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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 Fcntl qw(SEEK_SET SEEK_END SEEK_CUR); # for seek |
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my $usage=q/ |
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A simple fasta sequence(s) manipulation tool. |
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Usage: |
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seqmanip [-C] [-r<ranges>] [-L] [-D|-X] [-I] [-G] [-T|-t <frame>|-Z] |
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[-M|-m <ncount>] [-f <ranges_file>] [fasta file(s)...] |
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The input files should be one or more nucleotide or aminoacid sequences |
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in FASTA or raw format; if no files are given, input is expected at STDIN |
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Options: |
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-C reverse complement (is -r is given, first the subsequence is extracted |
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and only then reverse-complemented) |
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-l the line length for the output fasta record (default 70) |
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-r extract a range (subsequence) from the first input fasta sequence; |
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<range> can have one of the formats: |
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<start>..<end> or <start>-<end> or <start>:<len> |
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Multiple such intervals can be given after the -r option (comma or space |
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delimited) and they will be spliced together |
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This option doesn't work with -M or -n options. |
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-f same as -r but for multi-fasta\/seq input; expects a file containing |
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lines of this format: |
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<seqname> <range> |
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The format of <range> is the same with the -r above or it may be just |
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space delimited <start> <end> numbers; the output will be a multi-fasta |
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file with one subsequence for each line in the <ranges_file> |
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-M merge (concatenate) all input sequences into a single sequence |
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-m merge all input sequences separating them by <ncount> Ns |
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-d provides a custom defline for -M and -N options |
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-D add basic defline if the input doesn't provide one |
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-X exclude defline from the output (just print the sequence) |
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-L provide one-line output for each sequence |
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-T first frame translation (DNA to aminoacid) |
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-t <frame>th frame translation; <frame> could be 1,2,3,-1,-2,-3 |
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-E show exon\/splice-sites\/start\/stop info (requires -r) |
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-G show GFF output for the given range(s) (requires -r) |
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-Z raw reverse translate the output (aminoacid to DNA, rather useless) |
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-V only show a sequence if it's a valid, complete CDS |
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-q only show a sequence if it's longer than <minseqlen> |
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-n discard sequences with a percentage of Ns (or Xs) higher than <maxpercN> |
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-y remove spans of Ns longer than <maxnspan> replacing them by <maxnspan> Ns |
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-Y trim Ns from either end of sequence |
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-U cleanup\/remove extraneous characters(e.g. digits, dashes, stars) |
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from every input sequence |
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-R convert RNA to DNA (simply replacing U wih T) |
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-P convert all sequence letters to uppercase |
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-A use ANSI colors to highlight features in terminal (for -E option) |
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-O return longest ORF sequence for each input sequence (start..stop) |
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-Q same as -O but doesn't require a start codon |
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/; |
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my %codons=( |
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'AAA'=>'K', 'AAC'=>'N', 'AAG'=>'K', 'AAR'=>'K', 'AAT'=>'N', |
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'AAY'=>'N', 'ACA'=>'T', 'ACB'=>'T', 'ACC'=>'T', 'ACD'=>'T', |
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'ACG'=>'T', 'ACH'=>'T', 'ACK'=>'T', 'ACM'=>'T', 'ACN'=>'T', |
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'ACR'=>'T', 'ACS'=>'T', 'ACT'=>'T', 'ACV'=>'T', 'ACW'=>'T', |
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'ACY'=>'T', 'AGA'=>'R', 'AGC'=>'S', 'AGG'=>'R', 'AGR'=>'R', |
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'AGT'=>'S', 'AGY'=>'S', 'ATA'=>'I', 'ATC'=>'I', 'ATG'=>'M', |
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'ATH'=>'I', 'ATM'=>'I', 'ATT'=>'I', 'ATW'=>'I', 'ATY'=>'I', |
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'CAA'=>'Q', 'CAC'=>'H', 'CAG'=>'Q', 'CAR'=>'Q', 'CAT'=>'H', |
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'CAY'=>'H', 'CCA'=>'P', 'CCB'=>'P', 'CCC'=>'P', 'CCD'=>'P', |
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'CCG'=>'P', 'CCH'=>'P', 'CCK'=>'P', 'CCM'=>'P', 'CCN'=>'P', |
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'CCR'=>'P', 'CCS'=>'P', 'CCT'=>'P', 'CCV'=>'P', 'CCW'=>'P', |
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'CCY'=>'P', 'CGA'=>'R', 'CGB'=>'R', 'CGC'=>'R', 'CGD'=>'R', |
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'CGG'=>'R', 'CGH'=>'R', 'CGK'=>'R', 'CGM'=>'R', 'CGN'=>'R', |
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'CGR'=>'R', 'CGS'=>'R', 'CGT'=>'R', 'CGV'=>'R', 'CGW'=>'R', |
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'CGY'=>'R', 'CTA'=>'L', 'CTB'=>'L', 'CTC'=>'L', 'CTD'=>'L', |
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'CTG'=>'L', 'CTH'=>'L', 'CTK'=>'L', 'CTM'=>'L', 'CTN'=>'L', |
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'CTR'=>'L', 'CTS'=>'L', 'CTT'=>'L', 'CTV'=>'L', 'CTW'=>'L', |
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'CTY'=>'L', 'GAA'=>'E', 'GAC'=>'D', 'GAG'=>'E', 'GAR'=>'E', |
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'GAT'=>'D', 'GAY'=>'D', 'GCA'=>'A', 'GCB'=>'A', 'GCC'=>'A', |
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'GCD'=>'A', 'GCG'=>'A', 'GCH'=>'A', 'GCK'=>'A', 'GCM'=>'A', |
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'GCN'=>'A', 'GCR'=>'A', 'GCS'=>'A', 'GCT'=>'A', 'GCV'=>'A', |
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'GCW'=>'A', 'GCY'=>'A', 'GGA'=>'G', 'GGB'=>'G', 'GGC'=>'G', |
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'GGD'=>'G', 'GGG'=>'G', 'GGH'=>'G', 'GGK'=>'G', 'GGM'=>'G', |
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'GGN'=>'G', 'GGR'=>'G', 'GGS'=>'G', 'GGT'=>'G', 'GGV'=>'G', |
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'GGW'=>'G', 'GGY'=>'G', 'GTA'=>'V', 'GTB'=>'V', 'GTC'=>'V', |
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'GTD'=>'V', 'GTG'=>'V', 'GTH'=>'V', 'GTK'=>'V', 'GTM'=>'V', |
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'GTN'=>'V', 'GTR'=>'V', 'GTS'=>'V', 'GTT'=>'V', 'GTV'=>'V', |
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'GTW'=>'V', 'GTY'=>'V', 'MGA'=>'R', 'MGG'=>'R', 'MGR'=>'R', |
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'NNN'=>'X', 'RAY'=>'B', 'SAR'=>'Z', 'TAA'=>'.', 'TAC'=>'Y', |
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'TAG'=>'.', 'TAR'=>'.', 'TAT'=>'Y', 'TAY'=>'Y', 'TCA'=>'S', |
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'TCB'=>'S', 'TCC'=>'S', 'TCD'=>'S', 'TCG'=>'S', 'TCH'=>'S', |
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'TCK'=>'S', 'TCM'=>'S', 'TCN'=>'S', 'TCR'=>'S', 'TCS'=>'S', |
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'TCT'=>'S', 'TCV'=>'S', 'TCW'=>'S', 'TCY'=>'S', 'TGA'=>'.', |
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'TGC'=>'C', 'TGG'=>'W', 'TGT'=>'C', 'TGY'=>'C', 'TRA'=>'.', |
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'TTA'=>'L', 'TTC'=>'F', 'TTG'=>'L', 'TTR'=>'L', 'TTT'=>'F', |
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'TTY'=>'F', 'XXX'=>'X', 'YTA'=>'L', 'YTG'=>'L', 'YTR'=>'L' |
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); |
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getopts('AZTUPMEGNRXDVCLYOQr:d:m:q:l:t:f:y:n:') || die "$usage\n"; |
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#my %ranges; # seqname => [offset, len] only populated by -r or -f option; |
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my @ranges; # list of [chr, strand, defline, [[offset1,len1], [offset1,len2], ..]] |
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# 0 1 2 3 |
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#my @range_chrs; # just to keep track of the order of ranges requested |
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my $fai_loaded=0; |
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my %fai_h; # seqID => [fpos, linelen, delimlen, seqlen] |
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my $m_linerest; #for the merge case (-M) |
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my $linelen=$Getopt::Std::opt_l || 70; |
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my $user_defline=$Getopt::Std::opt_d || 'dummyname'; |
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my $ansicolors=$Getopt::Std::opt_A; |
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#some ansi colors: |
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my ($clred, $clgreen, $clreset)=("\e[1;33;41m", # bright yellow on red |
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"\e[0;32;40m", # green on black |
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"\e[0m") #reset colors |
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if $ansicolors; |
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my %toDNA=reverse(%codons); |
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@toDNA{'P','F','K','G'}=('CCC','TTT','AAA','GGG'); |
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my ($getOrf, $getOrfAny)=($Getopt::Std::opt_O, $Getopt::Std::opt_Q); |
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$getOrf=1 if $getOrfAny; |
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my $complement=$Getopt::Std::opt_C; |
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my $validateCDS=$Getopt::Std::opt_V; |
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my $exoninfo=$Getopt::Std::opt_E; |
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my $gffout=$Getopt::Std::opt_G; |
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my $rna2dna=$Getopt::Std::opt_R; |
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my $mergedist=$Getopt::Std::opt_m; |
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my $minseqlen=$Getopt::Std::opt_q; |
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my $maxnspan=$Getopt::Std::opt_y; |
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my $trimNs=$Getopt::Std::opt_Y; |
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my $maxnrepl=''; |
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if ($maxnspan) { |
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$maxnrepl='N' x $maxnspan; |
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$maxnspan++; |
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} |
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my $maxpercn=$Getopt::Std::opt_n; |
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my $mergesep; |
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if ($mergedist>0) { |
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$Getopt::Std::opt_M=1; |
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$mergesep='N' x $mergedist; |
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} |
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my $rangetarget; #if a specific seq target was provided |
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# if this is not set, then the first fasta sequence given as input |
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# will be used for range queries |
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# parse range information if available |
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if ($Getopt::Std::opt_r) { |
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my $rangetext=$Getopt::Std::opt_r; |
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my $rstrand='+'; |
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#if ($rangetext=~s/([\-\+])$//) { $rstrand=$2;} |
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if ($rangetext=~s/(\d+[\.\-\:_]+\d+)([\-\+])$/$1/) { $rstrand=$2; } |
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my @ar=split(/[\,\s]+/,$rangetext); #allow multiple ranges |
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my $seqtarget; |
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unless ($ar[0]=~m/^\d+\:\d+$/) { |
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if ($ar[0]=~s/^([\w\|\-\+\.]+)\://) { |
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# target chromosome given |
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$seqtarget=$1; |
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if ($seqtarget=~s/([\-\+])$//) { $rstrand=$1;} |
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$rangetarget=1; |
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} |
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} |
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if ($seqtarget) { # 0 1 2 3 |
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push(@ranges, [$seqtarget,$rstrand,'', []]); |
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} |
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else { |
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push(@ranges, ['-',$rstrand,'',[]]); |
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} |
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my $rdata=$ranges[0]->[3]; # [ ] |
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foreach my $rt (@ar) { |
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my ($rStart, $rLen)=&parseRange($rt); |
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push(@$rdata, [$rStart, $rLen]); |
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} |
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} |
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elsif ($Getopt::Std::opt_f) { # file with ranges to pull |
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my $frname=$Getopt::Std::opt_f; |
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my $using_stdin; |
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if ($frname eq '-' || $frname eq 'stdin') { |
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#open(FRNG, <&STDIN); |
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open(FRNG, "<&=STDIN") or die "Couldn't alias STDIN : $!"; |
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$using_stdin=1; |
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} |
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else { |
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open (FRNG, $frname) || die ("Error: cannot open seq ranges file '$frname'!\n"); |
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} |
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while (<FRNG>) { |
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chomp; |
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my $rstrand='+'; |
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my ($seqname, $rangetxt)=split(/\s+/,$_,2); |
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my $defline; |
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if ($seqname=~m/^([\w\|\-\+\.]+)\:(\d+[\.\-_]+\d*[\-\+]?)/) { |
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#chr:start-end format |
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# strand may follow chr or end |
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$seqname=$1; |
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$defline=$rangetxt; |
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$rangetxt=$2; |
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if ($seqname=~s/([\-\+])$//) { $rstrand=$1;} |
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elsif ($rangetxt=~s/(\d+[\.\-_]+\d+)([\-\+])$/$1/) { $rstrand=$2; } |
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} |
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else { #1st column is chr(strand), 2nd column is the interval |
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if ($seqname=~s/([\-\+])$//) { $rstrand=$1; } |
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$rangetxt=~s/(\d+)[\t ]+(\d+)/$1-$2/g; |
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my @rt=split(/\s+/,$rangetxt,2); |
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if ($rt[1]) { |
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$defline=$rt[1]; |
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$rangetxt=$rt[0]; |
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} |
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} |
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next unless $rangetxt; |
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push(@ranges, [$seqname, $rstrand, $defline, []]); |
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my $rdata=$ranges[-1]->[3]; |
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#$rangetxt=~s/(\d+)[\t ]+(\d+)/$1-$2/g; #could be space delimited |
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my @ar=split(/\,/,$rangetxt); |
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foreach my $rt (@ar) { |
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my ($rStart, $rLen)=&parseRange($rt); |
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push(@$rdata, [$rStart, $rLen]); |
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} |
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} |
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$rangetarget=1 if @ranges>0; |
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close(FRNG) unless $using_stdin; |
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} |
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my $seq; |
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my $seq_len; |
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my $count=0; |
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my $defline; |
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my $curseq; |
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my $seqcount; |
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print ">$user_defline\n" if ($Getopt::Std::opt_M && !$Getopt::Std::opt_X); |
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die("Error: target sequence(s) given but no input file!\n") |
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if ($rangetarget && (@ARGV==0 || ! -f $ARGV[0])); |
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my $qrange=(@ranges>0 && @ARGV>0 && -f $ARGV[0]); |
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if ($qrange) { #target |
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if (@ranges==1 && $ranges[0]->[0] eq '-') { #single fasta file |
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processRanges($ARGV[0], $ranges[0]); |
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} # single-fasta file |
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else { |
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#actual sequence names provided, need cdbfasta or samtools index |
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my $fasta=$ARGV[0]; |
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#die("Error: no fasta file $fasta!\n") unless -f $fasta; |
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my $faidx; |
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if ($fasta=~s/\.fai$//) { |
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$faidx=$fasta.'.fai'; |
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} |
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else { |
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$faidx=$fasta.'.fai' if -f $fasta.'.fai'; |
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} |
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unless ($faidx) { |
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if ($fasta=~s/\.cidx$//) { |
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$faidx=$fasta.'.cidx'; |
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} |
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else { |
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$faidx=$fasta.'.cidx' if -f $fasta.'.cidx'; |
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} |
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} |
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#print STDERR "info: using fasta index $faidx for $fasta.\n"; |
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die("Error: no index file for fasta file $fasta") unless $faidx; |
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die("Error: no fasta file $fasta!\n") unless -f $fasta; |
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foreach my $rd (@ranges) { |
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processRanges($fasta, $rd, $faidx); |
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} |
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} # cidx file needed |
| 254 |
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} # fast[er] range queries |
| 255 |
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else { # normal (serial) stream processing, very slow range processing for large sequences |
| 256 |
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while (<>) { |
| 257 |
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if (m/^(>.+)/) { |
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process_seq() if $curseq; #sequence is in $seq variable |
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$defline=$1; |
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($curseq)=($defline=~m/^>(\S+)/); |
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$seq_len=0; |
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next; |
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} |
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chomp; |
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tr/ \t\r\n//d; |
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$seq.=$_; |
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$seq_len+=length(); |
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process_seq() unless $curseq; #no defline = raw input: one sequence per line |
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} |
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process_seq() if $curseq; #sequence is in $seq variable |
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} |
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print "$m_linerest\n" if ($Getopt::Std::opt_M && $m_linerest); |
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#============================ |
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sub fai_load { |
| 278 |
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open(FAI, $_[0]) || die ("Error opening index file $_[0]!\n"); |
| 279 |
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while (<FAI>) { |
| 280 |
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my @t=split(/\t/);# 0=seqID 1=seqlen 2=fpos 3=linelen 4=linelen+dlen |
| 281 |
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next if m/^#/ && @t<5; |
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$fai_h{$t[0]}=[$t[2], $t[3], $t[4]-$t[3], $t[1]]; |
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# seqID => [fpos, linelen, delimlen, seqlen] |
| 284 |
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} |
| 285 |
|
|
close(FAI); |
| 286 |
|
|
$fai_loaded=1; |
| 287 |
|
|
} |
| 288 |
|
|
|
| 289 |
|
|
sub processRanges { |
| 290 |
|
|
#my ($fasta, $chr, $chr_rdata, $faidx, $udefline)=@_; |
| 291 |
|
|
my ($fasta, $r_data, $faidx)=@_; |
| 292 |
|
|
my $chr=$$r_data[0]; |
| 293 |
|
|
$chr='' if $chr eq '-'; |
| 294 |
|
|
my $chr_strand=$$r_data[1]; |
| 295 |
|
|
my $udefline=$$r_data[2]; |
| 296 |
|
|
my $chr_rdata=$$r_data[3]; |
| 297 |
|
|
my @intvs = sort { $main::a->[0] <=> $main::b->[0] } @$chr_rdata; #range intervals |
| 298 |
|
|
my ($fpos, $seqlen, $dlen, $flinelen); |
| 299 |
|
|
open(FA, $fasta) || die("Error opening fasta file $fasta\n"); |
| 300 |
|
|
$fpos=0; |
| 301 |
|
|
my $iscdb=($faidx=~m/\.cidx$/); |
| 302 |
|
|
if ($chr) { |
| 303 |
|
|
die("Error: target sequence given, but no fasta index\n") unless $faidx; |
| 304 |
|
|
if ($iscdb) { |
| 305 |
|
|
my $r=`cdbyank -a '$chr' -P $faidx`; |
| 306 |
|
|
my $syserr=$?; |
| 307 |
|
|
chomp($r); |
| 308 |
|
|
die("Error at cdbyank -a '$chr' -P $faidx (exit code $syserr)\n") if length($r)==0 || $syserr; |
| 309 |
|
|
$fpos=int($r); |
| 310 |
|
|
seek(FA, $fpos, SEEK_SET); |
| 311 |
|
|
} |
| 312 |
|
|
else { #fasta index |
| 313 |
|
|
#only load the first time |
| 314 |
|
|
fai_load($faidx) unless ($fai_loaded); |
| 315 |
|
|
my $cd=$fai_h{$chr}; |
| 316 |
|
|
die("Error retrieving $chr data from fasta index!\n") unless $cd; |
| 317 |
|
|
($fpos, $flinelen, $dlen, $seqlen)=@$cd; |
| 318 |
|
|
$intvs[-1]->[1]=$seqlen-$intvs[-1]->[0]+1 unless $intvs[-1]->[1]; |
| 319 |
|
|
if ($intvs[-1]->[1]<=0) { |
| 320 |
|
|
#invalid range |
| 321 |
|
|
$seq=''; |
| 322 |
|
|
$defline=''; |
| 323 |
|
|
return; |
| 324 |
|
|
} |
| 325 |
|
|
$defline = $udefline ? '>'.$udefline : ">$chr"; |
| 326 |
|
|
seek(FA, $fpos, SEEK_SET); |
| 327 |
|
|
} #samtools fai |
| 328 |
|
|
} #indexed access |
| 329 |
|
|
if ($iscdb || !$chr) { |
| 330 |
|
|
#for cdb or plain fasta we have to determine line length by reading the first 1k bytes |
| 331 |
|
|
my $rbuf; |
| 332 |
|
|
read(FA, $rbuf, 1024); |
| 333 |
|
|
my @lines=split(/[\n\r]+/,$rbuf); |
| 334 |
|
|
my @ldelim=($rbuf=~m/([\n\r]+)/gs); |
| 335 |
|
|
if (@ldelim<2) { #we need at least 2 full lines read |
| 336 |
|
|
my $radd; |
| 337 |
|
|
read(FA, $radd, 4096); |
| 338 |
|
|
$rbuf.=$radd; |
| 339 |
|
|
@lines=split(/[\n\r]+/,$rbuf); |
| 340 |
|
|
@ldelim=($rbuf=~m/([\n\r]+)/gs); |
| 341 |
|
|
} |
| 342 |
|
|
$dlen=length($ldelim[0]); |
| 343 |
|
|
die("Error determining line ending type for $fasta!\n") if ($dlen==0); |
| 344 |
|
|
$defline = $udefline ? ">$udefline" : $lines[0]; |
| 345 |
|
|
$flinelen=length($lines[1]); #line length in fasta record |
| 346 |
|
|
$fpos+=length($lines[0])+$dlen; |
| 347 |
|
|
seek(FA, $fpos, SEEK_SET); #reposition at the beginning of the sequence |
| 348 |
|
|
} |
| 349 |
|
|
#now we are positioned at the beginning of the fasta record sequence |
| 350 |
|
|
#seek(FA, $fpos+length($lines[0])+$dlen, SEEK_SET); |
| 351 |
|
|
$seq=''; |
| 352 |
|
|
my $revC=1 if $chr_strand eq '-'; |
| 353 |
|
|
my $rstart=$intvs[0]->[0]-1; #first range start position, 0-based |
| 354 |
|
|
my $rstartpos= ($rstart<$flinelen) ? $rstart : ($rstart+$dlen*(int($rstart/$flinelen))); |
| 355 |
|
|
my $fstartpos=$fpos+$rstartpos; |
| 356 |
|
|
seek(FA, $fstartpos, SEEK_SET); |
| 357 |
|
|
if ($intvs[-1]->[1]) { #ending for last interval is known |
| 358 |
|
|
my $rend=$intvs[-1]->[0]+$intvs[-1]->[1]-2; |
| 359 |
|
|
#$seq_len=$rend-$rstart+1; |
| 360 |
|
|
my $rendpos=($rend<$flinelen) ? $rend : ($rend+$dlen*(int($rend/$flinelen))); |
| 361 |
|
|
#print STDERR "pulling from $fstartpos to $rendpos\n"; |
| 362 |
|
|
my $readlen=$rendpos-$rstartpos+1; |
| 363 |
|
|
#my $fstartpos=$fpos+length($lines[0])+$dlen+$rstartpos; |
| 364 |
|
|
read(FA, $seq, $readlen) || die("Error reading $readlen bytes from fasta $fasta at offset $fstartpos\n"); |
| 365 |
|
|
close(FA); |
| 366 |
|
|
} |
| 367 |
|
|
else { #last interval goes to the end of sequence, but seqlen is not known |
| 368 |
|
|
my $rend=$intvs[-1]->[0]+$intvs[-1]->[1]-2; |
| 369 |
|
|
#$seq_len=$rend-$rstart+1; |
| 370 |
|
|
local $_; |
| 371 |
|
|
while (<FA> && !m/^>/) { |
| 372 |
|
|
$seq.=$_; |
| 373 |
|
|
} |
| 374 |
|
|
close(FA); |
| 375 |
|
|
} |
| 376 |
|
|
$seq=~tr/\n\r//d; |
| 377 |
|
|
$seq_len=length($seq); |
| 378 |
|
|
#now extract the ranges: |
| 379 |
|
|
my @rdata; |
| 380 |
|
|
my $txt_intvs; |
| 381 |
|
|
foreach my $r (@intvs) { |
| 382 |
|
|
push(@rdata, [$$r[0]-$rstart, $$r[1]]); |
| 383 |
|
|
#$spliceseq.=substr($subseq, $cstart, $clen); |
| 384 |
|
|
$txt_intvs.='|'.$$r[0].'-'.($$r[0]+$$r[1]-1); |
| 385 |
|
|
} |
| 386 |
|
|
$defline.=$txt_intvs.$chr_strand unless $udefline; |
| 387 |
|
|
process_seq(\@rdata, $rstart, $revC); |
| 388 |
|
|
} |
| 389 |
|
|
|
| 390 |
|
|
sub process_seq { |
| 391 |
|
|
#my $range = $rangekey ? $ranges{$rangekey} : $ranges{$_[0]}; |
| 392 |
|
|
return unless $seq; |
| 393 |
|
|
my ($range, $basepos, $revC)=@_; |
| 394 |
|
|
if ($maxnspan) { |
| 395 |
|
|
$seq=~s/[NX]{$maxnspan,}/$maxnrepl/ig; |
| 396 |
|
|
$seq_len=length($seq); |
| 397 |
|
|
} |
| 398 |
|
|
if ($Getopt::Std::opt_U) { |
| 399 |
|
|
$seq=~s/[<>\d\s\-\*\.\,\;\:,\x7B-\xFF]+//sg; |
| 400 |
|
|
$seq_len=length($seq); |
| 401 |
|
|
} |
| 402 |
|
|
if ($rna2dna) { |
| 403 |
|
|
$seq =~ tr/Uu/Tt/; |
| 404 |
|
|
} |
| 405 |
|
|
$seq=uc($seq) if $Getopt::Std::opt_P; |
| 406 |
|
|
if ($trimNs) { |
| 407 |
|
|
$seq=~s/^[NX]+//; |
| 408 |
|
|
$seq=~s/[NX]+$//; |
| 409 |
|
|
$seq_len=length($seq); |
| 410 |
|
|
} |
| 411 |
|
|
if ($minseqlen && $seq_len<$minseqlen) { |
| 412 |
|
|
$seq=''; |
| 413 |
|
|
$seq_len=0; |
| 414 |
|
|
return; |
| 415 |
|
|
} |
| 416 |
|
|
if ($maxpercn) { |
| 417 |
|
|
my $nN=($seq=~tr/AaCcGgTtUu//c); |
| 418 |
|
|
if ((($nN*100.0)/$seq_len)>$maxpercn) { |
| 419 |
|
|
$seq=''; |
| 420 |
|
|
$seq_len=0; |
| 421 |
|
|
return; |
| 422 |
|
|
} |
| 423 |
|
|
} |
| 424 |
|
|
# basepos is a 0 based offset |
| 425 |
|
|
unless ($range || @ranges==0) { |
| 426 |
|
|
$range=$ranges[0]->[3]; |
| 427 |
|
|
#print STDERR "using default, first ranges!\n"; #DEBUG |
| 428 |
|
|
} |
| 429 |
|
|
#print STDERR "key=$_[0], range=$$range[0] ($$range[1])\n"; |
| 430 |
|
|
#print STDERR "$range\t$seq\n"; |
| 431 |
|
|
|
| 432 |
|
|
$seqcount++; |
| 433 |
|
|
if ($Getopt::Std::opt_M) { #merge only; |
| 434 |
|
|
#merge all input |
| 435 |
|
|
if ($mergedist>0 && $seqcount>1) { |
| 436 |
|
|
$seq=$m_linerest.$mergesep.$seq; |
| 437 |
|
|
} |
| 438 |
|
|
else { |
| 439 |
|
|
$seq=$m_linerest.$seq; |
| 440 |
|
|
} |
| 441 |
|
|
$m_linerest=''; |
| 442 |
|
|
$seq_len=length($seq); |
| 443 |
|
|
for (my $p=0;$p<$seq_len;$p+=$linelen) { |
| 444 |
|
|
my $sline=substr($seq, $p, $linelen); |
| 445 |
|
|
if (length($sline)==$linelen) { |
| 446 |
|
|
print $sline."\n"; |
| 447 |
|
|
} |
| 448 |
|
|
else { |
| 449 |
|
|
$m_linerest=$sline; |
| 450 |
|
|
last; |
| 451 |
|
|
} |
| 452 |
|
|
} |
| 453 |
|
|
$seq=''; |
| 454 |
|
|
$seq_len=0; |
| 455 |
|
|
return; |
| 456 |
|
|
} |
| 457 |
|
|
my @seqranges; |
| 458 |
|
|
my $intr_ends=''; # 0 1 2 3 |
| 459 |
|
|
my @gfdata; #array of [exon_start, exon_len, cdsphase, diagram] |
| 460 |
|
|
if ($range) { #extract range |
| 461 |
|
|
my @intvs = sort { $main::a->[0] <=> $main::b->[0] } @$range; |
| 462 |
|
|
#print STDERR length($seq)." (seq_len=$seq_len)\n"; |
| 463 |
|
|
#print STDERR "beginning: ".substr($seq,0,10)."\n"; |
| 464 |
|
|
#print STDERR " ending: ".substr($seq,-10)."\n"; |
| 465 |
|
|
my $i=0; |
| 466 |
|
|
foreach my $rng (@intvs) { |
| 467 |
|
|
$i++; |
| 468 |
|
|
if ($$rng[1]>0) { |
| 469 |
|
|
push(@seqranges, substr($seq, $$rng[0]-1, $$rng[1])); |
| 470 |
|
|
my $ss_before=substr($seq, $$rng[0]-3,2); |
| 471 |
|
|
$ss_before='NN' unless length($ss_before)==2; |
| 472 |
|
|
my $ss_after=substr($seq, $$rng[0]+$$rng[1]-1,2); |
| 473 |
|
|
$ss_after='NN' unless length($ss_after)==2; |
| 474 |
|
|
$intr_ends.=$ss_before.$ss_after; |
| 475 |
|
|
push(@gfdata, [$$rng[0], $$rng[1], 0,'']); |
| 476 |
|
|
#print STDERR ">>$seq<<\n"; |
| 477 |
|
|
} |
| 478 |
|
|
#elsif ($$rng[1]<0) { # DON"T use this or mix ranges it's not consistent! |
| 479 |
|
|
# my $rseq=substr($seq, $$rng[0]-1, -$$rng[1]); |
| 480 |
|
|
# push(@seqranges, reverseComplement($rseq)); |
| 481 |
|
|
# push(@gfdata, [$$rng[0], $$rng[1], 0, '']); |
| 482 |
|
|
# } |
| 483 |
|
|
else { #0 length means to the end of sequence |
| 484 |
|
|
push(@seqranges, substr($seq, $$rng[0]-1)); |
| 485 |
|
|
push(@gfdata, [$$rng[0], length($seqranges[-1]), 0,'']); |
| 486 |
|
|
} |
| 487 |
|
|
}#for each range |
| 488 |
|
|
#print STDERR "intr_ends=$intr_ends\n"; |
| 489 |
|
|
} |
| 490 |
|
|
else { #no ranges requested, create a dummy one with the whole sequence |
| 491 |
|
|
push(@seqranges, $seq); |
| 492 |
|
|
push(@gfdata, [1, length($seqranges[-1]),0, '']); |
| 493 |
|
|
} |
| 494 |
|
|
# -- first and last codons |
| 495 |
|
|
#there is that rare case when the start/stop codons can be |
| 496 |
|
|
#broken/split by an intron |
| 497 |
|
|
my ($fcodon, $lcodon); |
| 498 |
|
|
if (@seqranges>1) { |
| 499 |
|
|
my $l=$#seqranges; |
| 500 |
|
|
($fcodon, $lcodon)=( uc(substr($seqranges[0].$seqranges[1],0,3)), |
| 501 |
|
|
uc(substr($seqranges[$l-1].$seqranges[$l],-3)) ); |
| 502 |
|
|
} |
| 503 |
|
|
else { # single-exon |
| 504 |
|
|
($fcodon, $lcodon)=( uc(substr($seqranges[0],0,3)), |
| 505 |
|
|
uc(substr($seqranges[-1],-3)) ); |
| 506 |
|
|
} |
| 507 |
|
|
my $trframe=$Getopt::Std::opt_t || $Getopt::Std::opt_T; |
| 508 |
|
|
my $splseq; |
| 509 |
|
|
$revC=($revC || $complement); |
| 510 |
|
|
foreach my $sq (@seqranges) { |
| 511 |
|
|
# -- complement requested? |
| 512 |
|
|
if ($revC) { |
| 513 |
|
|
$sq=reverseComplement($sq); |
| 514 |
|
|
#complement the range coordinates too! |
| 515 |
|
|
#$rStart=length($seq)-($rStart+$rLen)+2 if $range; |
| 516 |
|
|
$splseq=$sq.$splseq; |
| 517 |
|
|
} |
| 518 |
|
|
else { |
| 519 |
|
|
$splseq.=$sq; |
| 520 |
|
|
} |
| 521 |
|
|
} # for each range |
| 522 |
|
|
|
| 523 |
|
|
if (length($intr_ends)>4) { # have introns |
| 524 |
|
|
$intr_ends=substr($intr_ends,2,-2); |
| 525 |
|
|
if ($revC) { |
| 526 |
|
|
$intr_ends=reverseComplement($intr_ends); |
| 527 |
|
|
} |
| 528 |
|
|
} |
| 529 |
|
|
|
| 530 |
|
|
if ($revC) { |
| 531 |
|
|
@gfdata=reverse(@gfdata); |
| 532 |
|
|
($fcodon, $lcodon)=(reverseComplement($lcodon), |
| 533 |
|
|
reverseComplement($fcodon)); |
| 534 |
|
|
} |
| 535 |
|
|
# determine CDS phases |
| 536 |
|
|
my $initphase=0; #could be provided |
| 537 |
|
|
my $acclen=3-$initphase; |
| 538 |
|
|
foreach my $x (@gfdata) { |
| 539 |
|
|
#$$x[2]=($initframe+$acclen) % 3; |
| 540 |
|
|
$$x[2]=(3-$acclen%3) % 3; |
| 541 |
|
|
$acclen+=$$x[1]; |
| 542 |
|
|
} |
| 543 |
|
|
my $printflag=1; #should it be printed or not? |
| 544 |
|
|
# $splseq has the actual sequence to be processed |
| 545 |
|
|
# ========== vvvv - any other seq processing/trimming should be applied here: |
| 546 |
|
|
if ($getOrf) { |
| 547 |
|
|
my ($orf_start, $orf_end); |
| 548 |
|
|
($splseq, $orf_start, $orf_end)=getLongestOrf($splseq); |
| 549 |
|
|
if ($orf_start<=0) { |
| 550 |
|
|
$defline.=' ORF:none'; |
| 551 |
|
|
$orf_start=0;$orf_end=0; |
| 552 |
|
|
$splseq=''; |
| 553 |
|
|
$printflag=0; |
| 554 |
|
|
} |
| 555 |
|
|
else { |
| 556 |
|
|
$defline.=" ORF:$orf_start-$orf_end" if $defline; |
| 557 |
|
|
} |
| 558 |
|
|
} |
| 559 |
|
|
my $transl; |
| 560 |
|
|
if ($trframe) { |
| 561 |
|
|
$transl=&dna2prot($splseq, $trframe); #<trframe>th frame translate request |
| 562 |
|
|
$splseq=$transl; |
| 563 |
|
|
} |
| 564 |
|
|
elsif ($Getopt::Std::opt_Z) { |
| 565 |
|
|
$splseq=&prot2dna($splseq); #back-translate request |
| 566 |
|
|
} |
| 567 |
|
|
# ========== ^^^^ |
| 568 |
|
|
#------ output processing here: |
| 569 |
|
|
if ($validateCDS) { |
| 570 |
|
|
$transl=&dna2prot($splseq, $trframe) unless $transl; |
| 571 |
|
|
$printflag= ($splseq%3 == 0 && $codons{$fcodon} eq 'M' |
| 572 |
|
|
&& index($transl, '.')==length($transl)-1) |
| 573 |
|
|
} |
| 574 |
|
|
unless ($printflag) { |
| 575 |
|
|
$seq=''; # signal that it was processed |
| 576 |
|
|
$seq_len=0; |
| 577 |
|
|
return; |
| 578 |
|
|
} |
| 579 |
|
|
unless ($gffout) { |
| 580 |
|
|
if ($defline) { #format back to fasta |
| 581 |
|
|
print $defline."\n" unless ($Getopt::Std::opt_X); |
| 582 |
|
|
} |
| 583 |
|
|
else { #no defline found in the original file |
| 584 |
|
|
if ($Getopt::Std::opt_D && !$Getopt::Std::opt_X) { |
| 585 |
|
|
#my $defl='>SEQ'.$seqcount.'_'.length($seq); |
| 586 |
|
|
my $defl='>SEQ'.$seqcount.'_'.$seq_len; |
| 587 |
|
|
print "$defl\n"; |
| 588 |
|
|
} |
| 589 |
|
|
} |
| 590 |
|
|
} #print defline here |
| 591 |
|
|
unless ($gffout) { |
| 592 |
|
|
if ($Getopt::Std::opt_L) { #one line printing |
| 593 |
|
|
print $splseq."\n"; |
| 594 |
|
|
} |
| 595 |
|
|
else { # fasta multi-line printing |
| 596 |
|
|
for (my $p=0;$p<length($splseq);$p+=$linelen) { |
| 597 |
|
|
my $pl=substr($splseq, $p, $linelen)."\n"; |
| 598 |
|
|
print( ($trframe && $ansicolors) ? &colorize($pl, '.') : $pl ); |
| 599 |
|
|
} |
| 600 |
|
|
} |
| 601 |
|
|
} |
| 602 |
|
|
my @wmsg; |
| 603 |
|
|
if ($exoninfo || $gffout) { |
| 604 |
|
|
$transl=&dna2prot($splseq, $trframe) unless $transl; |
| 605 |
|
|
push(@wmsg,'NoStartCodon') if $codons{$fcodon} ne 'M'; |
| 606 |
|
|
#$wmsg.=';NoStopCodon' if $codons{$lcodon} ne '.'; |
| 607 |
|
|
push(@wmsg,'NoStopCodon') if substr($transl,-1) ne '.'; |
| 608 |
|
|
} |
| 609 |
|
|
|
| 610 |
|
|
if ($exoninfo) { #show exon info: |
| 611 |
|
|
print STDERR '----> Exon/CDS info ('.int(length($intr_ends)/4)." exons):\n"; |
| 612 |
|
|
my $afcodon=$fcodon; |
| 613 |
|
|
$afcodon=$clgreen.$fcodon.$clreset if ($fcodon eq 'ATG'); |
| 614 |
|
|
my @gfd;; |
| 615 |
|
|
my $pstrand=' '; |
| 616 |
|
|
if ($revC) { |
| 617 |
|
|
@gfd=map { $_->[0]+$_->[1]-1 } (@gfdata); |
| 618 |
|
|
$pstrand='-'; |
| 619 |
|
|
} |
| 620 |
|
|
else { @gfd=map { $_->[0] } @gfdata; } |
| 621 |
|
|
printf STDERR '%8d%s [%s~~', $basepos+$gfd[0],$pstrand,$afcodon; |
| 622 |
|
|
#print STDERR ' '.($basepos+int($gfdata[0]->[2])).' ['.$fcodon.'~~'; |
| 623 |
|
|
if (@gfdata>1) { # multi-exon |
| 624 |
|
|
my @splsites=unpack('(A4)*',$intr_ends); |
| 625 |
|
|
my $xn=1; |
| 626 |
|
|
foreach my $pair (@splsites) { |
| 627 |
|
|
my $don=substr($pair,0,2); |
| 628 |
|
|
$don=$clred.$don.$clreset if ($ansicolors && $don ne 'GT'); |
| 629 |
|
|
my $acc=substr($pair,-2); |
| 630 |
|
|
$acc=$clred.$acc.$clreset if ($ansicolors && $acc ne 'AG'); |
| 631 |
|
|
print STDERR '~~~]'.$don."\n"; |
| 632 |
|
|
#print STDERR ' '.($basepos+int($gfdata[$xn]->[2])).' '. |
| 633 |
|
|
# $acc. '[~~~~~'; |
| 634 |
|
|
printf STDERR '%8d%s %s[~~~~~', $basepos+$gfd[$xn], $pstrand,$acc; |
| 635 |
|
|
$xn++; |
| 636 |
|
|
} |
| 637 |
|
|
} #multi-exon |
| 638 |
|
|
my $alcodon=$lcodon; |
| 639 |
|
|
$alcodon=$clgreen.$lcodon.$clreset if $codons{uc($lcodon)} eq '.'; |
| 640 |
|
|
print STDERR $lcodon."]\n----------------------------"; |
| 641 |
|
|
if (@wmsg>0) { |
| 642 |
|
|
print STDERR "Warning: ".$clred.join($clreset.', '.$clred,@wmsg).$clreset; |
| 643 |
|
|
} |
| 644 |
|
|
print STDERR "\n"; |
| 645 |
|
|
} |
| 646 |
|
|
if ($gffout) { |
| 647 |
|
|
#show GFF output |
| 648 |
|
|
my $strand='+'; |
| 649 |
|
|
if ($revC) { |
| 650 |
|
|
@gfdata=reverse(@gfdata); #restore in fact, because we reversed it earlier |
| 651 |
|
|
$strand='-'; |
| 652 |
|
|
} |
| 653 |
|
|
my ($seqid)=($defline=~m/^>(\S+)/); |
| 654 |
|
|
my $warns=''; |
| 655 |
|
|
$warns=';'.join(';',@wmsg) if (@wmsg>0); |
| 656 |
|
|
print join("\t", $seqid, 'jigsaw', 'mRNA', $basepos+$gfdata[0]->[0], |
| 657 |
|
|
$basepos+$gfdata[-1]->[0]+$gfdata[-1]->[1]-1,'.',$strand,'.', 'ID=tjsm.XX;Name=tjsm.XX'.$warns)."\n"; |
| 658 |
|
|
foreach my $gfl (@gfdata) { |
| 659 |
|
|
print join("\t", $seqid, 'jigsaw', 'CDS', $basepos+$$gfl[0], |
| 660 |
|
|
$basepos+$$gfl[0]+$$gfl[1]-1,'.',$strand,$$gfl[2], 'Parent=tjsm.XX')."\n"; |
| 661 |
|
|
} |
| 662 |
|
|
} |
| 663 |
|
|
$seq=''; #processed! |
| 664 |
|
|
$seq_len=0; |
| 665 |
|
|
} |
| 666 |
|
|
|
| 667 |
|
|
|
| 668 |
|
|
sub parseRange { |
| 669 |
|
|
my $r=$_[0]; |
| 670 |
|
|
my ($rStart, $sep, $rLen)= ($r =~ m/^(\d+)([ \t\.\-\:_]+)(\d*)/); |
| 671 |
|
|
if ($rLen) { |
| 672 |
|
|
if ($sep ne ':') { # start-to-end format |
| 673 |
|
|
($rLen, $rStart) = ($rLen<$rStart) ? ($rStart-$rLen+1, $rLen) : ($rLen-$rStart+1, $rStart); |
| 674 |
|
|
} |
| 675 |
|
|
} |
| 676 |
|
|
#$rLen=-$rLen if ($rLen<0 && $r=~m/\d+\s*\-\s*$/); |
| 677 |
|
|
$rLen=-$rLen if ($rLen<0); |
| 678 |
|
|
return ($rStart, $rLen); #$rLen could be empty |
| 679 |
|
|
} |
| 680 |
|
|
|
| 681 |
|
|
|
| 682 |
|
|
sub colorize { |
| 683 |
|
|
#colorize all $p strings in $s |
| 684 |
|
|
my ($s, $p)=@_; |
| 685 |
|
|
#$red="\e[1;33;41m"; |
| 686 |
|
|
#$normal="\e[0m"; |
| 687 |
|
|
my $r="\e[1;33;41m"; # bright yellow on red |
| 688 |
|
|
my $b="\e[0m"; #reset colors |
| 689 |
|
|
$p=~s/\./\\./g; |
| 690 |
|
|
$s=~s/($p)/$r$1$b/g; |
| 691 |
|
|
return $s; |
| 692 |
|
|
} |
| 693 |
|
|
|
| 694 |
|
|
sub reverseComplement { |
| 695 |
|
|
my $s=reverse($_[0]); |
| 696 |
|
|
$s =~ tr/AaCcTtGgUuMmRrWwSsYyKkVvHhDdBb/TtGgAaCcAaKkYyWwSsRrMmBbDdHhVv/; |
| 697 |
|
|
return $s; |
| 698 |
|
|
} |
| 699 |
|
|
|
| 700 |
|
|
sub dna2prot { |
| 701 |
|
|
my $frame=$_[1] || 1; |
| 702 |
|
|
my $s; |
| 703 |
|
|
if ($frame<0) { |
| 704 |
|
|
$s=reverseComplement($_[0]); |
| 705 |
|
|
$frame=-$frame; |
| 706 |
|
|
} |
| 707 |
|
|
else { $s=$_[0]; } |
| 708 |
|
|
if ($frame==1) { $s= uc($s); } |
| 709 |
|
|
else { $s = uc(substr($s, $frame-1)); } |
| 710 |
|
|
#my @cods = ($s =~ m/([A-Z][A-Z][A-Z])/g); |
| 711 |
|
|
my @cods = unpack('(A3)*', $s); |
| 712 |
|
|
my $r; |
| 713 |
|
|
foreach my $c (@cods) { |
| 714 |
|
|
my $aa=$codons{$c} || 'X'; |
| 715 |
|
|
$r.=$aa; |
| 716 |
|
|
} |
| 717 |
|
|
return $r; |
| 718 |
|
|
} |
| 719 |
|
|
|
| 720 |
|
|
sub prot2dna { |
| 721 |
|
|
my $s= uc($_[0]); |
| 722 |
|
|
my @aa = ($s =~ m/([A-Z])/g); |
| 723 |
|
|
my $r; |
| 724 |
|
|
foreach my $a (@aa) { |
| 725 |
|
|
my $codon=$toDNA{$a} || 'N'; |
| 726 |
|
|
$r.=$codon; |
| 727 |
|
|
} |
| 728 |
|
|
return $r; |
| 729 |
|
|
} |
| 730 |
|
|
|
| 731 |
|
|
sub getLongestOrf { |
| 732 |
|
|
my ($seq)=@_; |
| 733 |
|
|
my $best=0; |
| 734 |
|
|
my ($bests,$beste)=(-1,-1); |
| 735 |
|
|
#my $bestorf=""; |
| 736 |
|
|
my $seqlen=length($seq); |
| 737 |
|
|
my @starts=(); |
| 738 |
|
|
my @ends=(); |
| 739 |
|
|
if ($getOrfAny) { # include start frames if not a stop codon directly |
| 740 |
|
|
for (my $frame=0;$frame<3;$frame++) { |
| 741 |
|
|
unless ($seq=~m/^.{$frame}(taa|tga|tag)/i) { |
| 742 |
|
|
push @starts,$frame+1; |
| 743 |
|
|
} |
| 744 |
|
|
} |
| 745 |
|
|
} |
| 746 |
|
|
while ($seq=~m/(atg)/gi) { |
| 747 |
|
|
push @starts,pos($seq)-2; |
| 748 |
|
|
} |
| 749 |
|
|
|
| 750 |
|
|
while ($seq=~m/(taa|tga|tag)/gi) { |
| 751 |
|
|
push @ends,pos($seq)-2; |
| 752 |
|
|
} |
| 753 |
|
|
push @ends,($seqlen-2,$seqlen-1,$seqlen); |
| 754 |
|
|
for my $s (@starts) { |
| 755 |
|
|
for my $e (@ends) { |
| 756 |
|
|
if ($e%3==$s%3 and $e>$s) { |
| 757 |
|
|
if ($e-$s>$best) { |
| 758 |
|
|
$best=$e-$s; |
| 759 |
|
|
($bests,$beste)=($s,$e); |
| 760 |
|
|
#$bestorf=substr($seq,$s-1,$e-$s+1); |
| 761 |
|
|
} |
| 762 |
|
|
last |
| 763 |
|
|
} |
| 764 |
|
|
else { |
| 765 |
|
|
next |
| 766 |
|
|
} |
| 767 |
|
|
} #for each end |
| 768 |
|
|
} #for each start |
| 769 |
|
|
if ($bests<=0) { |
| 770 |
|
|
return ('',0,0); |
| 771 |
|
|
} |
| 772 |
|
|
$beste+=2 if $beste<=length($seq)-2; #make it so it includes the stop codon! |
| 773 |
|
|
return (substr($seq,$bests-1,$beste-$bests+1), $bests, $beste); |
| 774 |
|
|
} |
