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#!/usr/bin/perl |
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use strict; |
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use Getopt::Std; |
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|
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my $usage = q/Usage: |
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ace2fasta.pl -o <contigs_fasta> [-c <components_file>] <acefile> |
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/; |
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umask 0002; |
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getopts('o:c:') || die($usage."\n"); |
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my $outfile=$Getopt::Std::opt_o || |
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die("$usage\nMust specify output file name!\n"); |
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open(CFASTA, '>'.$outfile) || die("Error creating file $outfile!\n"); |
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my $lnkfile=$Getopt::Std::opt_c; |
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if ($lnkfile) { |
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open(COMP, '>'.$lnkfile) || die("Error creating file $lnkfile!\n"); |
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} |
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|
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my $ctg; #current contig |
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my $ctgseq; #current contig sequence |
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my $ctglen; #current contig seq length |
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my $numseqs; |
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my @ctgcomp; #list of component sequence names |
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my %seqs; # seq => [ seqlen, strand, seqL, seqR, asmL, asmR ] |
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my %ctgnames; |
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while (<>) { |
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if (m/^CO\s+(\S+)\s+(\d+)\s+(\d+)/) { |
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my ($c, $l, $n)=($1, $2, $3); |
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#if ($c ne $ctg) { |
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&writeCtg() if $ctg; |
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undef %seqs; |
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undef @ctgcomp; |
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my $ctgdup=++$ctgnames{$c}; |
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$c='ASM_'.$c; |
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$c.='.'.($ctgdup-1) if ($ctgdup>1); |
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($ctg, $ctglen, $numseqs)=($c, $l, $n); |
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# } |
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$ctgseq=''; |
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my $seqline; |
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while (<>) { |
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($seqline)=(/^(\S+)/); |
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last unless $seqline; |
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$ctgseq.=$seqline; |
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} |
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} #contig start line |
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elsif (m/^AF (\S+) ([UC]) ([\-\d]+)/) { |
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my $strand=($2 eq 'U')?'+':'-'; |
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$seqs{$1}=[0, $strand, 0, 0, $3, 0]; #the untrimmed asmL position for now |
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} |
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elsif (m/^RD (\S+) (\d+) (\d+) (\d+)/) { |
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my ($seqname, $seqlen)=($1, $2); |
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my $seqd=$seqs{$seqname}; |
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push(@ctgcomp, $seqname); |
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die("Error at ACE parsing: no sequence found for RD $seqname\n") |
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unless $seqd; |
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$seqd->[0]=$seqlen; |
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my $rdseq=''; |
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my $seqline; |
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while ( defined($_=<>) && (($seqline)=(/(\S+)/))) { |
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$rdseq.=$seqline; |
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} |
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do { |
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$_=<>; |
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} until m/^QA (\d+) (\d+)/ || !defined($_); |
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die("Couldn't find the QA entry for RD $seqname!\n") unless defined($_); |
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($seqd->[2], $seqd->[3]) = ($1, $2); |
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my ($trimL, $trimR)=($seqd->[2]-1, $seqlen-$seqd->[3]); |
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$seqd->[5]=$seqd->[4]+$seqlen-$trimR-1; |
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$seqd->[4]+=$trimL; |
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} |
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} |
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|
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writeCtg() if $ctg; |
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|
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close(CFASTA); |
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close(COMP) if $lnkfile; |
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|
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sub writeCtg { |
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print CFASTA ">$ctg $numseqs\n"; |
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$ctgseq=~tr/-*\n\r//d; |
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# $ctglen=length($ctgseq); |
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print CFASTA join("\n", (unpack('(A72)*',$ctgseq)))."\n"; |
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if ($lnkfile) { |
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print COMP ">$ctg $numseqs $ctglen\n"; |
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foreach my $seqname (@ctgcomp) { |
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my $sd=$seqs{$seqname} || |
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die("Error: no seqdata for component $seqname!\n"); |
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print COMP $seqname.' '.join(' ',@$sd)."\n"; |
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} |
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} |
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|
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} |
