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NeatFreq_preprocess.pl
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NeatFreq_preprocess.pl
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#!/usr/bin/perl -w
#INITIAL SETUP
# J. Craig Venter Institute
# NeatFreq ver 1.0.1
# Written by Jamison M. McCorrison (jmccorri@jcvi.org)
use strict;
use File::Basename; #required for fileparse()
use Getopt::Std; #better command line input method
use Getopt::Long; #better command line input method
#OPEN LOG
my $NEATFREQ_INSTALL = `pwd`;
chomp $NEATFREQ_INSTALL;
open LOG, "> ./NeatFreq_preprocess.LOG.txt";
########################################################################################################################
# printl :
# print anything once to STDOUT and once to the LOG file -- pretty useful, eh?
########################################################################################################################
sub printl {
my $pr = shift;
#run STDOUT print
print $pr;
#run LOG print (when appropriate)
print LOG $pr;
}
########################################################################################################################
# outhelp:
# print help text
########################################################################################################################
sub outhelp {
printl("NeatFreq_preprocess.pl\n");
printl("\tRequired Flags:\n");
printl("\t-frag fragments.fast[a/q]\n\tAND/OR\n\t-pair pairs.interleaved.fast[a/q]\n\n");
printl("\tOptional Flags:\n");
printl("\t-q (toggles fastq mode, must be used with fastq files!)\n");
printl("\t-f <qv offset>\n");
printl("\t-N = provide NeatFreq install location (if not updated in script)\n\n");
exit;
}
################################################################################################################################################################################################################################################
# runsys :
################################################################################################################################################################################################################################################
sub runsys {
my $cmd = shift;
printl("++ RUN CMD : $cmd\n");
system("$cmd");
}
########################################################################################################################
# fixfasta:
########################################################################################################################
sub fixfasta {
my $fragfile = shift;
my $pairfile = shift;
my $fastq_status = shift;
my $mersize = shift;
printl("\n= 01 FIX IDS =\n");
if( (-s($fragfile)) && (-s($pairfile)) ){
runsys("$NEATFREQ_INSTALL/configure_automaton_for_neatfreq.pl -N $NEATFREQ_INSTALL -frg $fragfile -prs $pairfile -out AUTO_FORMAT");
runsys("cat AUTO_FORMAT.frg.fasta > allreads.fasta");
runsys("cat AUTO_FORMAT.prs.fasta >> allreads.fasta");
}
elsif(-s($fragfile)){
runsys("$NEATFREQ_INSTALL/lib/fastx_renamer -n COUNT -i $fragfile -o allreads.fasta");
}else{
runsys("$NEATFREQ_INSTALL/lib/fastx_renamer -n COUNT -i $pairfile -o allreads.fasta");
}
printl("\n\n= 02 TALLYMER =\n");
runsys("$NEATFREQ_INSTALL/lib/genometools-1.4.1/installed/bin/gt suffixerator -dna -pl -tis -suf -lcp -lossless -v -parts 4 -db allreads.fasta -indexname reads");
runsys("$NEATFREQ_INSTALL/lib/genometools-1.4.1/installed/bin/gt tallymer mkindex -mersize $mersize -minocc 1 -indexname tyr-reads-minocc1 -counts -pl -esa reads");
runsys("$NEATFREQ_INSTALL/lib/genometools-1.4.1/installed/bin/gt tallymer search -strand fp -output qseqnum qpos counts sequence -tyr tyr-reads-minocc1 -q allreads.fasta > allreads.mer_counts.minocc1.txt");
printl("\n\n= 03 CLEAN NONEXISTENT MERS (due to non-basecalls) =\n");
runsys("$NEATFREQ_INSTALL/clean_up_zero_mers_4_mernalysis.pl allreads.mer_counts.minocc1.txt allreads.mer_counts.minocc1.FIX.txt");
}
########################################################################################################################
# fixfastq:
########################################################################################################################
sub fixfastq {
my $fragfile = shift;
my $pairfile = shift;
my $fastq_status = shift;
my $mersize = shift;
my $offset = shift;
printl("\n= 01 FIX IDS AND CREATE FASTA EQUIVALENTS =\n");
if( (-s($fragfile)) && (-s($pairfile)) ){
if ($offset != 0){
runsys("$NEATFREQ_INSTALL/configure_automaton_fastq_for_neatfreq.pl -N $NEATFREQ_INSTALL -f $offset -frg $fragfile -prs $pairfile -out AUTO_FORMAT");
}else{
runsys("$NEATFREQ_INSTALL/configure_automaton_fastq_for_neatfreq.pl -N $NEATFREQ_INSTALL -frg $fragfile -prs $pairfile -out AUTO_FORMAT");
}
runsys("cat AUTO_FORMAT.frg.fastq > allreads.fastq");
runsys("cat AUTO_FORMAT.prs.fastq >> allreads.fastq");
runsys("$NEATFREQ_INSTALL/lib/fastq_to_fasta_qual allreads.fastq allreads.fasta allreads.fasta.qual");
runsys("$NEATFREQ_INSTALL/lib/fastq_to_fasta_qual AUTO_FORMAT.frg.fastq AUTO_FORMAT.frg.fasta AUTO_FORMAT.frg.fasta.qual");
runsys("$NEATFREQ_INSTALL/lib/fastq_to_fasta_qual AUTO_FORMAT.prs.fastq AUTO_FORMAT.prs.fasta AUTO_FORMAT.prs.fasta.qual");
}elsif(-s($fragfile)){
if ($offset != 0){
runsys("$NEATFREQ_INSTALL/lib/fastx_renamer -Q $offset -n COUNT -i $fragfile -o allreads.fastq");
if (!(-s("./allreads.fastq"))){ printl("ERROR : Offset incorrect (see error above, fix with -f flag).\n\nExiting..."); exit; }
}else{
runsys("$NEATFREQ_INSTALL/lib/fastx_renamer -n COUNT -i $fragfile -o allreads.fastq");
}
runsys("$NEATFREQ_INSTALL/lib/fastq_to_fasta_qual allreads.fastq AUTO_FORMAT.frg.fasta AUTO_FORMAT.frg.fasta.qual");
runsys("$NEATFREQ_INSTALL/lib/fastq_to_fasta_qual allreads.fastq allreads.fasta allreads.fasta.qual");
}else{
if ($offset != 0){
runsys("$NEATFREQ_INSTALL/lib/fastx_renamer -Q $offset -n COUNT -i $pairfile -o allreads.fastq");
if (!(-s("./allreads.fastq"))){ printl("ERROR : Offset incorrect (see error above, fix with -f flag).\n\nExiting..."); exit; }
}else{
runsys("$NEATFREQ_INSTALL/lib/fastx_renamer -n COUNT -i $pairfile -o allreads.fastq");
}
runsys("$NEATFREQ_INSTALL/lib/fastq_to_fasta_qual allreads.fastq AUTO_FORMAT.prs.fasta AUTO_FORMAT.prs.fasta.qual");
runsys("$NEATFREQ_INSTALL/lib/fastq_to_fasta_qual allreads.fastq allreads.fasta allreads.fasta.qual");
}
printl("\n\n= 02 TALLYMER =\n");
runsys("$NEATFREQ_INSTALL/lib/genometools-1.4.1/installed/bin/gt suffixerator -dna -pl -tis -suf -lcp -lossless -v -parts 4 -db allreads.fasta -indexname reads");
runsys("$NEATFREQ_INSTALL/lib/genometools-1.4.1/installed/bin/gt tallymer mkindex -mersize $mersize -minocc 1 -indexname tyr-reads-minocc1 -counts -pl -esa reads");
runsys("$NEATFREQ_INSTALL/lib/genometools-1.4.1/installed/bin/gt tallymer search -strand fp -output qseqnum qpos counts sequence -tyr tyr-reads-minocc1 -q allreads.fasta > allreads.mer_counts.minocc1.txt");
printl("\n\n= 03 CLEAN NONEXISTENT MERS (due to non-basecalls) =\n");
runsys("$NEATFREQ_INSTALL/clean_up_zero_mers_4_mernalysis.pl allreads.mer_counts.minocc1.txt allreads.mer_counts.minocc1.FIX.txt");
}
########################################################################################################################
# MAIN #
########################################################################################################################
MAIN : {
#command line input vars
my %Opts;
my ($fragfile, $pairfile, $fastq_status, $mersize, $offset, $cleanup);
my $NEW_NEATFREQ_INSTALL = `pwd`;
#pull in command line input
my $status = GetOptions(\%Opts, "help", "h", "q", "z", 'm=s'=> \$mersize, 'f=s'=> \$offset, 'N=s'=> \$NEW_NEATFREQ_INSTALL, 'frag=s'=> \$fragfile, 'pair=s'=> \$pairfile);
if ( exists $Opts{help} || exists $Opts{h}){ outhelp(); }
if ( exists $Opts{q} ){ $fastq_status = 1; }
else{ $fastq_status = 0; }
if ($mersize){
printl("\nUSING INPUT MER SIZE = $mersize\n");
}else{
printl("\nUSING DEFAULT MER SIZE = 19\n");
$mersize=19;
}
if ($offset){
printl("\nUSING INPUT QV OFFSET = $offset\n");
}else{
$offset = 0;
}
if (($NEW_NEATFREQ_INSTALL) && ($NEW_NEATFREQ_INSTALL ne $NEATFREQ_INSTALL)){
printl("Forcing use of user-selected NeatFreq install directory : $NEW_NEATFREQ_INSTALL\n");
if (!(-s("$NEW_NEATFREQ_INSTALL/NeatFreq.pl"))){
printl("\n\nERROR! : No NeatFreq install found in suggested install directory. \n\nExiting...\n");
exit;
}
$NEATFREQ_INSTALL = $NEW_NEATFREQ_INSTALL;
}
if (!(-s("$NEW_NEATFREQ_INSTALL/NeatFreq.pl"))){
printl("\n\nERROR! : No NeatFreq install found in suggested install directory. ( $NEW_NEATFREQ_INSTALL/NeatFreq.pl )\n\nExiting...\n");
exit;
}
if ( ($fragfile) && ($pairfile) && (-s("$fragfile")) && (-s("$pairfile")) ){
printl("\nUSING INPUT FRAGMENT-ONLY SEQUENCE FILE : $fragfile\n");
printl("\nUSING INPUT PAIRED END SEQUENCE FILE : $pairfile\n");
if ($fastq_status == 0){
fixfasta($fragfile, $pairfile, $fastq_status, $mersize);
}else{
fixfastq($fragfile, $pairfile, $fastq_status, $mersize, $offset);
}
}
elsif ( $fragfile ){
if (-s ("$fragfile")) {
printl("\nUSING INPUT FRAGMENT-ONLY SEQUENCE FILE : $fragfile\n");
}
else{
printl("\nPROBLEM FOUND : File $fragfile does not exist or has 0 byte size.\nExiting...");
#exit;
}
if ($fastq_status == 0){
fixfasta($fragfile, "NONE", $fastq_status, $mersize);
}else{
fixfastq($fragfile, "NONE", $fastq_status, $mersize, $offset);
}
}
elsif ( $pairfile ){
if (-s ("$pairfile")) {
printl("\nUSING INPUT PAIRED END SEQUENCE FILE : $pairfile\n");
}
else{
printl("\nPROBLEM FOUND : File $pairfile does not exist or has 0 byte size.\nExiting...");
#exit;
}
if ($fastq_status == 0){
fixfasta("NONE", $pairfile, $fastq_status, $mersize);
}else{
fixfastq("NONE", $pairfile, $fastq_status, $mersize, $offset);
}
}else{
printl("\nERROR : No input sequences found. See usage:\n\n");
outhelp();
}
# CLEAN UP
runsys("rm reads.des reads.esq reads.lcp reads.llv reads.ois reads.prj reads.sds reads.ssp reads.suf");
runsys("rm tyr-reads-minocc1.mbd tyr-reads-minocc1.mct tyr-reads-minocc1.mer");
runsys("rm allreads.mer_counts.minocc1.txt");
#Fix 'em
if (-s("allreads.mer_counts.minocc1.FIX.txt")){
if ($fragfile && $pairfile){
printl("\n\nSuccess! See NeatFreq input...\n");
printl("\t-r AUTO_FORMAT.frg.fasta\n");
printl("\t-rpairs AUTO_FORMAT.prs.fasta\n");
}
elsif ($fragfile){
runsys("mv allreads.fasta AUTO_FORMAT.frg.fasta");
runsys("mv allreads.fastq AUTO_FORMAT.frg.fastq");
printl("\n\nSuccess! See NeatFreq input...\n");
printl("\t-r AUTO_FORMAT.frg.fasta\n");
}
elsif ($pairfile ){
runsys("mv allreads.fasta AUTO_FORMAT.prs.fasta");
runsys("mv allreads.fastq AUTO_FORMAT.prs.fastq");
printl("\n\nSuccess! See NeatFreq input...\n");
printl("\t-rpairs AUTO_FORMAT.prs.fasta\n");
}
printl("\t-c allreads.mer_counts.minocc1.FIX.txt\n\n");
if ($fastq_status == 1){
#printl("\nTo extract quality scores following NeatFreq, use commands:\n");
#if ($fragfile){ printl("\t/usr/local/devel/BCIS/assembly/tools/extractFasta -i AUTO_FORMAT.frg.fastq -idlist DDD.REDUCED_COVERAGE_ID_LIST.txt -o NeatFreq_reduced_fragments.fastq\n"); }
#if ($pairfile ){ printl("\t/usr/local/devel/BCIS/assembly/tools/extractFasta -i AUTO_FORMAT.prs.fastq -idlist DDD.REDUCED_COVERAGE_ID_LIST.txt -o NeatFreq_reduced_pairs.fastq\n"); }
}
}
exit;
}