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#!/bin/bash
# Script for Biomaj PostProcess
# author : ofilangi, osallou
# date : 19/06/2007
# update : 22/10/2010 fix bug in generated alias file + a few cleanups
# 23/12/2015 use makeblastdb for ncbi blast+
#
# -title Title for database file [String] Optional
# -in Input file(s) for formatting [File In] Optional
# -logfile Logfile name: [File Out] Optional
# default = formatdb.log
# -dbtype nucl
# -parse_seqids
#
#----------
#GLOBAL DEF
#----------
BLASTDB_DIR="$datadir/index-blast"; # Path where aliases files should be generated
mkdir -p $BLASTDB_DIR
FORMATDB="makeblastdb"; # Path to formatdb executable
#----------
# FUNCTIONS
#----------
# createAlias: builds an alias file
# arg1: file to write to
# arg2: bank name
# arg3: db file list
createAlias() {
local file=$1;
local nomBanque=$2;
local lFiles=$3;
rm -f $file;
echo "#" > $file
echo "# Alias file created "`date` >>$file
echo "#" >>$file ;
echo "#">> $file ;
echo "TITLE "$nomBanque >> $file;
echo "#" >> $file;
echo "DBLIST "$lFiles >>$file;
echo "#" >> $file;
echo "#GILIST" >> $file;
echo "#" >> $file;
echo "#OIDLIST" >> $file;
echo "#" >> $file;
}
#-----
# MAIN
#-----
if (test $# -ne 4) then
echo "arguments:" 1>&2
echo "1: input files"
echo "2: working directory" 1>&2
echo "3: formatdb options (without -in for input file)" 1>&2
echo "4: bank name" 1>&2
echo `formatdb --help`;
exit -1
fi
relWorkDir=`echo "$2" | sed "s/\/*$//"` # remove useless trailing slash
workdir=$datadir/$dirversion/future_release
workdir=$workdir/$relWorkDir;
rm -rf $workdir;
mkdir -p $workdir ;
if ( test $? -ne 0 ) then
echo "Cannot create $workdir." 1>&2 ;
exit 1;
fi
cd $workdir
# Some vars for links creation
back="";
dir=$relWorkDir;
OLDIFS=$IFS;
IFS="/";
for i in $dir
do
back="../"$back;
done
IFS=$OLDIFS;
# Create links to input files into the working dir
listFile="";
for expression in $1
do
# the basename can be a regex
lsFile=`ls $datadir/$dirversion/future_release/$expression`;
if ( test $? -ne 0 ) then
echo "No input file found in dir `pwd`." 1>&2 ;
exit 1
fi
baseFile=`dirname $expression`;
for f in $lsFile
do
name=`basename $f`;
rm -f $4.p*;
rm -f $4.n*;
nameLink=`echo $name | cut -d"." -f1`;
ln -s $back/$baseFile/$name $nameLink;
if ( test $? -ne 0 ) then
echo "Cannot create link. [ln -s $back$f $name]" 1>&2 ;
exit 1
fi
if (test -z "$listFile") then
listFile=$nameLink;
else
listFile=$nameLink" "$listFile;
fi
done
done
echo "Input sequence file list: $listFile";
if (test -z "$listFile") then
echo "No input file found." 1>&2 ;
exit 1
fi
nameB=$4;
echo "Database name: $nameB";
echo "Working in "`pwd`;
echo "Launching formatdb [formatdb -in $listFile $3 -out $nameB]";
# Execute formatdb
$FORMATDB -in "$listFile" $3 -out $nameB;
formatdbResult=$?
if ( test $formatdbResult -ne 0 ) then
echo "Formatdb failed with status $formatdbResult" 1>&2 ;
exit 1
fi
echo "##BIOMAJ#blast###$2$nameB"
# Delete temp files and links
#-------------------------------------------------------------
rm -f $listFile;
rm -f formatdb.log
# Add generated files to biomaj postprocess dependance
echo "Generated files:";
for ff in `ls *`
do
echo $PP_DEPENDENCE$PWD/$ff;
done
goodPath=`readlink $datadir/$dirversion/future_release -s -n`;
if ( test $? -ne 0 ) then
echo "Failed to get version path: readlink returned with an error [$goodPath]" 1>&2 ;
exit 1
fi
# Search for nal files which are sometimes generated by formatdb.
lsAl=`ls *.?al 2> /dev/null`;
if ( test $? -ne 0 ) then
echo "No alias file found.";
lsAl="";
else
echo "Generated alias files:"
echo "$lsAl";
fi
# If nal files were generated, use them to generate nal files in $BLASTDB_DIR
for fileIndexVirtuel in $lsAl
do
echo "Found alias file: [$fileIndexVirtuel]";
listIndex=`more $fileIndexVirtuel | grep DBLIST`;
listFile2="";
for f in $listIndex
do
if (test $f != "DBLIST") then
listFile2=$goodPath/$relWorkDir/$f" "$listFile2;
fi
done
echo "Creating alias in [$BLASTDB_DIR/$fileIndexVirtuel]";
createAlias $BLASTDB_DIR/$fileIndexVirtuel $nameB "$listFile2"
done
# Else, if no nal file was generated by formatdb, create them
if (test -z "$lsAl") then
ext=`ls | grep .*hr$ | tail -c5 | head -c2`al;
echo "Creating alias file [$PWD/$4$ext]";
listNhr=`ls *.*hr | sed 's/\..hr$//g'`;
listFileNalRel=""; # List of blast db files, relative path
listFileNalAbs=""; # List of blast db files, absolute path
for f in $listNhr
do
listFileNalRel=$f" "$listFileNalRel;
listFileNalAbs=$goodPath/$relWorkDir/$f" "$listFileNalAbs;
done
createAlias $4$ext $nameB "$listFileNalRel";
echo $PP_DEPENDENCE$PWD/$4$ext;
echo "Creating alias in [$BLASTDB_DIR/$4$ext]";
createAlias $BLASTDB_DIR/$4$ext $nameB "$listFileNalAbs" ;
fi
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