Add gto_fasta_merge_streams and documentation

conda/build.sh

@@ -110,3 +110,4 @@ cp bin/gto_segment $PREFIX/bin/
 cp bin/gto_sum $PREFIX/bin/
 cp bin/gto_upper_bound $PREFIX/bin/
 cp bin/gto_word_search $PREFIX/bin/
+cp bin/gto_fasta_split_streams $PREFIX/bin/

conda/meta.yaml

@@ -5,10 +5,10 @@
 
 package:
     name: gto
-    version: '1.5.3'
+    version: '1.5.4'
 
 source:
-    git_rev: v1.5.3
+    git_rev: v1.5.4
     git_url: https://github.com/cobilab/gto.git
 
 requirements:

manual/manual.tex

@@ -84,7 +84,7 @@
 $^3$Department of Information and Communications Technologies, University of A Coru\~na, A Coru\~na, Spain\\
 $^4$Department of Virology, University of Helsinki, Helsinki, Finland\\
 ~\\
-Version 1.5.1
+Version 1.5.4
 }
 \date{}
 \maketitle

manual/sections/FASTA_tools/FASTA_tools.tex

@@ -39,6 +39,8 @@ \chapter{FASTA tools}
 
 \item \texttt{gto\char`_fasta\char`_split\char`_streams}: it splits and writes a FASTA file into three channels of information: headers, extra and DNA. 
 
+\item \texttt{gto\char`_fasta\char`_merge\char`_streams}: it merges the three channels of information (headers, extra and DNA) and writes it into a FASTA file.
+
 
 \end{enumerate}
 
@@ -56,4 +58,5 @@ \chapter{FASTA tools}
 \input{\FASTAToolsPath/FastaExtractPatternCoords.tex}
 \input{\FASTAToolsPath/FastaComplement.tex}
 \input{\FASTAToolsPath/FastaReverse.tex}
-\input{\FASTAToolsPath/FastaSpitStreams.tex}
+\input{\FASTAToolsPath/FastaSplitStreams.tex}
+\input{\FASTAToolsPath/FastaMergeStreams.tex}

manual/sections/FASTA_tools/FastaMergeStreams.tex

@@ -0,0 +1,39 @@
+\section{Program gto\char`_fasta\char`_merge\char`_streams}
+The \texttt{gto\char`_fasta\char`_merge\char`_streams} merges the three channels of information (headers, extra and DNA) and writes it into a FASTA file. \\
+For help type:
+\begin{lstlisting}
+./gto_fasta_merge_streams -h
+\end{lstlisting}
+In the following subsections, we explain the input and output paramters.
+
+\subsection*{Input parameters}
+
+The \texttt{gto\char`_fasta\char`_merge\char`_streams} program needs the three files resulting from the execution of the \texttt{gto\char`_fasta\char`_split\char`_streams} tool, and the output standard stream for computation. The output stream is a FASTA or Multi-FASTA file.\\
+The attribution is given according to:
+\begin{lstlisting}
+Usage: ./gto_fasta_merge_streams [options] [[--] args]
+   or: ./gto_fasta_merge_streams [options]
+
+It merges the three channels of information (headers, extra and DNA) and writes it into a FASTA file.
+
+    -h, --help            Show this help message and exit
+
+Basic options
+    -e, --extra=<str>     Output file for the extra information
+    -d, --dna=<str>       Output file for the DNA information
+    -H, --headers=<str>   Output file for the headers information
+    > output              Output FASTA file format (stdout)
+
+Example: ./gto_fasta_merge_streams -e <filename> -d <filename> -H <filename> > output.fasta
+\end{lstlisting}
+
+\subsection*{Output}
+
+The output of the \texttt{gto\char`_fasta\char`_merge\char`_streams} program is a FASTA or Multi-FASTA file.\\
+Using the three output files of the \texttt{gto\char`_fasta\char`_split\char`_streams} tool as input in this example, the output of this tool is the following:
+\begin{lstlisting}
+>AB000264 |acc=AB000264|descr=Homo sapiens mRNA 
+ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCCGGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAAGTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCCGCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGCTAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
+>AB000263 |acc=AB000263|descr=Homo sapiens mRNA 
+ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
+\end{lstlisting}

manual/sections/FASTA_tools/FastaSpitStreams.tex → manual/sections/FASTA_tools/FastaSplitStreams.tex

@@ -19,9 +19,12 @@ \subsection*{Input parameters}
     -h, --help            Show this help message and exit
 
 Basic options
+    -e, --extra=<str>     Output file for the extra information
+    -d, --dna=<str>       Output file for the DNA information
+    -H, --headers=<str>   Output file for the headers information
     < input.fastq         Input FASTA file format (stdin)
 
-Example: ./gto_fasta_split_streams < input.fastq
+Example: ./gto_fasta_split_streams -e <filename> -d <filename> -H <filename> < input.fasta
 \end{lstlisting}
 An example of such an input file is:
 \begin{lstlisting}
@@ -41,4 +44,4 @@ \subsection*{Input parameters}
 
 \subsection*{Output}
 
-The output of the \texttt{gto\char`_fasta\char`_split\char`_streams} program are three files containing the headers, extra information and DNA.
+The output of the \texttt{gto\char`_fasta\char`_split\char`_streams} program are three files containing the headers, extra information and DNA. The name of those files can be passed in the tool's paramenters. The default names are HEADERS.JV2, EXTRA.JV2 and DNA.JV2. 

src/FastaMergeStreams.c

@@ -0,0 +1,122 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include "argparse.h"
+#include <unistd.h>
+
+
+/* 
+ * This application merges FASTA into three channels of information: 
+ *        - HEADERS;
+ *        - EXTRA;
+ *        - DNA.
+ */
+int main(int argc, char *argv[])
+{
+
+  FILE *HEADERS, *EXTRA, *DNA;
+  int c, d = 0;
+  const char *output_headers = NULL;
+  const char *output_extra = NULL;
+  const char *output_dna = NULL;
+
+  char *programName = argv[0];
+  struct argparse_option options[] = {
+        OPT_HELP(),
+        OPT_GROUP("Basic options"),
+        OPT_STRING('e', "extra", &output_extra, "Output file for the extra information"),
+        OPT_STRING('d', "dna", &output_dna, "Output file for the DNA information"),
+        OPT_STRING('H', "headers", &output_headers, "Output file for the headers information"),
+        OPT_BUFF('>', "output", "Output FASTA file format (stdout)"),
+        OPT_END(),
+  };
+  struct argparse argparse;
+
+  char usage[250] = "\nExample: "; 
+  strcat(usage, programName);
+  strcat(usage, " -e <filename> -d <filename> -H <filename> > output.fasta\n");
+
+  argparse_init(&argparse, options, NULL, programName, 0);
+  argparse_describe(&argparse, "\nIt merges the three channels of information (headers, extra and DNA) and writes it into a FASTA file.", usage);
+  argc = argparse_parse(&argparse, argc, argv);
+
+  if(argc != 0)
+    argparse_help_cb(&argparse, options);
+
+  if(output_headers == NULL)
+    output_headers = "HEADERS.JV2";
+
+  if((HEADERS = fopen (output_headers, "r")) == NULL)
+  {
+    fprintf(stderr, "Error: could not open file!");
+    return 1;
+  }
+
+  if(output_extra == NULL)
+    output_extra = "EXTRA.JV2";
+
+  if((EXTRA = fopen (output_extra, "r")) == NULL)
+  {
+    fprintf(stderr, "Error: could not open file!");
+    return 1;
+  }
+
+  if(output_dna == NULL)
+    output_dna = "DNA.JV2";
+
+  if((DNA = fopen (output_dna, "r")) == NULL)
+  {
+    fprintf(stderr, "Error: could not open file!");
+    return 1;
+  }
+
+  while((c = fgetc(EXTRA)) != EOF)
+  {
+
+    if(c == '>')
+    {
+      fprintf(stdout, "%c", c);
+      while((c = fgetc(HEADERS)) != EOF)
+      {
+        if(c == EOF) goto x;
+        fprintf(stdout, "%c", c);
+        if(c == '\n') break;
+      }
+      continue;
+    }
+
+    switch(c)
+    {
+
+      case 0:
+        if((d = fgetc(DNA)) == EOF)
+        {
+          fprintf(stderr, "Error: invalid format!");
+          return 1;
+        }
+        fprintf(stdout, "%c", d); 
+        break;
+
+      case 1:
+        if((d = fgetc(DNA)) == EOF)
+        {
+          fprintf(stderr, "Error: invalid format!");
+          return 1;
+        }
+        fprintf(stdout, "%c", tolower(d));
+        break;
+
+        default:
+          fprintf(stdout, "%c", c);
+        break;      
+    }
+  }
+
+  x:
+
+  if(!HEADERS) fclose(HEADERS);
+  if(!EXTRA)   fclose(EXTRA);
+  if(!DNA)     fclose(DNA);
+  return EXIT_SUCCESS;
+}

src/FastaSplitStreams.c

@@ -33,7 +33,7 @@ int main(int argc, char *argv[])
 
   char usage[250] = "\nExample: "; 
   strcat(usage, programName);
-  strcat(usage, " -e <filename> -d <filename> -H <filename> < input.fastq\n");
+  strcat(usage, " -e <filename> -d <filename> -H <filename> < input.fasta\n");
 
   argparse_init(&argparse, options, NULL, programName, 0);
   argparse_describe(&argparse, "\nIt splits and writes a FASTA file into three channels of information: headers, extra and DNA.", usage);

src/GTO.c

@@ -15,7 +15,7 @@ int main(int argc, char *argv[])
   "                    ╚═════╝   ╚═╝    ╚═════╝                              \n"
   "                                                                          \n"
   "NAME                                                                      \n"
-  "      GTO v%u.%u.3,                                                       \n"
+  "      GTO v1.5.4,                                                         \n"
   "      The Genomics-Proteomics Toolkit.                                    \n"
   "                                                                          \n"
   "AUTHORS                                                                   \n"
@@ -243,6 +243,14 @@ int main(int argc, char *argv[])
   "          It uses the Chester-visual to visualize relative singularity    \n"
   "          regions.                                                        \n"
   "                                                                          \n"
+  "      [gto_fasta_split_streams]                                           \n"
+  "          It splits and writes a FASTA file into three channels of        \n"
+  "          information: headers, extra and DNA.                            \n"
+  "                                                                          \n"
+  "      [gto_fasta_merge_streams]                                           \n"
+  "          It merges the three channels of information (headers, extra     \n"
+  "          and DNA) and writes it into a FASTA file.                       \n"
+  "                                                                          \n"
   "Genomic Sequence Tools                                                    \n"
   "      [gto_genomic_count_bases]                                           \n"
   "          It counts the number of bases in sequence, FASTA or             \n"
@@ -399,7 +407,6 @@ int main(int argc, char *argv[])
   "      GTO: A toolkit to unify pipelines in genomic and proteomic research.\n",
   "      J. R. Almeida, A. J. Pinho, J. L. Oliveira, O. Fajarda, D. Pratas,  \n",
   "      SoftwareX, Volume 12, 2020, 100535,                                 \n",
-  "      doi: https://doi.org/10.1016/j.softx.2020.100535                    \n",
-  VERSION, RELEASE);
+  "      doi: https://doi.org/10.1016/j.softx.2020.100535                    \n");
   return EXIT_SUCCESS;
 }

src/Makefile

@@ -109,7 +109,8 @@ PROGS  	 	= $(BIN)/gto \
          	  $(BIN)/gto_amino_acid_from_fasta \
          	  $(BIN)/gto_amino_acid_from_fastq \
          	  $(BIN)/gto_amino_acid_from_seq \
-         	  $(BIN)/gto_fasta_split_streams 
+         	  $(BIN)/gto_fasta_split_streams \
+         	  $(BIN)/gto_fasta_merge_streams 
          	  #$(BIN)/gto_amino_acid_to_seq 
 
 
@@ -258,6 +259,8 @@ $(BIN)/gto_amino_acid_from_seq: AminoAcidFromSeq.c $(DEPS) $(OBJS)
 	$(CC) $(CFLAGS) -o $(BIN)/gto_amino_acid_from_seq AminoAcidFromSeq.c $(OBJS) $(LIBS)
 $(BIN)/gto_fasta_split_streams: FastaSplitStreams.c $(DEPS) $(OBJS)
 	$(CC) $(CFLAGS) -o $(BIN)/gto_fasta_split_streams FastaSplitStreams.c $(OBJS) $(LIBS)
+$(BIN)/gto_fasta_merge_streams: FastaMergeStreams.c $(DEPS) $(OBJS)
+	$(CC) $(CFLAGS) -o $(BIN)/gto_fasta_merge_streams FastaMergeStreams.c $(OBJS) $(LIBS)
 
 #$(BIN)/gto_amino_acid_to_seq: AminoAcidToSeq.c $(DEPS) $(OBJS)
 #	$(CC) $(CFLAGS) -o $(BIN)/gto_amino_acid_to_seq AminoAcidToSeq.c $(OBJS) $(LIBS)

tester/gto_fasta_merge_streams/DNA.JV2

@@ -0,0 +1 @@
+ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCCGGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAAGTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCCGCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGCTAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAAACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA

tester/gto_fasta_merge_streams/HEADERS.JV2

@@ -0,0 +1,2 @@
+AB000264 |acc=AB000264|descr=Homo sapiens mRNA 
+AB000263 |acc=AB000263|descr=Homo sapiens mRNA 

tester/gto_fasta_merge_streams/output.fasta

@@ -0,0 +1,4 @@
+>AB000264 |acc=AB000264|descr=Homo sapiens mRNA 
+ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCCGGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAAGTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCCGCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGCTAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
+>AB000263 |acc=AB000263|descr=Homo sapiens mRNA 
+ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA

tester/gto_fasta_merge_streams/runExample.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+../../bin/gto_fasta_merge_streams -e EXTRA.JV2 -H HEADERS.JV2 -d DNA.JV2 > output.fasta

tester/runAllTests.sh

@@ -213,4 +213,7 @@ sh runExample.sh
 cd ..
 cd gto_fasta_split_streams
 sh runExample.sh
+cd ..
+cd gto_fasta_merge_streams
+sh runExample.sh
 cd ..