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#!/bin/tcsh -f |
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|
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|
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set cdb=refseq.mammalian_np.CDS.fa.cidx |
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|
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if ($1"x" == "x") then |
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echo "Usage: prep_sim4.csh fasta_files.." |
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echo "" |
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echo "Must be run from the sim4search subdirectory" |
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echo "and expects a gblat_*.gff and/or gmap_*.gff3 file with gblat scanning results" |
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echo "and $cdb in the current directory to pull RefSeqs for sim4cc" |
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echo "" |
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echo "Example: prep_sim4.csh ../ga_??.fa" |
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exit 1 |
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endif |
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|
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# prepare the name translation table |
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|
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set f=$1; |
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|
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if (! -f $cdb ) then |
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echo "Error: missing file in current directory: $cdb" |
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exit 1 |
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endif |
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|
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set cdir=`pwd` |
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set pdir=$cdir:h |
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set gblat_gff=`ls gblat*.gf{f,f3}` |
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|
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if (! -f $gblat_gff ) then |
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echo "Error: no single gblat*.gf{f,f3} file found in current directory" |
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echo "make sure you're in <organism>/sim4search and the gblat results are there" |
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exit 1 |
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endif |
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set infiles=$gblat_gff |
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|
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set gmap_gff=`ls gmap*.gf{f,f3}` |
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if ( -f $gmap_gff ) then |
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#echo "Error: no single gmap*.gf{f,f3} file found in current directory" |
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#echo "make sure you're in <organism>/sim4search and the gblat/gmap results are there" |
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#exit 1 |
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set infiles="$infiles $gmap_gff" |
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endif |
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|
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set fp=$f:h |
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set ftx="$fp/seqn2fname.lst" |
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set dlst="" |
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set flst="" |
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/bin/rm -f $ftx |
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foreach f ( $* ) |
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set fn=$f:t |
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set bd=$fn:r |
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set sn=`head -1 $f | cut -f1 -d ' ' | cut -b2-` |
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#if (! -d $bd) mkdir $bd |
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echo "$sn\t$bd" >> $ftx |
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#/bin/rm -f $bd/$bd.refseq.gmap.gff3 |
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#/bin/rm -f $bd/$bd.unipr.pmap.gff3 |
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set flst = "$flst $fn" |
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end |
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echo "$fp/seqn2fname.lst created." |
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cat $infiles | trcol.pl -G $ftx | sort -u > anchored.lst |
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set simbat=sim4_grid.cmds |
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/bin/rm -f $simbat |
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gawk '{ print "qsim4cc -p75 -c75 -o wrk_sim4cc.gff3 -q \047"$2"\047"" '$cdir/$cdb' '$pdir/'"$1".fa"}' \ |
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anchored.lst > $simbat |
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|
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echo "$simbat file created, use gridx with it, e.g.:" |
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echo "gridx -q -N -O grdsim4logs -f sim4_grid.cmds -p40 -m gpertea" |
