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gpertea |
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#!/usr/bin/perl |
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use strict; |
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use Getopt::Std; |
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use FindBin;use lib $FindBin::Bin; |
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my $usage = q{ |
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Script for parsing RefSeq mRNAs in GenBank File Format. |
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Usage: |
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gbrna2fa.pl [-P][-R] genbank_format_stream |
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Use -P option in order to exclude the PREDICTED mRNAs and gene models. |
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Use -R option to only write the REVIEWED and VALIDATED entries |
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}; |
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umask 0002; |
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getopts('PR') || die($usage."\n"); |
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my %refseqtype=( |
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'INFERRED'=> 'inf', # usually not yet supported by experimental evidence |
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'MODEL' => 'mod', #usually predicted by GNOMON |
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'PREDICTED' => 'p', # only CDS is predicted in most cases, the mRNA is experimentally confirmed |
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# (it becomes 'px' then) |
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'PROVISIONAL' => 'pv', #usually based on experimental evidence, but not "reviewed" by NCBI |
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'VALIDATED' => 'v', # preliminary reviewed, but did not go through "final review" |
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'REVIEWED' => 'r' |
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); |
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#my $outfile=$Getopt::Std::opt_g; |
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#my $fastaout=$Getopt::Std::opt_F; |
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my %typeflt=('mod'=>1,'p'=>1,'inf'=>1,'px'=>1,'pv'=>1, 'v'=>1, 'r'=>1, 'gb'=>1); |
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my $nopred=$Getopt::Std::opt_P; |
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my $onlyrev=$Getopt::Std::opt_R; |
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if ($nopred || $onlyrev) { |
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@typeflt{'mod', 'inf', 'p'}=(0,0,0); |
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} |
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if ($onlyrev) { |
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@typeflt{'pv','px'}=(0,0); |
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} |
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my %gnames; |
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#if ($fastaout) { |
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# open(FASTAOUT, '>'.$fastaout)|| die ("Error creating file $fastaout\n"); |
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# } |
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#if ($outfile) { |
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# open(GFFOUT, '>'.$outfile) || die ("Error creating file $outfile\n"); |
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# select(GFFOUT); |
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# } |
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my ($bseq, $fseq, $descr, $bGI, $bACC, $blen, $org, $comment, $cds, $cdsprod, |
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$geneid, $freading, $seqreading); |
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my $skipLocus=0; |
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while (<>) { |
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chomp; |
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NEXTLINE: |
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if (m/^LOCUS/) { |
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($bseq, $blen)=(m/^LOCUS\s+(\S+)\s+(\d+)/); |
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die("Error parsing LOCUS tag info: $_\n") unless $blen; |
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if ($blen<20 || $blen>300000 || m/\s+DNA\s+linear\s+/) { |
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while(<>) { |
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chomp; |
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goto NEXTLINE if m/^LOCUS/; |
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} |
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} |
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} |
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elsif (m/^DEFINITION\s+(.+)/) { |
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$descr=$1; |
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while (<>) { |
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chomp; |
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if (m/^[A-Z]+\s+/) { |
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$descr=~tr/\t \n\r/ /s; |
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goto NEXTLINE; |
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} |
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$descr.=' '.$_; |
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} |
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$descr=~tr/\t \n\r/ /s; |
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next; |
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} |
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elsif (m/^ACCESSION\s+(\S+)/) { |
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$bACC=$1; |
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next; |
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} |
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elsif (m/^VERSION/) { |
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($bACC, $bGI)=(m/([\w\.]+)\s+GI:(\d+)/); |
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die("Error parsing GI# from VERSION tag ($_)") unless $bGI>1; |
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next; |
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} |
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elsif (m/^SOURCE\s+(.+)/) { |
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$org=$1; |
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next; |
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} |
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elsif (m/^COMMENT\s+(.+)/) { |
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$comment=$1; |
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while (<>) { |
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chomp; |
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if (m/^\s*[A-Z]+\s+/) { |
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goto NEXTLINE; |
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} |
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$comment.=' '.$_; |
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} |
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next; |
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} |
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elsif (m/^FEATURES\s+/) { |
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$freading=1; |
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next; |
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} |
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# elsif (m/^BASE COUNT/) { |
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# $freading=0; |
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# next; |
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# } |
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elsif (m/^CONTIG\s+/) { |
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$freading=0; |
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$seqreading=0; |
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} |
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elsif (m/^ORIGIN\s+/) { |
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$freading=0; |
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$seqreading=1; |
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next; |
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} |
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elsif (m/^\/\/$/) { |
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$freading=0; |
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$seqreading=0; |
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my $defline=$bACC; |
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my ($ctype)=($comment=~m/^([A-Z]+)\s+/); |
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my $rtype; |
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if ($ctype && ($rtype=$refseqtype{$ctype})) { |
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$rtype.='x' if $comment=~m/is supported by experimental/; |
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#$defline=$rtype.'|'.$bACC; |
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} |
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else { |
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$rtype='gb'; |
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} |
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$defline=$rtype.'|'.$bACC; |
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# non refseq entries will not have rtype set |
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if (length($fseq)>20 && $typeflt{$rtype}==1) { |
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$descr=~s/\,\s+mRNA\.$//; |
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$descr=~s/\.$//; |
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$descr=~s/\s*\(\Q$geneid\E\)// if $geneid; |
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$descr=~s/^$org\s+//; |
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if ($cdsprod) { |
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$cdsprod=~tr/\t \n\r/ /s; |
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if (!$descr || $descr=~m/hypothetical/i) { |
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$descr=$cdsprod; |
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} |
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else { |
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#print STDERR "{$descr}\n{$cdsprod}\n"; |
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$descr.=' product:'.$cdsprod |
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unless (index(lc($descr), lc($cdsprod))>=0 || $cdsprod=~m/hypothetical protein/i); |
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} |
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} |
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$defline.=' gid:'.$geneid if $geneid; |
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$defline.=' '.$cds if $cds; |
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$defline.=' '.$descr; |
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$defline.=' {'.$org.'}'; |
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$defline =~ tr/ \t/ /s; |
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print &fastafmt(\$fseq, $defline); |
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} |
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$fseq=''; |
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$descr=''; |
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$bseq=''; |
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$geneid=''; |
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$comment=''; |
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$cds=''; |
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$cdsprod=''; |
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$comment=''; |
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next; |
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} |
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#-- remaining lines parsing: |
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if ($freading) { |
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my ($featname, $frange)=(m/^\s+([\w\'\-]+)\s+(.+)/); |
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die("Error parsing $bACC feature at: $_\n") unless $featname && $frange; |
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if ($frange=~m/\(/ && $frange!~m/\)$/) { #wrapped composite intervals line |
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do { |
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$_=<>; |
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last unless $_; |
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chomp; |
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$frange.=$_; |
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} until (m/\)$/); |
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} #unwrapped the composite intervals (multi-exons) |
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if ($featname eq 'CDS') { |
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$cds.='|' if $cds; |
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$frange=~s/\.\./-/g; |
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$frange=~tr/ //d; |
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# for join() ranges or partial < > |
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$frange=~ s/^[^\d]*(\d+).+?(\d+)\)?$/$1-$2/; |
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$cds.='CDS:'.$frange; |
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} |
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my @attrs; |
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my $endattr; |
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#print STDERR "..reading attributes for $featname ($frange)\n"; |
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while (<>) { #read all attributes for this feature |
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unless (m/^\s+\/\w+/) { |
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$endattr=1; |
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last; |
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} |
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chomp; |
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if (m/^\s+\/([\w\-]+)=(.+)/) { |
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my ($a, $av)=($1, $2); |
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my ($fattr, $fattr_dta)=&parseAttr($featname, $a,$av); #this will read the next line(s) if necessary |
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if ($fattr eq 'gene' && !$geneid) { |
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$geneid=$fattr_dta; |
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#$gname =~ tr/"//d; #" |
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next; |
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} |
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if ($featname eq 'CDS' && $fattr eq 'product') { |
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$cdsprod=$fattr_dta; |
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# if (!$descr || $descr=~m/hypothetical/i) { |
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# $descr=$fattr_dta; |
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# } |
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# else { $cdsprod=' product:'.$fattr_dta; } |
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next; |
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} |
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if ($fattr eq 'organism') { |
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$org=$fattr_dta; |
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#$org=~tr/"//d; #" |
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} |
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} # /attr=attrvalue parsing |
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# store all attributes and their values -- for the current feature only |
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#elsif ($fattr ne 'translation') { |
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# push(@attrs, $fattr.'='.$fattr_dta); |
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# } |
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} #attribute parsing loop |
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#&writeFeature($featname, $frange, $gname, @attrs); |
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goto NEXTLINE if $endattr; |
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next; |
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}# FEATURES section reading |
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if ($seqreading && m/^\s+\d+\s+(.+)/) { |
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my $s=$1; |
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$s=~tr/ \t\n//d; |
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$fseq.=uc($s); |
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} |
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}#while input lines |
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#close(FASTAOUT) if $fastaout; |
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sub parseAttr { |
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my ($fn, $a, $adta)=@_; |
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#print STDERR "[[ parseAttr($fn, $a, $adta) ]]\n"; |
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$adta=~s/^\s+//;$adta=~s/\s+$//; #trim |
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#die("Invalid attribute string for $fn\:$a ($adta)\n") unless $adta=~m/^"/; |
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if ($adta=~m/^"/) { |
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while ($adta!~m/\"$/) { |
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$_=<>; |
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chomp; |
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tr/ \t/ /s; #remove extra spaces |
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$adta.=$_; |
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} |
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} |
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$adta=~s/^\"//;$adta=~s/\"$//; #remove quotes |
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$adta=~tr/\t \n\r/ /s; |
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return ($a, $adta); |
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} |
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sub fastafmt { # (seqref, defline, linelen) |
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my $seqr=shift(@_); |
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my $defline=shift(@_); |
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my $linelen=shift(@_) || 60;; |
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my $rec; |
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$rec=">$defline\n" if $defline; |
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my $seqlen=length($$seqr); |
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my $pos=0; |
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while ($pos<$seqlen) { |
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$rec.= substr($$seqr,$pos,$linelen)."\n"; |
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$pos+=$linelen; |
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} |
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return $rec; |
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} |
