ProtExcluder.npl

#! /usr/bin/perl -w

$usage = "Protexcluder.pl -f bpsofflankingtoremove(default=50)  blastx/blastpfile fastafile \n";

# to exclude the portion matching protein subject in a nucleotide sequence file

if (@ARGV < 2) {die "$usage";}

use Getopt::Std;

getopts("f:");

$Len  = defined $opt_f ? $opt_f : 50;

`rm -f $ARGV[1].ssi`;

`_prexc_matchtract.pl $ARGV[0] > $ARGV[0].mt`;

`_prexc_countaanu.pl $ARGV[0].mt > $ARGV[0].mtca`;

`_prexc_rmlowcomplexitymathc.pl  $ARGV[0].mtca 3 60 >  $ARGV[0].mtca_3_60`;

`_prexc_blastformatProt.pl $ARGV[0] > $ARGV[0].f`;

`_prexc_rmlowcomfromBF.pl $ARGV[0].mtca_3_60 $ARGV[0].f > $ARGV[0].fnolow`;

`sort -k 6,6 -k 3,3n $ARGV[0].fnolow > $ARGV[0].fnolows`;

`_prexc_mergequeryBF.pl $ARGV[0].fnolows $Len > $ARGV[0].fnolowm50`;

`_prexc_unmatchedregionBF.pl $ARGV[0].fnolowm50 $Len > $ARGV[0].fnolowm50MSP`;

`_prexc_mspesl-sfetch.pl $ARGV[1] $ARGV[0].fnolowm50MSP 0 $ARGV[0].fnolowm50seq`;

`_prexc_mergeunmatchedregion.pl $ARGV[0].fnolowm50seq > $ARGV[0].fnolowm50seqm`;

`_prexc_GCcontent.pl $ARGV[0].fnolowm50seqm > $ARGV[0].fnolowm50seqmGC`;

`_prexc_rmshortseq_noN.pl $ARGV[0].fnolowm50seqmGC $ARGV[0].fnolowm50seqm 50 > $ARGV[0].fnolowm50seqmns`;

`_prexc_getanycolumnuni.pl $ARGV[0].fnolow 6 > $ARGV[0].fnolowlist`;

`_prexc_rmlistedseq.pl $ARGV[0].fnolowlist $ARGV[1] >  $ARGV[1]nPr`;

`cat $ARGV[1]nPr $ARGV[0].fnolowm50seqmns > temp`;

`_prexc_fasta-reformat.pl temp 50 > $ARGV[1]noProtFinal`;