diff --git a/README.md b/README.md
index 215b4264b6c579268cafc8ba8da7b3e1d2a66bc5..e7968461b2075cc5a025f417d38ba486f923bb53 100644
--- a/README.md
+++ b/README.md
@@ -8,34 +8,47 @@ The source code of _eFASTA_ is inside the _src_ directory and could be compiled
#### Building an executable jar file
-On computers with [Oracle JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html) (6 or higher) installed, a Java executable jar file could be created. In a command-line window, go to the _src_ directory and type:
+Clone this repository with the following command line:
+```bash
+git clone https://gitlab.pasteur.fr/GIPhy/eFASTA.git
+```
+On computers with [Oracle JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html) (6 or higher) installed, a Java executable jar file can be created. In a command-line window, go to the _src_ directory and type:
```bash
javac EFASTA.java
echo Main-Class: EFASTA > MANIFEST.MF
jar -cmvf MANIFEST.MF EFASTA.jar EFASTA.class
rm MANIFEST.MF EFASTA.class
```
-This will create the executable jar file `EFASTA.jar` that could be launched with the following command line model:
+This will create the executable jar file `EFASTA.jar` that could be run with the following command line model:
```bash
java -jar EFASTA.jar [options]
```
#### Building a native code binary
-On computers with the [GNU compiler GCJ](https://gcc.gnu.org/onlinedocs/gcc-4.2.4/gcj/) installed, a binary could also be built. In a command-line window, go to the _src_ directory, and type:
+Clone this repository with the following command line:
+```bash
+git clone https://gitlab.pasteur.fr/GIPhy/eFASTA.git
+```
+On computers with [GraalVM](https://www.graalvm.org/downloads/) installed, a native executable can be built. In a command-line window, go to the _src_ directory, and type:
```bash
-make
+javac EFASTA.java
+native-image EFASTA eFASTA
+rm EFASTA.class
```
-This will create the executable binary file `eFASTA` that could be launched with the following command line model:
+This will create the native executable `eFASTA` that can be run with the following command line model:
```bash
./eFASTA [options]
```
+
## Usage
-Launch _eFASTA_ without option to read the following documentation:
+Run _eFASTA_ without option to read the following documentation:
```
+ eFASTA
+
USAGE: eFASTA <options>
where options are:
@@ -52,17 +65,17 @@ Launch _eFASTA_ without option to read the following documentation:
leading to the writing of its amino acid translation
(standard genetic code) into a second FASTA-formatted
output file [basename].faa
- -fcds to search for the full CDS (starting and ending by start
- and stop codons, respectively) that includes the region
+ -fcds to search for the full CDS (starting and ending by START
+ and STOP codons, respectively) that includes the region
specified by option -c
- -orf to search for the ORF (starting and ending by stop codons)
+ -orf to search for the ORF (starting and ending by STOP codons)
that includes the region specified by option -c
- -start, -init <string> (only with options -cds and -fcds) several alternate start
+ -start, -init <string> (only with options -cds and -fcds) several alternate START
codons (non ATG) could be specified with this option:
PROK = ATG GTG TTG
PROK+ = ATG GTG TTG CTG ATT
PROK++ = ATG GTG TTG CTG ATT ATC ATA
- -stop (only with options -cds, fcds and -orf) to include the stop
+ -stop (only with options -cds, -fcds or -orf) to include the STOP
codon in the outputed sequences
```
@@ -74,7 +87,7 @@ The directory _example_ contains the FASTA-formatted file _Ecoli.O104H4.plsm.fna
```bash
eFASTA -f Ecoli.O104H4.plsm.fna -c CP003291:31400-31293
```
-This command line allows writing the file _seq.fna_ containing the following nucleotide segment:
+This command line creates the file _seq.fna_ containing the following nucleotide segment:
```
>CP003291.1 plasmid pAA-EA11::31400-31293
GGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATGGCCTTCCAACCGAGTTGGCGAACTCCTG
@@ -84,7 +97,7 @@ GGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATG
```bash
eFASTA -f Ecoli.O104H4.plsm.fna -c CP003291:31400-31293 -orf
```
-This command line allows writing the file _seq.fna_ with the smallest ORF containing the specified region:
+This command line creates the file _seq.fna_ with the smallest ORF containing the specified region:
```
>CP003291.1 plasmid pAA-EA11::31433-31266
GTACAGGGCTGGAGCTTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATGGCCTTCCAACCGAGTTGGCGAACTCCTGCCATGGAACGTAGTACTCACCAATAAA
@@ -95,11 +108,11 @@ as well as the file _seq.faa_ containing its translation (standard genetic code
VQGWSLCALLYGLIGTCRLNGIDPEAYLRHILSVLPEWPSNRVGELLPWNVVLTNK
```
-##### Open Reading Frame (ORF) with codons stop
+##### Open Reading Frame (ORF) with codons STOP
```bash
eFASTA -f Ecoli.O104H4.plsm.fna -c CP003291:31400-31293 -orf -stop
```
-This command line allows writing the two files _seq.fna_ and _seq.faa_ containing the ORF and its translation, respectively, with the two ending-up stop codons:
+This command line creates the two files _seq.fna_ and _seq.faa_ containing the ORF and its translation, respectively, with the two ending-up codons STOP:
```
>CP003291.1 plasmid pAA-EA11::31436-31263
TGAGTACAGGGCTGGAGCTTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATGGCCTTCCAACCGAGTTGGCGAACTCCTGCCATGGAACGTAGTACTCACCAATAAATAA
@@ -113,23 +126,23 @@ TGAGTACAGGGCTGGAGCTTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGC
```bash
eFASTA -f Ecoli.O104H4.plsm.fna -c CP003291:31400-31293 -fcds
```
-This command line allows writing the file _seq.fna_ with the the smallest putative CDS containing the specified region:
+This command line creates the file _seq.fna_ with the the smallest putative CDS containing the specified region:
```
>CP003291.1 plasmid pAA-EA11::31433-31266
GTACAGGGCTGGAGCTTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATGGCCTTCCAACCGAGTTGGCGAACTCCTGCCATGGAACGTAGTACTCACCAATAAA
```
-as well as the file _seq.faa_ containing its translation (standard genetic code):
+as well as the file _seq.faa_ containing its translation (standard genetic code):
```
>CP003291.1 plasmid pAA-EA11::31433-31266
VQGWSLCALLYGLIGTCRLNGIDPEAYLRHILSVLPEWPSNRVGELLPWNVVLTNK
```
-Of note, it is the same results as with option `-orf` because the stop codon TGA is occuring first (before any start codon ATG).
+Of note, it is the same results as with option `-orf` because the STOP codon TGA is occurring first (before any START codon ATG).
-##### Coding Sequence (CDS) with alternate codon start
+##### Coding Sequence (CDS) with alternate codon START
```bash
eFASTA -f Ecoli.O104H4.plsm.fna -c CP003291:31400-31293 -fcds -start PROK
```
-This command line allows writing the two files _seq.fna_ and _seq.faa_ containing the CDS and its translation, respectively, by considering each of the three codons ATG, GTG and TTG as a putative start codon:
+This command line creates the two files _seq.fna_ and _seq.faa_ containing the CDS and its translation, respectively, by considering each of the three codons ATG, GTG and TTG as a putative codon START:
```
>CP003291.1 plasmid pAA-EA11::31418-31266
TTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATGGCCTTCCAACCGAGTTGGCGAACTCCTGCCATGGAACGTAGTACTCACCAATAAA
@@ -139,11 +152,11 @@ TTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCT
MCALLYGLIGTCRLNGIDPEAYLRHILSVLPEWPSNRVGELLPWNVVLTNK
```
-##### Coding Sequence (CDS) with alternate start codon and stop codon
+##### Coding Sequence (CDS) with alternate codons START and codon STOP
```bash
eFASTA -f Ecoli.O104H4.plsm.fna -c CP003291:31400-31293 -fcds -start PROK -stop
```
-This command line allows writing the two files _seq.fna_ and _seq.faa_ containing the CDS and its translation, respectively, by considering each of the three codons ATG, GTG and TTG as a putative start codon, and including the termination codon:
+This command line creates the two files _seq.fna_ and _seq.faa_ containing the CDS and its translation, respectively, by considering each of the three codons ATG, GTG and TTG as a putative codon START, and including the termination codon:
```
>CP003291.1 plasmid pAA-EA11::31418-31263
TTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATGGCCTTCCAACCGAGTTGGCGAACTCCTGCCATGGAACGTAGTACTCACCAATAAATAA
diff --git a/src/EFASTA.java b/src/EFASTA.java
index 4077964b4b927aea38e56b81cafc3f6fc299cddd..cf9ddcb0031374f89c19cd4651dd513f249617c8 100644
--- a/src/EFASTA.java
+++ b/src/EFASTA.java
@@ -1,30 +1,30 @@
/*
- ####################################################################
- EFASTA: extracting nucleotide segments from FASTA file
-
- Copyright (C) 2017,2018 Alexis Criscuolo
+ ########################################################################################################
- 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 3 of the License, or
+ EFASTA: extracting nucleotide segments from FASTA file
+
+ Copyright (C) 2017-2020 Institut Pasteur
+
+ 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 3 of the License, or
(at your option) any later version.
- This program 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.
+ This program 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 <http://www.gnu.org/licenses/>.
-
- Contact:
- Institut Pasteur
- Bioinformatics and Biostatistics Hub
- C3BI, USR 3756 IP CNRS
- Paris, FRANCE
+ You should have received a copy of the GNU General Public License along with this program. If not, see
+ <http://www.gnu.org/licenses/>.
+
+ Contact:
+ Alexis Criscuolo alexis.criscuolo@pasteur.fr
+ Genome Informatics & Phylogenetics (GIPhy) giphy.pasteur.fr
+ Bioinformatics and Biostatistics Hub research.pasteur.fr/team/hub-giphy
+ USR 3756 IP CNRS research.pasteur.fr/team/bioinformatics-and-biostatistics-hub
+ Dpt. Biologie Computationnelle research.pasteur.fr/department/computational-biology
+ Institut Pasteur, Paris, FRANCE research.pasteur.fr
- alexis.criscuolo@pasteur.fr
- ####################################################################
+ ########################################################################################################
*/
import java.io.*;
@@ -32,7 +32,7 @@ import java.util.*;
public class EFASTA {
//### constants ##########
- final static String VERSION = "1.2.180511ac";
+ final static String VERSION = "1.2b.201024ac";
final static String[] CODON = {"AAA" , "AAC" , "AAG" , "AAT" , // A A -
"ACA" , "ACC" , "ACG" , "ACT" , // . C -
"AGA" , "AGC" , "AGG" , "AGT" , // . G -
@@ -97,9 +97,9 @@ public class EFASTA {
// ###########################
if ( args.length < 2 ) {
System.out.println("");
- System.out.println(" eFASTA v." + VERSION);
+ System.out.println(" eFASTA v." + VERSION + " Copyright (C) 2017-2020 Institut Pasteur");
System.out.println("");
- System.out.println(" USAGE: eFASTA <options>");
+ System.out.println(" USAGE: eFASTA [options]");
System.out.println("");
System.out.println(" where options are:");
System.out.println("");
@@ -115,20 +115,20 @@ public class EFASTA {
System.out.println(" leading to the writing of its amino acid translation");
System.out.println(" (standard genetic code) into a second FASTA-formatted");
System.out.println(" output file [basename].faa");
- System.out.println(" -fcds to search for the full CDS (starting and ending by start");
- System.out.println(" and stop codons, respectively) that includes the region");
+ System.out.println(" -fcds to search for the full CDS (starting and ending by START");
+ System.out.println(" and STOP codons, respectively) that includes the region");
System.out.println(" specified by option -c");
- System.out.println(" -orf to search for the ORF (starting and ending by stop codons)");
+ System.out.println(" -orf to search for the ORF (starting and ending by STOP codons)");
System.out.println(" that includes the region specified by option -c");
- System.out.println(" -start, -init <string> (only with options -cds and -fcds) several alternate start");
+ System.out.println(" -start, -init <string> (only with options -cds and -fcds) several alternate START");
System.out.println(" codons (non ATG) could be specified with this option:");
System.out.println(" PROK = ATG GTG TTG");
System.out.println(" PROK+ = ATG GTG TTG CTG ATT");
System.out.println(" PROK++ = ATG GTG TTG CTG ATT ATC ATA");
- System.out.println(" -stop (only with options -cds, fcds and -orf) to include the stop");
+ System.out.println(" -stop (only with options -cds, -fcds or -orf) to include the STOP");
System.out.println(" codon in the outputed sequences");
System.out.println("");
- System.exit(1);
+ System.exit(0);
}
// ###########################
diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index 861a98c6d60b12f1499bb18d954f30612d4ef6e4..0000000000000000000000000000000000000000
--- a/src/Makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-GCJ=gcj
-GCJFLAGS=-fsource=1.6 -march=native -msse2 -O3 -minline-all-stringops -fomit-frame-pointer -momit-leaf-frame-pointer -fstrict-aliasing -fno-store-check -fno-bounds-check -funroll-all-loops -Wall
-OTHERFLAGS=-funsafe-math-optimizations -ffast-math
-MAIN=EFASTA
-EXEC=eFASTA
-
-eFASTA: EFASTA.java
- $(GCJ) $(GCJFLAGS) --main=$(MAIN) $(MAIN).java -o $(EXEC)