scbi_fqbin 0.2.2 → 0.2.3

data/test/old/ext/Makefile

@@ -0,0 +1,187 @@
+
+SHELL = /bin/sh
+
+#### Start of system configuration section. ####
+
+srcdir = .
+topdir = /Users/dariogf/.rvm/rubies/ruby-1.9.2-p0/include/ruby-1.9.1
+hdrdir = /Users/dariogf/.rvm/rubies/ruby-1.9.2-p0/include/ruby-1.9.1
+arch_hdrdir = /Users/dariogf/.rvm/rubies/ruby-1.9.2-p0/include/ruby-1.9.1/$(arch)
+VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
+prefix = $(DESTDIR)/Users/dariogf/.rvm/rubies/ruby-1.9.2-p0
+rubylibprefix = $(libdir)/$(RUBY_BASE_NAME)
+exec_prefix = $(prefix)
+vendorhdrdir = $(rubyhdrdir)/vendor_ruby
+sitehdrdir = $(rubyhdrdir)/site_ruby
+rubyhdrdir = $(includedir)/$(RUBY_BASE_NAME)-$(ruby_version)
+vendordir = $(rubylibprefix)/vendor_ruby
+sitedir = $(rubylibprefix)/site_ruby
+ridir = $(datarootdir)/$(RI_BASE_NAME)
+mandir = $(datarootdir)/man
+localedir = $(datarootdir)/locale
+libdir = $(exec_prefix)/lib
+psdir = $(docdir)
+pdfdir = $(docdir)
+dvidir = $(docdir)
+htmldir = $(docdir)
+infodir = $(datarootdir)/info
+docdir = $(datarootdir)/doc/$(PACKAGE)
+oldincludedir = $(DESTDIR)/usr/include
+includedir = $(prefix)/include
+localstatedir = $(prefix)/var
+sharedstatedir = $(prefix)/com
+sysconfdir = $(prefix)/etc
+datadir = $(datarootdir)
+datarootdir = $(prefix)/share
+libexecdir = $(exec_prefix)/libexec
+sbindir = $(exec_prefix)/sbin
+bindir = $(exec_prefix)/bin
+rubylibdir = $(rubylibprefix)/$(ruby_version)
+archdir = $(rubylibdir)/$(arch)
+sitelibdir = $(sitedir)/$(ruby_version)
+sitearchdir = $(sitelibdir)/$(sitearch)
+vendorlibdir = $(vendordir)/$(ruby_version)
+vendorarchdir = $(vendorlibdir)/$(sitearch)
+
+CC = gcc
+CXX = g++
+LIBRUBY = $(LIBRUBY_SO)
+LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
+LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
+LIBRUBYARG_STATIC = -l$(RUBY_SO_NAME)-static
+OUTFLAG = -o 
+COUTFLAG = -o 
+
+RUBY_EXTCONF_H = 
+cflags   =  $(optflags) $(debugflags) $(warnflags)
+optflags = -O3
+debugflags = -ggdb
+warnflags = -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wshorten-64-to-32 -Wno-long-long
+CFLAGS   = -fno-common $(cflags)  -fno-common -pipe 
+INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir)
+DEFS     = 
+CPPFLAGS =  -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE $(DEFS) $(cppflags)
+CXXFLAGS = $(CFLAGS) $(cxxflags)
+ldflags  = -L. 
+dldflags = -Wl,-undefined,dynamic_lookup -Wl,-multiply_defined,suppress -Wl,-flat_namespace
+ARCH_FLAG = 
+DLDFLAGS = $(ldflags) $(dldflags)
+LDSHARED = $(CC) -dynamic -bundle
+LDSHAREDXX = $(CXX) -dynamic -bundle
+AR = ar
+EXEEXT = 
+
+RUBY_BASE_NAME = ruby
+RUBY_INSTALL_NAME = ruby
+RUBY_SO_NAME = ruby.1.9.1
+arch = x86_64-darwin10.5.0
+sitearch = $(arch)
+ruby_version = 1.9.1
+ruby = /Users/dariogf/.rvm/rubies/ruby-1.9.2-p0/bin/ruby
+RUBY = $(ruby)
+RM = rm -f
+RM_RF = $(RUBY) -run -e rm -- -rf
+RMDIRS = $(RUBY) -run -e rmdir -- -p
+MAKEDIRS = mkdir -p
+INSTALL = /usr/bin/install -c
+INSTALL_PROG = $(INSTALL) -m 0755
+INSTALL_DATA = $(INSTALL) -m 644
+COPY = cp
+
+#### End of system configuration section. ####
+
+preload = 
+
+libpath = . $(libdir)
+LIBPATH =  -L. -L$(libdir)
+DEFFILE = 
+
+CLEANFILES = mkmf.log
+DISTCLEANFILES = 
+DISTCLEANDIRS = 
+
+extout = 
+extout_prefix = 
+target_prefix = 
+LOCAL_LIBS = 
+LIBS = $(LIBRUBYARG_SHARED)  -lpthread -ldl -lobjc 
+SRCS = mk_fbin.c
+OBJS = mk_fbin.o
+TARGET = bin
+DLLIB = $(TARGET).bundle
+EXTSTATIC = 
+STATIC_LIB = 
+
+BINDIR        = $(bindir)
+RUBYCOMMONDIR = $(sitedir)$(target_prefix)
+RUBYLIBDIR    = $(sitelibdir)$(target_prefix)
+RUBYARCHDIR   = $(sitearchdir)$(target_prefix)
+HDRDIR        = $(rubyhdrdir)/ruby$(target_prefix)
+ARCHHDRDIR    = $(rubyhdrdir)/$(arch)/ruby$(target_prefix)
+
+TARGET_SO     = $(DLLIB)
+CLEANLIBS     = $(TARGET).bundle 
+CLEANOBJS     = *.o  *.bak
+
+all:    $(DLLIB)
+static: $(STATIC_LIB)
+.PHONY: all install static install-so install-rb
+.PHONY: clean clean-so clean-rb
+
+clean-rb-default::
+clean-rb::
+clean-so::
+clean: clean-so clean-rb-default clean-rb
+		@-$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES)
+
+distclean-rb-default::
+distclean-rb::
+distclean-so::
+distclean: clean distclean-so distclean-rb-default distclean-rb
+		@-$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
+		@-$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
+		@-$(RMDIRS) $(DISTCLEANDIRS)
+
+realclean: distclean
+install: install-so install-rb
+
+install-so: $(RUBYARCHDIR)
+install-so: $(RUBYARCHDIR)/$(DLLIB)
+$(RUBYARCHDIR)/$(DLLIB): $(DLLIB)
+	@-$(MAKEDIRS) $(@D)
+	$(INSTALL_PROG) $(DLLIB) $(@D)
+install-rb: pre-install-rb install-rb-default
+install-rb-default: pre-install-rb-default
+pre-install-rb: Makefile
+pre-install-rb-default: Makefile
+$(RUBYARCHDIR):
+	$(MAKEDIRS) $@
+
+site-install: site-install-so site-install-rb
+site-install-so: install-so
+site-install-rb: install-rb
+
+.SUFFIXES: .c .m .cc .cxx .cpp .C .o
+
+.cc.o:
+	$(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.cxx.o:
+	$(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.cpp.o:
+	$(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.C.o:
+	$(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.c.o:
+	$(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
+
+$(DLLIB): $(OBJS) Makefile
+	@-$(RM) $(@)
+	$(LDSHARED) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
+
+
+
+$(OBJS): $(hdrdir)/ruby.h $(hdrdir)/ruby/defines.h $(arch_hdrdir)/ruby/config.h

data/test/old/ext/Makefile.dario

@@ -0,0 +1,34 @@
+OS := $(shell uname)
+
+CFLAGS=
+
+ifeq ($(OS), Linux)
+	CFLAGS=-fPIC -O3
+endif
+
+CC=gcc
+DEPFILE=.depend
+PROGS=mk_fbin rd_seq_fbin iterate_fbin
+OBJS=libreria_gz.o
+LIBS=-lz
+LIB_NAME=liblibreria_gz
+
+all: $(OBJS) $(PROGS) lib
+
+$(PROGS):
+	$(CC) $(CFLAGS) $(OBJS) $(LIBS) $@.c -o $@
+
+.c.o:
+	$(CC) $(CFLAGS) -c -o $@ $<
+
+lib:
+ifeq ($(OS), Linux)
+	$(CC) -shared -Wl,-soname,$(LIB_NAME).so.1 -o $(LIB_NAME).so $(OBJS) $(LIBS) 
+endif
+
+ifeq ($(OS), Darwin)
+	$(CC) $(LIBS) -dynamiclib -o $(LIB_NAME).dylib -dylib $(OBJS)
+endif
+ 
+clean:
+	rm -f *.o $(PROGS) *.dylib *.so*

data/test/old/ext/extconf.rb

@@ -0,0 +1,8 @@
+require 'mkmf'
+require 'rbconfig'
+
+dir_config("bin")
+
+have_library("libfbin")
+
+create_makefile("bin")

data/test/old/ext/mk_fbin.c

@@ -0,0 +1,24 @@
+#include "libfbin.h"
+#include <stdio.h>
+#include <ctype.h>
+
+
+/*******************************************************/
+/* main                                                */
+/*******************************************************/
+int main(int argc, char *argv[])
+{
+  // check params
+  if (argc!=5)
+  {
+    printf("Usage %s fasta_file qual_file extras_file output_file\n\n",argv[0]);
+    return -1;
+  }
+ 
+  // process file
+//  int res=process_biofile(argv[1],argv[2],argv[3],argv[4]);
+  int res=process_biofile(argv[1],argv[2],argv[3] ,argv[4]);
+
+  return res;
+}
+

data/test/old/ext/sample/extras.txt

@@ -0,0 +1,4 @@
+>FX9YN3P05C43XJ
+extras1
+>FX9YN3P05C9OK8_I_IZQ
+extras2

data/test/old/ext/sample/f1.fasta

@@ -0,0 +1,10 @@
+>FX9YN3P05C1ZOQ
+TTTAGTAATTGAGACACCACCATGATTCAATGTGTGTATTTAGTTCTCATAGTAGTGTTCTATATCAAGGCCAATGCACCATGGTGCTCAAACCCAATAGTCAATCTTCTCTTCAATCCATGGGAAGAATAATTATGGGTGCTTGTATGAAGTTTCATGATCAAAATGGTGCCAATATGGTGACATGGAATGCATACATATTCTATAAAACATGCATGTG
+>FX9YN3P05C1QG2
+AATGGTGGAATTGGAGGATCTAATGCATTGAGGAGCTGAGGTCAGAGACTTTGATGCAGGATGGGGTGCATTCTTTCCAGTACATGTATGGGTGTGGCTTGGAAGAGTGACTTGATGTGCTGAGCGGGC
+>FX9YN3P05C43XJ
+CCCTCATATTTGTAGATTTCATATTTTTAAGTATATTATATCAGATATATTGTGTCGAACTATACAATGGAATATCCATGGTTGTTTACATATCACTTCTTCCATGCAACTAAAATTGGAATAACCCTTACTTCAAATCAATAAACAAGCTCTGATGTCATAGCTCAATAAACAATCATGAAGCATCATTAAGCAATCCTCCAAGCATTAGATCACTGAGCGGGCTGG
+>FX9YN3P05C9OK8_I_IZQ
+CAGAGAGGGCTGTGCAGGGCAATACCTGTACAGTAAAATGGAATTCATGATGAAAAGTACCAAGGTACTCTGCTACCTCTTTGGCAGCCTTTAAATCTGGCGATCCCTGCTCAGA
+>FX9YN3P05C9OK8_I_DER
+CACAAAGAAACAGATTATAGAAGAGGTTTGTTTCAACCATTTTAATGGGTGGATTTTTCGTGGTCTACTTGTAGAAATATACTCTAATGTATTTTTTTTTTTCAATAAATTAATCTGGGACTAATCGTCAATGAGCCTGCA

data/test/old/ext/sample/f1.fasta.qual

@@ -0,0 +1,10 @@
+>FX9YN3P05C1ZOQ
+21 21 21 31 34 29 34 34 34 34 34 34 35 35 35 35 28 27 27 30 34 34 34 34 34 36 35 35 34 34 36 36 36 36 36 34 34 34 34 34 34 34 34 34 34 32 26 27 27 31 34 34 34 34 30 30 30 30 30 34 34 34 34 34 34 32 32 32 32 32 32 32 34 34 31 31 31 31 30 30 30 26 26 26 30 30 31 32 34 34 34 34 34 34 34 34 30 31 30 32 34 34 31 31 31 34 30 30 30 32 26 20 20 20 31 31 26 26 26 32 32 32 31 31 31 31 27 30 30 31 24 24 18 18 15 22 18 18 18 30 27 32 24 24 25 25 31 32 32 25 25 25 32 34 34 34 34 30 30 30 34 34 34 34 34 34 34 34 34 34 34 25 25 25 25 34 32 32 32 32 34 34 29 24 24 24 24 24 32 32 32 32 34 34 34 34 34 34 34 34 32 32 18 18 18 24 26 34 34 23 23 14 34 34 34 34 30 23 23 23
+>FX9YN3P05C1QG2
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 33 33 33 
+>FX9YN3P05C43XJ 
+36 36 36 36 36 36 36 36 39 39 39 40 39 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 38 38 38 40 40 40 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 31 21 21 21 21 31 31 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 35 35 35 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 31 31 31 35 36 36 36 36 36 31 31 31 35 35 35 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 35 35 35 36 36 36 36 36 36 36 36 36 36 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 33 33 
+>FX9YN3P05C9OK8_I_IZQ 
+35 35 35 35 35 35 35 35 40 40 40 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 39 39 40 39 38 38 38 40 40 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
+>FX9YN3P05C9OK8_I_DER
+35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 34 34 34 35 35 35 35 31 31 30 30 30 25 25 25 21 30 30 35 35 35 35 35 35 33 33 25 25 25 25 25 34 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 29 29 29 34 34 34 35 35 35 35 33 26 26 20 20 20 20 14 14 14 14 14 14 14 14 14 14 14 15 23 23 15 15 15 15 28 28 28 35 35 25 25 19 22 22 26 22 30 30 30 30 30 30 28 28 28 30 30 30 30 30 30 30 28 28 28 28

data/test/old/ext/sample/main.c

@@ -0,0 +1,86 @@
+#include "libreria_gz.h"
+#include <stdio.h>
+#include <ctype.h>
+
+
+/*******************************************************/
+/* main                                                */
+/*******************************************************/
+int main(int argc, char *argv[])
+{
+
+char *fasta=NULL;
+char *qual=NULL;
+char *extras=NULL;
+int size=5000;
+            
+if (argc!=4)
+{
+  printf("Usage %s fasta_file qual_file output_file\n\n",argv[0]);
+  exit(-1);
+}
+ 
+
+
+// prueba de lectura
+printf ("Comienzo\n");
+
+//int res=read_seq("data/F143CJN01.fbin","F143CJN01D96I9", &fasta, &qual, &extras);
+//int res=read_seq("fasta_filt_w_dict.fbin","F143CJN01D96I9", &fasta, &qual, &extras);
+
+// prueba de escritura
+/*int res=write_seq("borrar","S143CJN01D96I9", "primero","QUANTAQUANTAQUANTAQUANTAQUANTA","");
+    res=write_seq("borrar","3CJN01D96I9", "el de enmedio","QUANTAQUANTAQUANTAQUANTAQUANTA","");
+    res=write_seq("borrar","3CJsdasdaN01D96I9", "ultimo","QUANTAQUANTAQUANTAQUANTAQUANTA","");
+*/
+//init_dicts(dict_fasta,dict_qual,32767);
+//int res=process_biofile("data/F143CJN01.fasta","/tmp/prueba2gz.fbin");
+int res=process_biofile(argv[1],argv[3]);
+
+//res=read_seq("fasta_filt_w_dict.fbin","F143CJN01D96I9", &fasta, &qual, &extras);
+/*
+int res=read_seq("prueba2.fbin","F143CJN01DI5MZ", &fasta, &qual, &extras);
+printf ("-------------------------------------------------------------\n");
+printf ("RES of read_seq1 call is :%d\n",res);
+if ( res==0 ) printf ("fasta:%s\n size:%d\n",fasta,sizeof(fasta));
+if ( res==0 ) printf ("qual:%s\n",qual);
+if (( res==0 )&& (extras!=NULL)) printf ("extras:%s\n",extras);
+if ( fasta!=NULL ) {free(fasta);fasta=NULL;}
+if ( qual!=NULL ) {free(qual);qual=NULL;}
+if ( extras!=NULL ) {free(extras);extras=NULL;}
+*/
+//int res=read_seq("/tmp/prueba2gz.fbin","F143CJN01BO14N", &fasta, &qual, &extras);
+//int res=read_seq("/tmp/prueba2gz.fbin","F143CJN01D2X26", &fasta, &qual, &extras);
+//res=read_seq("prueba2gz.fbin","F143CJN01EBIJN", &fasta, &qual, &extras);
+res=read_seq(argv[3],"F143CJN01DZW7L", &fasta, &qual, &extras);
+//res=read_seq("prueba2gz.fbin","F143CJN01EN6AH", &fasta, &qual, &extras);
+printf ("-------------------------------------------------------------\n");
+printf ("RES of read_seq2 call is :%d\n",res);
+if ( res==0 ) printf ("fasta:%s\n fasta size:%d\n",fasta,strlen(fasta));
+if ( res==0 ) printf ("qual:%s\n",qual);
+if (( res==0 )&& (extras!=NULL)) printf ("extras:%s\n",extras);
+if ( fasta!=NULL ) {free(fasta);fasta=NULL;}
+if ( qual!=NULL ) {free(qual);qual=NULL;}
+if ( extras!=NULL ) {free(extras);extras=NULL;}
+
+printf ("***************************\n");
+printf ("Sequential reads\n");
+
+initialize_sequential_reads(argv[3]);
+char *sname=NULL;
+while (read_data_sequential(&sname, &fasta, &qual, &extras)==0)
+{
+	printf ("***************************\n");
+	printf ("RES of read_seq2 call is :%d, sname:%s\n",res,sname);
+	if ( res==0 ) printf ("fasta:%s fasta size:%d\n",fasta,strlen(fasta));
+	if ( res==0 ) printf ("qual:%s",qual);
+	if (( res==0 )&& (extras!=NULL)) printf ("extras:%s\n",extras);
+	if ( fasta!=NULL ) {free(fasta);fasta=NULL;}
+	if ( qual!=NULL ) {free(qual);qual=NULL;}
+	if ( extras!=NULL ) {free(extras);extras=NULL;}
+}
+close_sequential_reads();
+
+return res;
+}
+

data/test/old/ext/usage_instructions.txt

@@ -0,0 +1,62 @@
+
+Manual of the YAGFF (Yet Another Genetic File Format)
+OGF (Optimized Genetic Format)
+
+
+First a call to :
+        error=initialize_writes(outname,1);
+
+Is needed to initialize the files.
+
+Its arguments are:
+
+- the name of the main output file and to this the suffix .index will be
+  appended for the index file.
+
+- The mode of the write:
+	1 : create a new file
+	2 : append data to already existing files
+
+It returns 
+	 0 if everything goes fine, 
+	-1 if there is a problem with already existing files, like an incorrect
+		version number 
+	-2 if there is a problem creating or opening files
+
+In case of error it writes it on stderr
+
+
+Then request to write can be done:
+
+int error_wr=write_seq(sname, fasta,qual,extras);
+
+Where sname is a char* with the name of the sequence, and fasta, qual and
+extras are char* with the fasta, qual and extras data.
+
+At the end a call to : closes_writes();
+is needed to close the opened files
+
+
+
+The reads are even easier:
+
+int read_seq(char *filename, char *seq_name, char **fasta, char **qual, char **extras)
+The arguments are:
+filename: is a char* used as input the name of the main file, .index is appended for the index file
+seq_name :  char* that contains the name of the searched sequence
+
+And the result are returned in :
+fasta, qual and extras, if they point to NULL they are malloced to bufsize=150000 bytes (defined inside the function)
+else they are used without checking its size
+
+
+
+For doing sequential reads an untested procedure is implemented:
+
+int initialize_sequential_reads(char *filename);
+
+// return -9 on EOF
+int read_data_sequential(char **seq_name, char **fasta, char **qual, char **extras)
+int close_sequential_reads();
+
+