moved all to bin folder

medvedevgroup · Jul 23, 2020 · bb7b12d · bb7b12d
1 parent 075630e
commit bb7b12d
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diff --git a/INSTALL b/INSTALL
@@ -40,13 +40,13 @@ cd $PPATH/
 
 rm -rf $PPATH/dependencies/bcalm
 rm -rf $PPATH/dependencies/dsk
-rm -rf $PPATH/aux/essAuxCompress
-rm -rf $PPATH/aux/essAuxDecompress
-rm -rf $PPATH/aux/essAuxDsk
-rm -rf $PPATH/aux/essAuxDsk2ascii
-rm -rf $PPATH/aux/essAuxBcalm
-rm -rf $PPATH/aux/essAuxMFCompressC
-rm -rf $PPATH/aux/essAuxMFCompressD
+rm -rf $PPATH/bin/essAuxCompress
+rm -rf $PPATH/bin/essAuxDecompress
+rm -rf $PPATH/bin/essAuxDsk
+rm -rf $PPATH/bin/essAuxDsk2ascii
+rm -rf $PPATH/bin/essAuxBcalm
+rm -rf $PPATH/bin/essAuxMFCompressC
+rm -rf $PPATH/bin/essAuxMFCompressD
 make -f $PPATH/dependencies/mfc1.01/Makefile.linux clean
 
 cd src/ ; make ; cd ../
@@ -69,9 +69,8 @@ cd dsk
 sh INSTALL
 failureMessage "DSK installation"
 echo $PWD
-ln build/bin/dsk ../../aux/essAuxDsk
-ln build/bin/dsk2ascii ../../aux/essAuxDsk2ascii
-
+mv build/bin/dsk ../../bin/essAuxDsk
+mv build/bin/dsk2ascii ../../bin/essAuxDsk2ascii
 
 echo "Now installing BCALM........"
 cd ../../
@@ -82,17 +81,21 @@ mkdir build;  cd build;  cmake ..;
 failureMessage cmake
 make -j 8 #after this we are inside build
 failureMessage "BCALM installation"
-ln bcalm ../../../aux/essAuxBcalm
+mv bcalm ../../../bin/essAuxBcalm
 
 echo "Now installing MFCompress........"
 cd ../../../
 cd dependencies/mfc1.01/
 make -f Makefile.linux
 failureMessage "MFC installation"
-ln MFCompressC ../../aux/essAuxMFCompressC
-ln MFCompressD ../../aux/essAuxMFCompressD
+mv MFCompressC ../../bin/essAuxMFCompressC
+mv MFCompressD ../../bin/essAuxMFCompressD
+make -f Makefile.linux clean
 
 cd ../../
+rm -rf dependencies/dsk
+rm -rf dependencies/bcalm
+
 #export PATH="$PWD/bin:$PATH"
 
-echo "ESS-Compress v2.0 installation (from source) was successful!!"
+echo "ESS-Compress v2.0 installation (from source) was successful!!"
diff --git a/README.md b/README.md
@@ -19,9 +19,12 @@ A tool to compress a set of k-mers represented in FASTA/FASTQ file(s).
 `cd essCompress-v2.0/`
 
 
-3. You will see two scripts in the directory: `essCompress` and `essDecompress`.
-	- Use the command `./essCompress` and `./essDecompress` to get directions on how to use the tool.
+3. You will see two executables in the directory named `essCompress` and `essDecompress`.
 
+	- You can either refer to these two executables
+	directly when compressing/decompressing (using the command `./essCompress` and `./essDecompress`),
+
+	- Or, you can move/copy the executables in `essCompress-v2.0/bin` to the `bin` directory that is already in your PATH. For instance, considering `/usr/bin` is already in PATH, you need to run the command `mv ess* /usr/bin` to move all executables for ESS-Compress software. An alternative to moving/copying executables is adding the location of `essCompress-v2.0/bin` to your PATH.
 
 
 ## Quick start with a step-by-step example
@@ -39,7 +42,7 @@ CCCCCCCCCCA
 ```
 We can compress it using k=11 as follows
 ```
-./essCompress -k 11 -i examples/smallExample.fa
+./bin/essCompress -k 11 -i examples/smallExample.fa
 ```  
 Now `ls examples` will show both original input file and compressed file in the same directory:
 
@@ -52,7 +55,7 @@ smallExample.fa.essc is a compressed binary file generated by MFCompress, so it
 
 To decompress into a readable format, you can run
 ```
-./essDecompress examples/smallExample.fa.essc   
+./bin/essDecompress examples/smallExample.fa.essc   
 ```
 
 You'll now see the decompressed file example.fa.essd in the same directory.   
@@ -63,7 +66,7 @@ You'll now see the decompressed file example.fa.essd in the same directory.
 AAAAAAACCCCCCCCCCA
 ```
 Notice that the decompressed fasta file is not the same as the original file, but it contains the same k-mers as smallExample.fa. You can double check this using the command   
-`./aux/essAuxValidate 11 examples/smallExample.fa examples/smallExample.fa.essd`   
+`./bin/essAuxValidate 11 examples/smallExample.fa examples/smallExample.fa.essd`   
 If they contain the same k-mers (i.e. 11-mers), you will see an output like this:
 
 ```
@@ -85,7 +88,7 @@ If they contain the same k-mers (i.e. 11-mers), you will see an output like this
 	   -f                Fast compression mode: uses less memory, but achieves smaller compression ratio.
 	   -v                Enable verbose mode: print more useful information.
 	   -c                Verify correctness: check that all the distinct k-mers in the input file appears exactly once in compressed file.
-	   -h                Print this help.
+	   -h                Print this Help.
 
 
 #### Input for essCompress
@@ -98,13 +101,13 @@ File input format can be
 	1. a single fasta or fastq file (either gzipped or not)   
 	2. a single text file containing the list of multiple fasta/fastq files (one file per line)	 
 
-To pass a single file as input and compress: `./essCompress -i examples/11mers.fa -k 11`
+To pass a single file as input and compress: `./bin/essCompress -i examples/11mers.fa -k 11`
 
 To pass several files as input, generate the list of files (one file per line) as follows:
 
 ```
 ls -1 examples/*.fa > list_reads   
-./essCompress -i list_reads -k 5
+./bin/essCompress -i list_reads -k 5
 ```
 
 ESS-Compress uses BCALM 2 under the hood, which does not care about paired-end information, all given reads contribute to k-mers in the graph (as long as such k-mers pass the abundance threshold).
@@ -147,7 +150,7 @@ cd ESSCompress
 ./INSTALL
 ```
 
-Upon successful execution of this script, you will see linux binaries for [BCALM](https://github.com/GATB/bcalm) (`essAuxBcalm`), [DSK](https://github.com/GATB/dsk) (`essAuxDsk` and `essAuxDsk2ascii`) and [MFCompress](http://bioinformatics.ua.pt/software/mfcompress/) (`essAuxMFCompressC` and `essAuxMFCompressD`) in the `aux` folder, along with `essAuxValidate`, `essAuxCompress` and `essAuxDecompress`.
+Upon successful execution of this script, you will see linux binaries for [BCALM](https://github.com/GATB/bcalm) (`essAuxBcalm`), [DSK](https://github.com/GATB/dsk) (`essAuxDsk` and `essAuxDsk2ascii`) and [MFCompress](http://bioinformatics.ua.pt/software/mfcompress/) (`essAuxMFCompressC` and `essAuxMFCompressD`) in the `bin` folder, along with `essAuxValidate`, `essAuxCompress` and `essAuxDecompress`. All of these are auxiliary executables. The main two executables are `essCompress` and `essDecompress`.
 
 
 

diff --git a/aux/essAuxValidate → bin/essAuxValidate b/aux/essAuxValidate → bin/essAuxValidate
diff --git a/essCompress → bin/essCompress b/essCompress → bin/essCompress
@@ -1,5 +1,5 @@
 #!/bin/bash
-#Last modified: Jul 23, 9 AM
+#Last modified: Jul 23, 11 AM
 
 DDEBUG=0
 TMPDIRNAME=$(echo "tmp_ess_$(date +"%s")")
@@ -29,23 +29,27 @@ function abspath {
     fi
 }
 
-PPATH=$(abspath $(dirname $0))
+PPATH="$(abspath $(dirname $0))/../"
 
 Help()
 {
    # Display Help
    #echo "Description of the script functions here."
    #echo
    echo "Syntax: ./essCompress [parameters] "
+   echo
    echo "mandatory arguments:"
-   echo "-i [filepath]     Full path for input file."
-   echo "-k [INT]          k-mer size (must be >=4)"
+   echo "-k [int]          k-mer size (must be >=4)"
+   echo "-i [input-file]   Path to input file. Input file can be either of these 2 formats:"
+   echo "                     1. a single fasta/fastq file (either gzipped or not)   "
+   echo "                     2. a single text file containing the list of multiple fasta/fastq files (one file per line)	"
+   echo
    echo "optional arguments:"
-   echo "-a [INT]          DEFAULT=1. Sets a threshold X, such that k-mers that appear less than X times in the input dataset are filtered out. "
+   echo "-a [int]          Default=1. Sets a threshold X, such that k-mers that appear less than X times in the input dataset are filtered out. "
    echo "-f                Fast compression mode: uses less memory, but achieves smaller compression ratio."
-   echo "-h                Print this Help."
    echo "-v                Enable verbose mode: print more useful information."
    echo "-c                Verify correctness: check that all the distinct k-mers in the input file appears exactly once in compressed file."
+   echo "-h                Print this Help."
    echo
    exit
 }
@@ -66,10 +70,10 @@ validate(){
    DECOMPRESSED_FILE=$3
    echo "-------"
    echo "Verifying correctness of ESS-Compress core algorithm...";
-   $PPATH/aux/essAuxDsk -file $UNITIG_FILE -kmer-size $K -abundance-min 1  -verbose 0 -out unitigs.h5
-   $PPATH/aux/essAuxDsk -file $DECOMPRESSED_FILE -kmer-size $K -abundance-min 1  -verbose 0 -out spss.h5
-   $PPATH/aux/essAuxDsk2ascii -file unitigs.h5 -out unitigs.txt  -verbose 0
-   $PPATH/aux/essAuxDsk2ascii -file spss.h5 -out spss.txt  -verbose 0
+   $PPATH/bin/essAuxDsk -file $UNITIG_FILE -kmer-size $K -abundance-min 1  -verbose 0 -out unitigs.h5
+   $PPATH/bin/essAuxDsk -file $DECOMPRESSED_FILE -kmer-size $K -abundance-min 1  -verbose 0 -out spss.h5
+   $PPATH/bin/essAuxDsk2ascii -file unitigs.h5 -out unitigs.txt  -verbose 0
+   $PPATH/bin/essAuxDsk2ascii -file spss.h5 -out spss.txt  -verbose 0
    #echo "doing highly  accurate validation................"
    #echo "Sorting k-mers for validation................"
    #sort -k 1 -n unitigs.txt -o sorted_unitigs.txt; sort -k 1 -n spss.txt -o sorted_spss.txt
@@ -100,19 +104,19 @@ essCompress_prior(){
    ## get unitigs
    if [ "$K" -gt "10" ]; then
       if [[ VERBOSEMODE -eq 0 ]]; then
-            /usr/bin/time  -f "%M\t%e" --output-file=mem_bcalm $PPATH/aux/essAuxBcalm -in $L -out kmers -kmer-size $K  -abundance-min $A -verbose 0 > bcalm_output
+            /usr/bin/time  -f "%M\t%e" --output-file=mem_bcalm $PPATH/bin/essAuxBcalm -in $L -out kmers -kmer-size $K  -abundance-min $A -verbose 0 > bcalm_output
       else
             echo "Running BCALM2 to get compacted de Bruijn graph..."
-            /usr/bin/time  -f "%M\t%e" --output-file=mem_bcalm $PPATH/aux/essAuxBcalm -in $L -out kmers -kmer-size $K  -abundance-min $A -verbose 0
+            /usr/bin/time  -f "%M\t%e" --output-file=mem_bcalm $PPATH/bin/essAuxBcalm -in $L -out kmers -kmer-size $K  -abundance-min $A -verbose 0
       fi
 
 
    elif [ "$K" -gt "3" ]; then
       if [[ VERBOSEMODE -eq 0 ]]; then
-            /usr/bin/time  -f "%M\t%e" --output-file=mem_bcalm $PPATH/aux/essAuxBcalm -in $L -out kmers -kmer-size $K  -abundance-min $A -minimizer-size 2 -verbose 0 > bcalm_output
+            /usr/bin/time  -f "%M\t%e" --output-file=mem_bcalm $PPATH/bin/essAuxBcalm -in $L -out kmers -kmer-size $K  -abundance-min $A -minimizer-size 2 -verbose 0 > bcalm_output
       else
             echo "Running BCALM2 to get compacted de Bruijn graph..."
-            /usr/bin/time  -f "%M\t%e" --output-file=mem_bcalm $PPATH/aux/essAuxBcalm -in $L -out kmers -kmer-size $K  -abundance-min $A -minimizer-size 2 -verbose 0
+            /usr/bin/time  -f "%M\t%e" --output-file=mem_bcalm $PPATH/bin/essAuxBcalm -in $L -out kmers -kmer-size $K  -abundance-min $A -minimizer-size 2 -verbose 0
       fi
 
    else
@@ -143,21 +147,21 @@ essCompress_main(){
 
    cd $O2  #this is inside tmp_ess/
 
-   /usr/bin/time  -f "%M\t%e" --output-file=mem_ess_$TYPE $PPATH/aux/essAuxCompress -i $L -k $K -t $TYPE -v $VERBOSEMODE
+   /usr/bin/time  -f "%M\t%e" --output-file=mem_ess_$TYPE $PPATH/bin/essAuxCompress -i $L -k $K -t $TYPE -v $VERBOSEMODE
    failureMessage "ESS-Compress core"
 
    if [[ "$TYPE" -eq "0" ]]; then
       cat kmers.ess | tr "[" "g" | tr "]" "t" | tr "+" "a" | tr "-" "c" | awk -F=' ' '{print ""$1}' > kmers_acgt.ess
       var=$(echo ">2.0\_$K\_0") ;  sed -i "1s/.*/$var/" kmers_acgt.ess
-      /usr/bin/time  -f "%M\t%e" --output-file=mem_mfc_$TYPE $PPATH/aux/essAuxMFCompressC kmers_acgt.ess
+      /usr/bin/time  -f "%M\t%e" --output-file=mem_mfc_$TYPE $PPATH/bin/essAuxMFCompressC kmers_acgt.ess
       failureMessage MFC
       mv kmers_acgt.ess.mfc $FULLFINALMFC
 
       echo "Output is in '$FULLFINALMFC'".
    elif [[ "$TYPE" -eq  "1" ]]; then
       cat kmers.esstip | tr "{" "a" | tr "}" "c" | tr "(" "g" | tr ")" "t" | awk -F=' ' '{print ""$1}' > kmers_acgt.esstip
       var=$(echo ">2.0\_$K\_1") ;  sed -i "1s/.*/$var/" kmers_acgt.esstip
-      /usr/bin/time  -f "%M\t%e" --output-file=mem_mfc_$TYPE $PPATH/aux/essAuxMFCompressC kmers_acgt.esstip
+      /usr/bin/time  -f "%M\t%e" --output-file=mem_mfc_$TYPE $PPATH/bin/essAuxMFCompressC kmers_acgt.esstip
       failureMessage MFC
       mv kmers_acgt.esstip.mfc $FULLFINALMFC
 
@@ -174,18 +178,18 @@ essCompress_main(){
       if [[ "$TYPE" -eq "0" ]]; then
 
          var=$(echo ">2.0\_$K\_0") ; sed -i "1s/.*/$var/" kmers.ess
-         /usr/bin/time  -f "%M\t%e" --output-file=mem_dec_$TYPE $PPATH/aux/essAuxDecompress kmers.ess
+         /usr/bin/time  -f "%M\t%e" --output-file=mem_dec_$TYPE $PPATH/bin/essAuxDecompress kmers.ess
 
          validate $K $KMERS_FA kmers.ess.spss
 
       elif [[ "$TYPE" -eq  "1" ]]; then
 
          var=$(echo ">2.0\_$K\_1") ;  sed -i "1s/.*/$var/" kmers.esstip
-         /usr/bin/time  -f "%M\t%e" --output-file=mem_dec_$TYPE $PPATH/aux/essAuxDecompress kmers.esstip
+         /usr/bin/time  -f "%M\t%e" --output-file=mem_dec_$TYPE $PPATH/bin/essAuxDecompress kmers.esstip
 
          validate $K $KMERS_FA kmers.esstip.spss
       else
-         /usr/bin/time  -f "%M\t%e" --output-file=mem_mfc_$TYPE $PPATH/aux/essAuxMFCompressC kmers.ust.spss
+         /usr/bin/time  -f "%M\t%e" --output-file=mem_mfc_$TYPE $PPATH/bin/essAuxMFCompressC kmers.ust.spss
          validate $K $KMERS_FA kmers.ust.spss
       fi
 

diff --git a/essDecompress → bin/essDecompress b/essDecompress → bin/essDecompress
@@ -48,7 +48,7 @@ failureMessage(){
    fi
 }
 #set -e
-PPATH=$(abspath $(dirname $0))
+PPATH="$(abspath $(dirname $0))/../"
 
 if [[ -z "$1" ]]; then
     Help
@@ -68,7 +68,7 @@ input_directory=$(dirname $INPUTFILE)
 
 ENAME=$(basename $INPUTFILE .essc)
 ENAME="$ENAME.essd"
-$PPATH/aux/essAuxMFCompressD $INPUTFILE 
+$PPATH/bin/essAuxMFCompressD $INPUTFILE 
 x=$(echo $?)
 if [ $x -eq 0 ]
    then
@@ -93,12 +93,12 @@ cd $TMPDIRNAME
 
 if [[ "$ISTIP" -eq "1" ]]; then
     cat $MFCDFILE | tr "a" "{" | tr "c" "}" | tr "g" "(" | tr "t" ")" | awk -F=' ' '{print ""$1}' > $ENAME
-    $PPATH/aux/essAuxDecompress $ENAME 
+    $PPATH/bin/essAuxDecompress $ENAME 
     failureMessage "ESS-Decompress (core algorithm)"
     mv kmers.esstip.spss ../$ENAME 
 else
     cat $MFCDFILE | tr "a" "+" | tr "c" "-" | tr "g" "[" | tr "t" "]" | awk -F=' ' '{print ""$1}' > $ENAME
-    $PPATH/aux/essAuxDecompress $ENAME 
+    $PPATH/bin/essAuxDecompress $ENAME 
     failureMessage "ESS-Decompress (core algorithm)"
     mv kmers.ess.spss ../$ENAME 
 fi

diff --git a/src/Makefile b/src/Makefile
@@ -6,15 +6,15 @@ CFLAGS=-w -std=c++11 -O3
 all: make_directories essC essD
 
 essC:
-	$(CC) $(CFLAGS) -o ../aux/essAuxCompress ess.cpp
+	$(CC) $(CFLAGS) -o ../bin/essAuxCompress ess.cpp
 
 essD:
-	$(CC) $(CFLAGS) -o ../aux/essAuxDecompress decoder.cpp
+	$(CC) $(CFLAGS) -o ../bin/essAuxDecompress decoder.cpp
 
 .PHONY: make_directories
 make_directories:
-	mkdir -p ../aux/
+	mkdir -p ../bin/
 
 clean:
-	rm -rf *.o ../aux/essAuxCompress ../aux/essAuxDecompress ../aux/essAuxBcalm ../aux/essAuxDsk ../aux/essAuxDsk2ascii ../aux/essAuxMFCompressC ../aux/essAuxMFCompressD ../dependencies/bcalm ../dependencies/dsk 
+	rm -rf *.o ../bin/essAuxCompress ../bin/essAuxDecompress ../bin/essAuxBcalm ../bin/essAuxDsk ../bin/essAuxDsk2ascii ../bin/essAuxMFCompressC ../bin/essAuxMFCompressD ../dependencies/bcalm ../dependencies/dsk 
 	cd ../dependencies/mfc1.01; make -f Makefile.linux clean