERY_ORIENTATION + QUERY_START + REFERENCE + ROUND_NUMBER + ROUND_SEQ_FOUND + ROUND_SEQ_NEW + SCORE + SCORE_BITS + SEARCHING + SUBJECT_ALI + SUBJECT_ANNOTATION + SUBJECT_END + SUBJECT_FRAME + SUBJECT_LENGTH + SUBJECT_NAME + SUBJECT_ORIENTATION + SUBJECT_START + TAIL_OF_REPORT + UNMATCHED =head2 NOTES ON THE SCANNER @@ -312,13 +345,15 @@ and those that are modified by the parser, namely: QUERY_LENGTH, SUBJECT_LENGTH, EVALUE, GAPS. -=head1 TO DO +=head1 TODO Add more tokens to the scanner as the need for that appears. =head1 AUTHOR -Apuã Paquola, IQ-USP Bioinformatics Lab, apua@iq.usp.br +Apuã Paquola, IQ-USP Bioinformatics Lab, apua@iq.usp.br + +Laszlo Kajan , Technical University of Munich, Germany =head1 SEE ALSO Index: libzerg-perl-1.0.4/Zerg/Zerg.xs =================================================================== --- libzerg-perl-1.0.4.orig/Zerg/Zerg.xs 2005-01-10 23:57:35.000000000 +0100 +++ libzerg-perl-1.0.4/Zerg/Zerg.xs 2011-09-22 21:44:27.000000000 +0200 @@ -1,6 +1,6 @@ /* - Copyright (C) 2002 Apuã Paquola - Instituto de Química - - Universidade de São Paulo - Brasil + Copyright (C) 2002 Apuã Paquola - Instituto de Química - + Universidade de São Paulo - Brasil This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -94,7 +94,14 @@ } switch (name[1 + 5]) { case 'A': - if (strEQ(name + 1, "UERY_ANNOTATION")) { /* Q removed */ + if (strEQ(name + 1, "UERY_ALI")) { /* Q removed */ +#ifdef QUERY_ALI + return QUERY_ALI; +#else + goto not_there; +#endif + } + else if (strEQ(name + 1, "UERY_ANNOTATION")) { /* Q removed */ #ifdef QUERY_ANNOTATION return QUERY_ANNOTATION; #else @@ -159,6 +166,45 @@ } static double +constant_R(char *name, int len, int arg) +{ + if (strEQ(name + 1, "EFERENCE")) { /* R removed */ +#ifdef REFERENCE + return REFERENCE; +#else + goto not_there; +#endif + } + else if (strEQ(name + 1, "OUND_NUMBER")) { /* R removed */ +#ifdef ROUND_NUMBER + return ROUND_NUMBER; +#else + goto not_there; +#endif + } + else if (strEQ(name + 1, "OUND_SEQ_FOUND")) { /* R removed */ +#ifdef ROUND_SEQ_FOUND + return ROUND_SEQ_FOUND; +#else + goto not_there; +#endif + } + else if (strEQ(name + 1, "OUND_SEQ_NEW")) { /* R removed */ +#ifdef ROUND_SEQ_NEW + return ROUND_SEQ_NEW; +#else + goto not_there; +#endif + } + errno = EINVAL; + return 0; + +not_there: + errno = ENOENT; + return 0; +} + +static double constant_SC(char *name, int len, int arg) { if (2 + 3 > len ) { @@ -200,7 +246,14 @@ } switch (name[2 + 6]) { case 'A': - if (strEQ(name + 2, "BJECT_ANNOTATION")) { /* SU removed */ + if (strEQ(name + 2, "BJECT_ALI")) { /* SU removed */ +#ifdef SUBJECT_ALI + return SUBJECT_ALI; +#else + goto not_there; +#endif + } + else if (strEQ(name + 2, "BJECT_ANNOTATION")) { /* SU removed */ #ifdef SUBJECT_ANNOTATION return SUBJECT_ANNOTATION; #else @@ -270,6 +323,14 @@ switch (name[1 + 0]) { case 'C': return constant_SC(name, len, arg); + case 'E': + if (strEQ(name + 2, "ARCHING")) { /* SE removed */ +#ifdef SEARCHING + return SEARCHING; +#else + goto not_there; +#endif + } case 'U': return constant_SU(name, len, arg); } @@ -284,6 +345,13 @@ static double constant_D(char *name, int len, int arg) { + if (strEQ(name + 1, "ATABASE")) { /* D removed */ +#ifdef DATABASE + return DATABASE; +#else + goto not_there; +#endif + } if (1 + 11 >= len ) { errno = EINVAL; return 0; @@ -380,6 +448,14 @@ goto not_there; #endif } + case 'C': + if (strEQ(name + 1, "ONVERGED")) { /* C removed */ +#ifdef CONVERGED + return CONVERGED; +#else + goto not_there; +#endif + } case 'D': return constant_D(name, len, arg); case 'E': @@ -392,6 +468,14 @@ goto not_there; #endif } + case 'H': + if (strEQ(name + 1, "SP_METHOD")) { /* H removed */ +#ifdef HSP_METHOD + return HSP_METHOD; +#else + goto not_there; +#endif + } case 'I': if (strEQ(name + 0, "IDENTITIES")) { /* removed */ #ifdef IDENTITIES @@ -412,8 +496,18 @@ return constant_P(name, len, arg); case 'Q': return constant_Q(name, len, arg); + case 'R': + return constant_R(name, len, arg); case 'S': return constant_S(name, len, arg); + case 'T': + if (strEQ(name + 0, "TAIL_OF_REPORT")) { /* removed */ +#ifdef TAIL_OF_REPORT + return TAIL_OF_REPORT; +#else + goto not_there; +#endif + } case 'U': if (strEQ(name + 0, "UNMATCHED")) { /* removed */ #ifdef UNMATCHED Index: libzerg-perl-1.0.4/Zerg/Report/Report.pm =================================================================== --- libzerg-perl-1.0.4.orig/Zerg/Report/Report.pm 2006-03-07 18:19:10.000000000 +0100 +++ libzerg-perl-1.0.4/Zerg/Report/Report.pm 2011-09-23 21:25:38.141700224 +0200 @@ -17,6 +17,7 @@ # package Zerg::Report; use strict; +use Carp; use Zerg; our $VERSION = '1.0.4'; @@ -30,14 +31,10 @@ my $file = shift; - my $blast_report = (); - - Zerg::zerg_open_file($file); + if( defined($file) ){ Zerg::zerg_open_file($file); } Zerg::zerg_unignore_all(); - $self->{report} = $blast_report; - bless $self,$class; return $self; @@ -49,7 +46,7 @@ my $self=shift; - my $blast_report = $self->{report}; + my $blast_report = undef; my ($c,$v,$hit_counter,$hsp_counter); @@ -59,6 +56,8 @@ while((($c, $v)= Zerg::zerg_get_token()) && $c) { + if( !defined($blast_report) ){ $blast_report = {}; } + if($c==BLAST_VERSION) { $blast_report->{blast_version}=$v; @@ -86,96 +85,104 @@ $blast_report->{hits}[$hit_counter]{"subject_name"}=$v; } elsif($c==SUBJECT_ANNOTATION) - { - $blast_report->{hits}[$hit_counter]{"subject_annotation"}=$v; - } - elsif($c==SUBJECT_LENGTH) - { - $blast_report->{hits}[$hit_counter]{"subject_length"}=$v; - } - elsif($c==SCORE_BITS) - { + { + $blast_report->{hits}[$hit_counter]{"subject_annotation"}=$v; + } + elsif($c==SUBJECT_LENGTH) + { + $blast_report->{hits}[$hit_counter]{"subject_length"}=$v; + } + elsif($c==SCORE_BITS) + { $hsp_counter++; $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score_bits"}=$v; - } - elsif($c==SCORE) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score"}=$v; - } - elsif($c==EVALUE) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"evalue"}=$v; - } - elsif($c==IDENTITIES) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"identities"}=$v; - } - elsif($c==ALIGNMENT_LENGTH) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"alignment_length"}=$v; - } - elsif($c==PERCENT_IDENTITIES) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_identities"}=$v; - } - elsif($c==GAPS) - { - - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"gaps"}=$v; - } - elsif($c==QUERY_ORIENTATION) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_orientation"}=$v; - } - elsif($c==SUBJECT_ORIENTATION) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_orientation"}=$v; - } + } + elsif($c==SCORE) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score"}=$v; + } + elsif($c==EVALUE) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"evalue"}=$v; + } + elsif($c==IDENTITIES) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"identities"}=$v; + } + elsif($c==ALIGNMENT_LENGTH) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"alignment_length"}=$v; + } + elsif($c==PERCENT_IDENTITIES) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_identities"}=$v; + } + elsif($c==GAPS) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"gaps"}=$v; + } + elsif($c==QUERY_ORIENTATION) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_orientation"}=$v; + } + elsif($c==SUBJECT_ORIENTATION) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_orientation"}=$v; + } elsif($c==QUERY_START) { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"}=$v; - + if( $v && !$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"}=$v; } + } + elsif($c==QUERY_ALI) + { + if( $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_ali"} .= $v; } } elsif($c==QUERY_END) { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_end"}=$v; + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_end"}=$v; } elsif($c==SUBJECT_START) { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_start"}=$v; + if( $v && !$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_start"}=$v; } + } + elsif($c==SUBJECT_ALI) + { + if( $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_ali"} .= $v; } } elsif($c==SUBJECT_END) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_end"}=$v; - } - elsif($c==POSITIVES) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"positives"}=$v; - } - elsif($c==PERCENT_POSITIVES) - { + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_end"}=$v; + } + elsif($c==POSITIVES) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"positives"}=$v; + } + elsif($c==PERCENT_POSITIVES) + { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_positives"}=$v; - } - elsif($c==QUERY_FRAME) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_frame"}=$v; - } - elsif($c==SUBJECT_FRAME) - { - $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_frame"}=$v; - } - elsif($c==UNMATCHED) - { - die "Syntax error in blast report\n"; - } - elsif($c==END_OF_REPORT) - { - my $r=$blast_report; - $blast_report=(); - return $r; - } + } + elsif($c==QUERY_FRAME) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_frame"}=$v; + } + elsif($c==SUBJECT_FRAME) + { + $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_frame"}=$v; + } + elsif($c==ROUND_NUMBER) + { + $blast_report->{round_begins}[$v-1] = $hit_counter + 1; + } + elsif($c==UNMATCHED) + { + confess("Syntax error in blast report: '$v'"); + } + elsif($c==END_OF_REPORT) + { + return $blast_report; + } } - return (); + return $blast_report; } sub closeFile @@ -218,8 +225,9 @@ foreach my $hit (@{$r->{hits}}) { foreach my $hsp (@{$hit->{hsps}}) - { - print "$r->{query_name} $hit->{subject_name} $hsp->{score_bits}\n"; } + { + print "$r->{query_name} $hit->{subject_name} $hsp->{score_bits}\n"; + } } } @@ -227,15 +235,15 @@ =head1 DESCRIPTION - Zerg::Report uses Zerg to parse a file containing multiple BLAST - reports and, for each report, stores the obtained fields in a data - structure made of arrays and hashes. Please consult the Zerg man - page to see which fields are extracted. + Zerg::Report uses Zerg to parse a file - or STDIN if file is not given - + containing one or multiple BLAST reports and, for each report, stores + the obtained fields in a data structure made of arrays and hashes. + Please consult the Zerg man page to see which fields are extracted. The method getReport() reads a BLAST report from the input file and returns a reference to a data structure like the one in the example - below. When no report is found, it returns false. It dies from - syntax errors in BLAST reports. + below. When no report is found, it returns undef. It dies from + syntax errors in BLAST reports with a stack backtrace. Example of a data structure returned by getReport(): @@ -245,26 +253,27 @@ 'byte_offset' => 4981, 'query_length' => '444', 'query_annotation' => '' - + 'round_begins' => [ 0, 129, 201 ], # indicates the first hit in each round of iterated blast 'hits' => [ { 'subject_annotation' => '(NC_003210) similar to cation (calcium) transporting ATPase [Listeria monocytogenes EGD-e]', 'hsps' => [ { - 'query_end' => '428', - 'subject_end' => '151', - 'identities' => '59', - 'score' => '252', - 'percent_positives' => '57', - 'gaps' => '0', - 'score_bits' => '101', - 'alignment_length' => '142', - 'evalue' => '2e-21', - 'percent_identities' => '41', - 'positives' => '83', - 'query_start' => '3', - 'subject_start' => '22', - 'query_frame' => '+3' + 'query_end' => '82', + 'subject_ali' => 'ASELEIFAALIECEA-GSTDYDGMLAVASVVMNRVNHRYYPDTITGVIYQSGQFSPVASGKLDKVLKRGIKSSCLEVAKDA', + 'query_ali' => 'DAQTRKLAAIAYGEASGANDANEIGGIAWAVANRARAWGGK-TVDGLLAADPNYTYAVKDG-NQRYAKLMKATEAAIAADP', + 'subject_end' => '328', + 'identities' => '15', + 'score' => '87', + 'percent_positives' => '41', + 'gaps' => '3', + 'score_bits' => '37.9', + 'alignment_length' => '81', + 'evalue' => '0.40', + 'percent_identities' => '18', + 'positives' => '34', + 'query_start' => '4', + 'subject_start' => '249' } ], 'subject_length' => '880', @@ -275,11 +284,13 @@ =head1 AUTHORS -Apuã Paquola , Abimael Machado -IQ-USP Bioinformatics Lab +Apuã Paquola , Abimael Machado IQ-USP Bioinformatics Lab + +Laszlo Kajan , Technical University of Munich, Germany =head1 SEE ALSO Zerg =cut +# vim:et:ts=2:ai: debian/patches/series0000644000000000000000000000004211636711335012034 0ustar new_tokens debian-changes-1.0.4-1 debian/compat0000644000000000000000000000000211775572147010404 0ustar 8 debian/control0000644000000000000000000000241011775572154010604 0ustar Source: libzerg-perl Section: perl Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , Andreas Tille Build-Depends: debhelper (>= 8), libzerg0-dev Standards-Version: 3.9.3 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/libzerg-perl/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/libzerg-perl/trunk/ DM-Upload-Allowed: yes Homepage: http://code.google.com/p/libzerg/ Package: libzerg-perl Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends} Description: fast perl module for parsing the output of NCBI BLAST programs The Zerg library contains a C/flex lexical scanner for BLAST reports and a set of supporting functions. It is centered on a "get_token" function that scans the input for specified lexical elements and, when one is found, returns its code and value to the user. . It is intended to be fast: for that the authors used flex, which provides simple regular expression matching and input buffering in the generated C scanner. And it is intended to be simple in the sense of providing just a lexical scanner, with no features whose support could slow down its main function. debian/changelog0000644000000000000000000000241312231040320011023 0ustar libzerg-perl (1.0.4-3build1) devel; urgency=low * Rebuild for Perl 5.18. -- Colin Watson Sun, 20 Oct 2013 21:45:04 +0100 libzerg-perl (1.0.4-3) unstable; urgency=low [ Andreas Tille ] * debian/upstream: - copy of libzerg upstream file * debian/control: - Added myself to uploaders - Standards-Version: 3.9.3 (no changes needed) - Removed build dependency from cdbs [ Charles Plessy ] * mv debian/upstream-metadata.yaml debian/upstream [ Laszlo Kajan ] * Fixed watch file; moved from cdbs to dh build. * debian/compat and dh build dep for version 7 to allow Ubuntu Lucid (LTS) builds without modification (Lucid has version 7 of dh) * Fixed Build-Depends issue, now libzerg0-dev, thanks to Michael Terry . (Closes: #680425) -- Laszlo Kajan Fri, 06 Jul 2012 15:32:27 +0200 libzerg-perl (1.0.4-2) unstable; urgency=low * added new tokens from libzerg-1.0.7-2 * Report.pm now understands blastpgp output, i.e. rounds of iteration -- Laszlo Kajan Thu, 22 Sep 2011 18:43:25 +0200 libzerg-perl (1.0.4-1) unstable; urgency=low * Initial release (Closes: #641799) -- Laszlo Kajan Fri, 16 Sep 2011 11:52:32 +0200