diff trimal_repo/source/readAl.cpp @ 0:b15a3147e604 draft

"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal_repo/source/readAl.cpp	Fri Mar 25 17:10:43 2022 +0000
@@ -0,0 +1,383 @@
+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+    readAl v1.4: a tool for automated alignment conversion among different
+                 formats.
+
+    2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+              [scapella, tgabaldon]@crg.es
+
+    This file is part of readAl.
+
+    readAl 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, the last available version.
+
+    readAl 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 readAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#include <stdlib.h>
+#include <string.h>
+
+#include "alignment.h"
+#include "defines.h"
+#include "utils.h"
+
+void menu(void);
+
+int main(int argc, char *argv[]) {
+
+  /* Input alignment */
+  alignment inAlig;
+
+  /* Local variables */
+  string align_format;
+  int i, outformat = -1;
+  char *infile = NULL, *outfile = NULL;
+  bool errors = false, reverse = false, shortNames = false, format = false, \
+    type = false, info = false;
+
+  /* If there is no parameters: Inform about readAl options and finish */
+  if(argc == 1) {
+    menu();
+    return 0;
+  }
+
+  i = 1;
+  /* If option -h has been used, inform about readAl options and finish */
+  if(!strcmp(argv[i], "-h") && (i+1 == argc)) {
+    menu();
+    return 0;
+  }
+
+  /* Inform about current readAl version/revision/build and finish */
+  if(!strcmp(argv[i], "--version") && (i+1 == argc)) {
+      cout << endl << "readAl v" << VERSION << ".rev" << REVISION << " build["
+        << BUILD << "]" << endl << endl;
+    return 0;
+  }
+
+  /* Catch different input options and then check whether there is a valid
+   * combination of parameters */
+  while(i < argc) {
+
+    /* Input alignment option: -in */
+    if(!strcmp(argv[i], "-in") && (i+1 != argc) && (infile == NULL)) {
+      /* Allocate memory for storing input alignment filename */
+      infile = new char[strlen(argv[++i]) + 1];
+      strcpy(infile, argv[i]);
+
+      /* Load input alignment and inform about it if something is wrong */
+      if(!inAlig.loadAlignment(infile)) {
+        cerr << endl << "ERROR: Alignment not loaded: \"" << infile
+          << "\" Check the file's content." << endl << endl;
+        errors = true;
+      }
+    }
+
+    /* Output filename option: -out */
+    else if(!strcmp(argv[i], "-out") && (i+1 != argc) && (outfile == NULL)) {
+      /* Allocate memory for storing output alignment filename */
+      outfile = new char[strlen(argv[++i]) + 1];
+      strcpy(outfile, argv[i]);
+    }
+
+    /* Get information about input file format */
+    else if(!strcmp(argv[i], "-format") && (!format))
+      format = true;
+
+    /* Get information about input file residues type */
+    else if(!strcmp(argv[i], "-type") && (!type))
+      type = true;
+
+    /* Get general information about input file: seqs number, average seq length,
+     * etc */
+    else if(!strcmp(argv[i], "-info") && (!info))
+      info = true;
+
+    /* Get input sequences reverse option: -reverse */
+    else if(!strcmp(argv[i], "-reverse") && (!reverse))
+      reverse = true;
+
+    /* For all output format options is checked if more
+     * than one output format has been required */
+
+    /* Set output alignment format to CLUSTAL: -clustal */
+    else if(!strcmp(argv[i], "-clustal") && (outformat == -1))
+      outformat = 1;
+
+    /* Set output alignment format to FASTA: -fasta */
+    else if(!strcmp(argv[i], "-fasta") && (outformat == -1))
+      outformat = 8;
+
+   /* Set output alignment format to FASTA and ask for using only
+    * up to 10 characters for sequences name: -fasta_m10 */
+    else if(!strcmp(argv[i], "-fasta_m10") && (outformat == -1)) {
+      outformat = 8;
+      shortNames = true;
+    }
+
+    /* Set output alignment format to NBRF/PIR: -nbrf */
+    else if(!strcmp(argv[i], "-nbrf") && (outformat == -1))
+      outformat = 3;
+
+    /* Set output alignment format to NEXUS: -nexus */
+    else if(!strcmp(argv[i], "-nexus") && (outformat == -1))
+      outformat = 17;
+
+    /* Set output alignment format to MEGA: -mega */
+    else if(!strcmp(argv[i], "-mega") && (outformat == -1))
+      outformat = 21;
+
+    /* Set output alignment format to PHYLIP3.2 (sequential): -phylip3.2 */
+    else if(!strcmp(argv[i], "-phylip3.2") && (outformat == -1))
+      outformat = 11;
+
+    /* Set output alignment format to PHYLIP3.2 (sequential) and ask for
+     * using only up to 10 characters for sequences name: -phylip3.2_m10 */
+    else if(!strcmp(argv[i], "-phylip3.2_m10") && (outformat == -1)) {
+      outformat = 11;
+      shortNames = true;
+    }
+
+    /* Set output alignment format to PHYLIP (interleaved): -phylip */
+    else if(!strcmp(argv[i], "-phylip") && (outformat == -1))
+      outformat = 12;
+
+    /* Set output alignment format to PHYLIP (interleaved) and ask for
+     * using only up to 10 characters for sequences name: -phylip_m10 */
+    else if(!strcmp(argv[i], "-phylip_m10") && (outformat == -1)) {
+      outformat = 12; shortNames = true;
+    }
+
+    /* Set output alignment format to PHYLIP compatible with programs
+     * such as PAML: -phylip_paml */
+    else if(!strcmp(argv[i], "-phylip_paml") && (outformat == -1))
+      outformat = 13;
+
+    /* Set output alignment format to PHYLIP compatible with programs such as
+     * PAML and ask for using only up to 10 characters for sequences name:
+     * -phylip_paml_m10 */
+    else if(!strcmp(argv[i], "-phylip_paml_m10") && (outformat == -1)) {
+      outformat = 13;
+      shortNames = true;
+    }
+
+    /* Set output alignment format to HTML, that means residues will be colored
+     * according to its physic-chemical properties using CLUSTAL color scheme:
+     * -html */
+    else if(!strcmp(argv[i], "-html") && (outformat == -1))
+      outformat = 100;
+
+    /* Get unaligned sequences from input file: -onlyseqs */
+    else if(!strcmp(argv[i], "-onlyseqs") && (outformat == -1))
+      outformat = 99;
+
+    /* Inform about no valid options */
+    else {
+      cerr << endl << "ERROR: Parameter \"" << argv[i] << "\" not valid."
+        << endl << endl;
+      errors = true;
+    }
+    i++;
+
+    /* If any error has been detected, break input options loop
+     * and then process detected error */
+    if(errors)
+      break;
+  }
+
+  /* Final verifications to detect any possible mistake in the input options */
+  /* It is mandatory to provide an input file. Otherwise, inform about it */
+  if((infile == NULL) && (!errors)) {
+    cerr << endl << "ERROR: An input file has to be defined." << endl << endl;
+    errors = true;
+  }
+
+  /* It is mandatory to choose an option for processing input alignment */
+  if((outformat == -1) && (!reverse) && (!format) && (!type) && (!info)
+    && (!errors)) {
+    cerr << endl << "ERROR: An option has to be chosen." << endl << endl;
+    errors = true;
+  }
+
+  /* Only one option can be selected when an output file is not defined */
+  if((outfile == NULL) && ((outformat != -1) || reverse) && (format || type \
+    || info) && (!errors)) {
+    cerr << endl << "ERROR: Only one option can be selected: either an output "
+      << "format or get information about input file when an output file is "
+      << "not defined" << endl << endl;
+    errors = true;
+  }
+
+  /* Does not make any sense to define any output file when
+   * only information about input alignment is requested */
+  if(((outfile != NULL) && outformat == -1 && !reverse) && (format || type \
+    || info) && (!errors)) {
+    cerr << endl << "ERROR: An output file should not be provided when only "
+      << "information about input alignment is requested" << endl << endl;
+    errors = true;
+  }
+
+  /* If no error has been detected, process input file */
+  if(!errors) {
+
+    /* Print information about input alignment */
+    if((format) || (type) || (info)) {
+      cout << "## Input filename\t'" << infile << "'" << endl;
+
+      if(format) {
+        /* Input file format */
+        if (inAlig.getInputFormat() == 1)
+          align_format = "clustal";
+        else if (inAlig.getInputFormat() == 3)
+          align_format = "nbrf/pir";
+        else if (inAlig.getInputFormat() == 8)
+          align_format = "fasta";
+        else if (inAlig.getInputFormat() == 11)
+          align_format = "phylip3.2";
+        else if (inAlig.getInputFormat() == 12)
+          align_format = "phylip";
+        else if (inAlig.getInputFormat() == 17)
+          align_format = "nexus";
+        else if (inAlig.getInputFormat() == 21)
+          align_format = "mega_interleaved";
+        else if (inAlig.getInputFormat() == 22)
+          align_format = "mega_sequential";
+        else
+          align_format = "unknown";
+
+        /* Inform about if sequences are aligned or not */
+        cout << "## Input file format\t" << align_format << endl
+          << "## Input file aligned\t" << (inAlig.isFileAligned() ? "YES":"NO")
+          << endl;
+      }
+
+      if(type) {
+        /* Inform about biological datatype */
+        if (inAlig.getTypeAlignment() == DNAType)
+          cout << "## Input file datatype\tnucleotides:dna" << endl;
+        else if (inAlig.getTypeAlignment() == DNADeg)
+          cout << "## Input file datatype\tnucleotides:dna_degenerate_codes"
+            << endl;
+        else if (inAlig.getTypeAlignment() == RNAType)
+          cout << "## Input file datatype\tnucleotides:rna" << endl;
+        else if (inAlig.getTypeAlignment() == RNADeg)
+          cout << "## Input file datatype\tnucleotides:rna_degenerate_codes"
+            << endl;
+        else if (inAlig.getTypeAlignment() == AAType)
+          cout << "## Input file datatype\tamino-acids" << endl;
+        else
+          cout << "## Input file datatype\tunknown" << endl;
+      }
+
+      if(info)
+        inAlig.printAlignmentInfo(cout);
+    }
+
+    if((outfile != NULL) || (outformat != -1) || reverse || shortNames) {
+      /* Set output format */
+      if(outformat != -1 || shortNames)
+        inAlig.setOutputFormat(outformat, shortNames);
+      /* Ask for getting the reverse of input file */
+      if(reverse)
+        inAlig.setReverse();
+
+      /* If a outfile has been provided, try to generate output file */
+      if(outfile != NULL) {
+        if(!inAlig.saveAlignment(outfile)) {
+          cerr << endl << "ERROR: Impossible to generate OUTPUT file." << endl
+            << endl;
+          return -1;
+        }
+      /* ... otherwise dump outfile content to standard output */
+      } else {
+        inAlig.printAlignment();
+      }
+    }
+  }
+
+  /* Deallocate local memory */
+  delete [] infile;
+  delete [] outfile;
+
+  /* Inform about readAl execution */
+  return (errors == true ? -1 : 0);
+}
+
+void menu(void) {
+
+  cout << endl
+    << "readAl v" << VERSION << ".rev" << REVISION << " build[" << BUILD
+    << "]. " << AUTHORS << endl << endl
+
+    << "readAl webpage: http://trimal.cgenomics.org" << endl << endl
+
+    << "This program is free software: you can redistribute it and/or modify "
+    << endl
+    << "it under the terms of the GNU General Public License as published by "
+    << endl
+    << "the Free Software Foundation, the last available version." << endl
+    << endl
+
+    << "Basic usage" << endl
+    << "\treadal -in <inputfile> -out <outputfile> [options]." << endl << endl
+
+    << "\t-h                   " << "Show this information." << endl
+    << "\t--version            " << "Show readAl version." << endl << endl
+
+    << "\t-in <inputfile>      " << "Input file in several formats." << endl
+    << "\t-out <outputfile>    " << "Output file name (default STDOUT)." << endl
+    << endl
+
+    << "\t-format              " << "Print information about input file format "
+    << "and if sequences are aligned or not." << endl
+
+    << "\t-type                " << "Print information about biological "
+    << "sequences datatype (e.g. nucleotides:dna, nucleotides:rna, aminoacids, etc)"
+    << endl
+
+    << "\t-info                " << "Print information about sequences number, "
+    << "average sequence length, max & min sequence length"
+    << endl << endl
+
+    << "\t-onlyseqs            " << "Generate output with only residues from "
+    << "input file" << endl << endl
+
+    << "\t-html                " << "Output residues colored according their "
+    << "physicochemical properties. HTML file." << endl << endl
+
+    << "\t-reverse             " << "Output the reverse of sequences in "
+    << "input file." << endl << endl
+
+    << "\t-nbrf                " << "Output file in NBRF/PIR format" << endl
+    << "\t-mega                " << "Output file in MEGA format" << endl
+
+    << "\t-nexus               " << "Output file in NEXUS format" << endl
+    << "\t-clustal             " << "Output file in CLUSTAL format" << endl
+    << endl
+
+    << "\t-fasta               " << "Output file in FASTA format" << endl
+    << "\t-fasta_m10           " << "Output file in FASTA format. Sequences "
+    << "name up to 10 characters." << endl << endl
+
+    << "\t-phylip              " << "Output file in PHYLIP/PHYLIP4 format"
+    << endl
+    << "\t-phylip_m10          " << "Output file in PHYLIP/PHYLIP4 format. "
+    << "Sequences name up to 10 characters." << endl
+    << "\t-phylip_paml         " << "Output file in PHYLIP format compatible "
+    << "with PAML" << endl
+    << "\t-phylip_paml_m10     " << "Output file in PHYLIP format compatible "
+    << "with PAML. Sequences name up to 10 characters." << endl
+    << "\t-phylip3.2           " << "Output file in PHYLIP3.2 format" << endl
+    << "\t-phylip3.2_m10       " << "Output file in PHYLIP3.2 format. Sequences"
+    << " name up to 10 characters." << endl << endl;
+}