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vadr_seed.pm
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vadr_seed.pm
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#!/usr/bin/env perl
#
# version: 1.6.3 [Dec 2023]
#
# vadr_seed.pm
# Eric Nawrocki
# EPN, Fri Mar 27 10:28:01 2020
#
# Perl module used by v-annotate.pl script related to the -s option to
# use blastn for the classification, and coverage determination
# stages, and to accelerate the alignment stage. Alignment
# acceleration achieved by using a alignment seed region from the
# blastn alignment (possibly the full alignment) as a fixed alignment
# and only aligning the flanking terminal 5' and/or 3' regions with
# cmalign or glsearch, if necessary.
#
#########################
# Naming conventions used in this file:
#
# - Hash data structures use the abbreviation 'H', typically at the end of
# a variable name (e.g. %length_H)
#
# - Array data structures use the abbreviation 'A', typically at the end of
# a variable name (e.g. @accession_A)
#
# - Multidimensional arrays/hashes use concatenated 'H's and 'A's, e.g.:
# @size_AA is a two dimensional array, and %info_HHA is a two dimensional
# hash of arrays
#
# - File handles typically start or end with 'FH', e.g. $log_FH, or a hash
# of file handles that is used commonly is %FH_HR.
#
##
#
# See vadr.pm for additional notes
#
use strict;
use warnings;
require "vadr.pm";
require "sqp_opts.pm";
require "sqp_ofile.pm";
require "sqp_seq.pm";
require "sqp_seqfile.pm";
require "sqp_utils.pm";
#########################################################################################
#
# List of subroutines in this file, divided into categories.
#
# Subroutines related to running and parsing blastn:
# run_blastn_and_summarize_output()
# parse_blastn_results()
# blastn_pretblout_to_tblout()
# parse_blastn_indel_strings()
# parse_blastn_indel_token()
# parse_blastn_indel_file_to_get_seed_info()
#
# Subroutines related to joining alignments:
# join_alignments_and_add_unjoinbl_alerts()
# join_alignments_helper()
# update_overflow_info_for_joined_alignments
#
# Subroutines related to seeds:
# seed_info_to_subseqs()
# process_seed_seq_and_mdl_coords()
# prune_seed_given_minimum_length_segment()
# prune_seed_of_terminal_short_segments()
# check_seed_overlap_with_start_stop_codons()
# pick_best_seed_info()
#
# Subroutines related to minimap2:
# run_minimap2()
# parse_minimap2_to_get_seed_info()
# parse_minimap2_cigar_to_seed_coords()
#
#########################################################################################
#################################################################
# Subroutine: run_blastn_and_summarize_output()
# Incept: EPN, Fri Mar 27 11:11:24 2020
#
# Purpose: Run all input sequences as queries against a
# blastn db of the model sequences and summarize
# the output with parse_blast.pl.
#
# Arguments:
# $execs_HR: ref to executables with "esl-ssplit" and "cmsearch"
# defined as keys
# $db_file: name of blast db file to use
# $seq_file: name of sequence file with all sequences to run against
# $out_root: string for naming output files
# $stg_key: stage key, "rpn.cls" or "std.cls"
# $nseq: number of sequences in $seq_file
# $progress_w: width for outputProgressPrior output
# $opt_HHR: REF to 2D hash of option values, see top of sqp-opts.pm for description
# $ofile_info_HHR: REF to 2D hash of output file information
#
# Returns: void
#
# Dies: If blastn executable doesn't exist or command fails
#################################################################
sub run_blastn_and_summarize_output {
my $sub_name = "run_blastn_and_summarize_output";
my $nargs_expected = 9;
if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
my ($execs_HR, $db_file, $seq_file, $out_root, $stg_key,
$nseq, $progress_w, $opt_HHR, $ofile_info_HHR) = @_;
my $FH_HR = $ofile_info_HHR->{"FH"};
my $log_FH = $FH_HR->{"log"}; # for convenience
my $ncpu = opt_Get("--cpu", $opt_HHR);
if($ncpu == 0) { $ncpu = 1; }
if(($stg_key ne "rpn.cls") && ($stg_key ne "std.cls")) {
ofile_FAIL("ERROR in $sub_name, unrecognized stage key: $stg_key, should be rpn.cls or std.cls", 1, $FH_HR);
}
my $do_keep = opt_Get("--keep", $opt_HHR);
my $stg_desc = ($stg_key eq "rpn.cls") ?
sprintf("Preprocessing for N replacement: blastn classification ($nseq seq%s)", (($nseq > 1) ? "s" : "")) :
sprintf("Classifying sequences with blastn ($nseq seq%s)", (($nseq > 1) ? "s" : ""));
my $start_secs = ofile_OutputProgressPrior($stg_desc, $progress_w, $log_FH, *STDOUT);
my $blastn_out_file = $out_root . ".$stg_key.blastn.out";
my $opt_str = "-num_threads $ncpu -query $seq_file -db $db_file -out $blastn_out_file";
if($stg_key eq "rpn.cls") { # rpn.cls, use --r_* options
$opt_str .= " -word_size " . opt_Get("--r_blastnws", $opt_HHR);
$opt_str .= " -reward " . opt_Get("--r_blastnrw", $opt_HHR);
$opt_str .= " -penalty " . opt_Get("--r_blastnpn", $opt_HHR);
$opt_str .= " -xdrop_gap_final " . opt_Get("--r_blastnxd", $opt_HHR);
if(! opt_Get("--r_blastngdf", $opt_HHR)) {
$opt_str .= " -gapopen " . opt_Get("--r_blastngo", $opt_HHR);
$opt_str .= " -gapextend " . opt_Get("--r_blastnge", $opt_HHR);
}
if(opt_IsUsed("--r_blastntk", $opt_HHR)) {
$opt_str .= " -task blastn";
}
}
else { # not rpn.cls, use --s_* options
$opt_str .= " -word_size " . opt_Get("--s_blastnws", $opt_HHR);
$opt_str .= " -reward " . opt_Get("--s_blastnrw", $opt_HHR);
$opt_str .= " -penalty " . opt_Get("--s_blastnpn", $opt_HHR);
$opt_str .= " -xdrop_gap_final " . opt_Get("--s_blastnxd", $opt_HHR);
if(! opt_Get("--s_blastngdf", $opt_HHR)) {
$opt_str .= " -gapopen " . opt_Get("--s_blastngo", $opt_HHR);
$opt_str .= " -gapextend " . opt_Get("--s_blastnge", $opt_HHR);
}
if(opt_IsUsed("--s_blastntk", $opt_HHR)) {
$opt_str .= " -task blastn";
}
}
my $blastn_cmd = $execs_HR->{"blastn"} . " $opt_str";
# default values for vadr 1.1 to 1.3 were:
# --s_blastngo 0
# --s_blastnge 2.5
# --s_blastnrw 1
# --s_blastnpn -2
# --s_blastnxd 100
# For more info, see https://www.ncbi.nlm.nih.gov/books/NBK279684/,
# search for BLASTN reward/penalty values and then look at table D1.
# Note that blastn is really megablast unless -task blastn is use
# (and vadr does NOT use -task blastn by default so it is using megablast)
utl_RunCommand($blastn_cmd, opt_Get("-v", $opt_HHR), 0, $FH_HR);
ofile_AddClosedFileToOutputInfo($ofile_info_HHR, "$stg_key.blastn.out", $blastn_out_file, 0, $do_keep, "blastn output");
# now summarize its output
# use --splus to skip alignment parsing of hits to negative strand of subject
# that's important because parse_blast.pl doesn't have the code to deal with
# such alignments (it was written for blastx originally for which subject is
# always +) but that's okay because those hits are to negative strand of
# the sequence (actually negative strand of the subject/model but blastn revcomps
# the subject instead of the query like cmsearch/cmscan would do), and we don't care
# about negative strand hit indel info.
my $blastn_summary_file = $out_root . ".$stg_key.blastn.summary.txt";
my $parse_cmd = $execs_HR->{"parse_blast"} . " --program n --input $blastn_out_file --splus > $blastn_summary_file";
utl_RunCommand($parse_cmd, opt_Get("-v", $opt_HHR), 0, $ofile_info_HHR->{"FH"});
ofile_AddClosedFileToOutputInfo($ofile_info_HHR, "$stg_key.blastn.summary", $blastn_summary_file, 0, $do_keep, "parsed (summarized) blastn output");
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
return;
}
#################################################################
# Subroutine: parse_blastn_results()
# Incept: EPN, Thu Oct 4 15:25:00 2018
# [based on parse_blastx_results() which was
# modified from parse_blastx_results() subroutine
# Alejandro Schaffer in compare_predictions.pl]
#
# Purpose: Parse blastn summary file and output a summary file
# and create one of two sets of output files:
#
# Output mode 1: 1 file, produced if $seq2mdl_HR is undef
#
# "blastn.{rpn.cls,std.cls}.pretblout" file: cmsearch --trmF3 output
# format file with each hit on a separate line and
# individual hit scores reported for each hit. This is
# later processed by blastn_pretblout_to_tblout() to sum
# bit scores for all hits with the same model/seq/strand
# so we can classify sequences the same way we do in
# default mode (cmsearch based classification).
#
# Output mode 2: 2 files produced per model with >= 1 matching
# sequence, produced if $seq2mdl_HR is defined.
#
# "search.{rpn.cls,std.cls,rpn.cdt,std.cdt}.<mdlname>.tblout":
# cmsearch --tblout format file with each hit for a
# sequence on + strand that is classified to model
# <mdlname>.
#
# "blastn.{rpn.cls,std.cls,rpn.cdt,std.cdt}.<mdlname>.indel.txt":
# one line per sequence with all inserts and deletes in
# all blastn hit alignments for each sequence that is
# classified to <mdlname> on strand +.
#
# Arguments:
# $blastn_summary_file: path to blastn summary file to parse
# $seq_len_HR: REF to hash of sequence lengths
# $seq2mdl_HR: REF to hash mapping each sequence to the model
# it is classified to, if undef serves as flag
# that we will create set 1 of output files
# $mdl_name_AR: REF to array of model names that are keys in
# %{$seq2mdl_HR}, can be undef if $seq2mdl_HR is undef
# $out_root: output root for the file names
# $stg_key: stage key, "rpn.cls" or "std.cls" for classification
# or "rpn.cdt" or "std.cdt" for coverage determination
# $opt_HHR: REF to 2D hash of option values, see top of sqp_opts.pm for description
# $ofile_info_HHR: REF to 2D hash of output file information, ADDED TO HERE
#
# Returns: void
#
# Dies: If blastn fails.
#
#################################################################
sub parse_blastn_results {
my $sub_name = "parse_blastn_results";
my $nargs_exp = 8;
if(scalar(@_) != $nargs_exp) { die "ERROR $sub_name entered with wrong number of input args"; }
my ($blastn_summary_file, $seq_len_HR, $seq2mdl_HR, $mdl_name_AR,
$out_root, $stg_key, $opt_HHR, $ofile_info_HHR) = @_;
my $FH_HR = (defined $ofile_info_HHR->{"FH"}) ? $ofile_info_HHR->{"FH"} : undef;
if(($stg_key ne "rpn.cls") && ($stg_key ne "rpn.cdt") &&
($stg_key ne "std.cls") && ($stg_key ne "std.cdt")) {
ofile_FAIL("ERROR in $sub_name, unrecognized stage key: $stg_key, should be rpn.cls, rpn.cdt, std.cls, or std.cdt", 1, $FH_HR);
}
if((($stg_key eq "rpn.cdt") || ($stg_key eq "std.cdt")) &&
(! defined $seq2mdl_HR)) {
ofile_FAIL("ERROR in $sub_name, stage key is $stg_key but seq2mdl_HR is undef", 1, $FH_HR);
}
my $pretblout_FH = undef; # defined if output mode 1 (if ! defined $seq2mdl_HR)
my %tblout_FH_H = (); # defined if output mode 2 (if defined $seq2mdl_HR)
my %indel_FH_H = (); # defined if output mode 2 (if defined $seq2mdl_HR)
my $outfile_key = undef; # a key for an output file in %{$ofile_info_HHR}
my $small_value = 0.000001;
my $min_bitsc = opt_Get("--s_blastnsc", $opt_HHR) - $small_value;
if(($stg_key eq "rpn.cls") || ($stg_key eq "rpn.cdt")) {
$min_bitsc = opt_Get("--r_blastnsc", $opt_HHR) - $small_value;
}
my $do_keep = opt_Get("--keep", $opt_HHR) ? 1 : 0;
my $mdl_name = undef;
if(! defined $seq2mdl_HR) {
# output mode 1, open the pretblout output file
#
# We write to this file as we parse the $blastn_summary_file but we
# have to post-process it in blastn_pretblout_to_tblout so that the
# top hit per model/sequence/strand trio includes the *summed* score
# for that model/strand/strand instead of just the hit score. This
# way we will match the cmsearch --trmF3 output downstream steps
# expect.
ofile_OpenAndAddFileToOutputInfo($ofile_info_HHR, "$stg_key.blastn.pretblout", $out_root . ".$stg_key.blastn.pretblout", 0, $do_keep, "blastn output converted to cmsearch --trmF3 tblout format (hit scores)");
$pretblout_FH = $ofile_info_HHR->{"FH"}{"$stg_key.blastn.pretblout"};
printf $pretblout_FH ("%-30s %-30s %8s %9s %9s %6s %6s %3s %11s\n",
"#modelname/subject", "sequence/query", "bitscore", "start", "end", "strand", "bounds", "ovp", "seqlen");
}
else { # $seq2mdl_HR is defined
# output mode 2, for each model in @{$mdl_name_AR}, open the
# coverage determination tblout files in cmsearch --tblout
# format (not --trmF3 output format) and the indel files
foreach $mdl_name (@{$mdl_name_AR}) {
$outfile_key = "$stg_key.$mdl_name.tblout";
ofile_OpenAndAddFileToOutputInfo($ofile_info_HHR, $outfile_key, $out_root . "." . $outfile_key, 0, $do_keep, "blastn output converted to cmsearch tblout format for model $mdl_name");
$tblout_FH_H{$mdl_name} = $ofile_info_HHR->{"FH"}{$outfile_key};
$outfile_key = "$stg_key.$mdl_name.indel";
ofile_OpenAndAddFileToOutputInfo($ofile_info_HHR, $outfile_key, $out_root . "." . $outfile_key, 0, $do_keep, "blastn indel information for model $mdl_name");
$indel_FH_H{$mdl_name} = $ofile_info_HHR->{"FH"}{$outfile_key};
}
}
# open and parse input blastn summary file
utl_FileValidateExistsAndNonEmpty($blastn_summary_file, "blastn summary file", $sub_name, 1, $FH_HR);
open(IN, $blastn_summary_file) || ofile_FileOpenFailure($blastn_summary_file, $sub_name, $!, "reading", $FH_HR);
my $line_idx = 0;
my $seq_name = undef; # sequence name this hit corresponds to (query)
my $seq_len = undef; # length of query sequence
my $cur_FH = undef; # current file handle
my %cur_H = (); # values for current hit (HSP)
my %scsum_HHH = (); # 3D hash with summed scores for model/seq/strand trios:
# key 1: model/subject
# key 2: sequence/query
# key 3: strand ("+" or "-")
# value: summed bit score for all hits for this model/sequence/strand trio
#
# Order of lines in <IN>:
# -----per-query/target-block---
# QACC
# QDEF ignored
# QLEN
# MATCH ignored
# HACC
# HDEF ignored
# SLEN
# ------per-HSP-block------
# HSP
# BITSCORE
# RAWSCORE ignored
# EVALUE
# HLEN ignored
# IDENT ignored
# GAPS ignored
# STRAND
# STOP
# DEL
# MAXDE
# INS
# MAXINS
# QRANGE
# SRANGE
# ------per-HSP-block------
# END_MATCH
while(my $line = <IN>) {
chomp $line;
$line_idx++;
if($line ne "END_MATCH") {
my @el_A = split(/\t/, $line);
if(scalar(@el_A) != 2) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, did not read exactly 2 tab-delimited tokens in line $line", 1, $FH_HR);
}
my ($key, $value) = (@el_A);
if($key eq "QACC") {
$cur_H{$key} = $value;
if(! defined $seq_len_HR->{$value}) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, unexpected sequence name $value in line $line", 1, $FH_HR);
}
}
elsif($key eq "QLEN") {
if(! defined $cur_H{"QACC"}) {
ofile_FAIL("ERROR in $sub_name, ing $blastn_summary_file, read QLEN line before QACC line (line: $line_idx)", 1, $FH_HR);
}
$cur_H{$key} = $value;
if($value !~ /^\d+$/) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, unable to parse query length in line $line", 1, $FH_HR);
}
if($value != $seq_len_HR->{$cur_H{"QACC"}}) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read query length of $value from QLEN line for query " . $cur_H{"QACC"} . ", but expected " . $seq_len_HR->{$cur_H{"QACC"}} . " from seq_len_HR, on line: $line", 1, $FH_HR);
}
}
elsif($key eq "HACC") {
if(! defined $cur_H{"QACC"}) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read HACC line $line before QACC line (line: $line_idx)\n", 1, $FH_HR);
}
$cur_H{$key} = $value;
}
elsif($key eq "HLEN") {
if((! defined $cur_H{"QACC"}) || (! defined $cur_H{"HACC"})) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read HLEN line $line before one or both of QACC and HACC lines (line: $line_idx)\n", 1, $FH_HR);
}
$cur_H{$key} = $value;
if($value !~ /^\d+$/) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, unable to parse subject length in line $line", 1, $FH_HR);
}
}
elsif($key eq "HSP") {
if((! defined $cur_H{"QACC"}) || (! defined $cur_H{"HACC"})) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read HSP line before one or both of QACC and HACC lines (line: $line_idx)\n", 1, $FH_HR);
}
$cur_H{$key} = $value;
if($value !~ /^(\d+)$/) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, unable to parse blastn summary HSP line $line", 1, $FH_HR);
}
}
elsif($key eq "BITSCORE") {
if((! defined $cur_H{"QACC"}) || (! defined $cur_H{"HACC"}) || (! defined $cur_H{"HSP"})) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read BITSCORE line before one or more of QACC, HACC, or HSP lines (line: $line_idx)\n", 1, $FH_HR);
}
$cur_H{$key} = $value;
if(($value !~ /^\d+\.\d+$/) && ($value !~ /^\d+$/) && ($value !~ /^\d+\.\d+e[+-]\d+/)) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, unable to parse blastn summary BITSCORE line $line", 1, $FH_HR);
}
}
elsif($key eq "EVALUE") {
if((! defined $cur_H{"QACC"}) || (! defined $cur_H{"HACC"}) || (! defined $cur_H{"HSP"}) || (! defined $cur_H{"BITSCORE"})) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read EVALUE line before one or more of QACC, HACC, HSP, or BITSCORE lines (line: $line_idx)\n", 1, $FH_HR);
}
$cur_H{$key} = $value;
}
elsif($key =~ m/^[SQ]STRAND$/) {
if((! defined $cur_H{"QACC"}) || (! defined $cur_H{"HACC"}) || (! defined $cur_H{"HSP"}) || (! defined $cur_H{"BITSCORE"})) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read QSTRAND OR SSTRAND line before one or more of QACC, HACC, HSP, or BITSCORE lines (line: $line_idx)\n", 1, $FH_HR);
}
if($value =~ /^([\+\-])$/) {
$cur_H{$key} = $1;
# all query strands should be + (unless blastn is reverse complementing queries and running those too)
if(($key eq "QSTRAND") && ($cur_H{$key} ne "+")) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, query strand not + line $line", 1, $FH_HR);
}
}
else {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, unable to parse blastn summary $key line $line ($key $value)", 1, $FH_HR);
}
}
elsif(($key eq "STOP") || ($key eq "DEL") || ($key eq "INS")) {
if((! defined $cur_H{"QACC"}) || (! defined $cur_H{"HACC"}) || (! defined $cur_H{"HSP"}) || (! defined $cur_H{"BITSCORE"}) || (! defined $cur_H{"QSTRAND"}) || (! defined $cur_H{"SSTRAND"})) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read $key line before one or more of QACC, HACC, HSP, BITSCORE or FRAME lines (line: $line_idx)\n", 1, $FH_HR);
}
if(($value ne "") && ($value ne "BLASTNULL")) {
$cur_H{$key} = $value;
}
}
elsif($key eq "SRANGE") {
# we don't require all of QACC, HACC, HSP, BITSCORE and STRAND even though we should have them
# sometimes we don't (may be a bug in parse-blastn.pl), we only require QACC
if(! defined $cur_H{"QACC"}) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read $key line before QACC line (line: $line_idx)\n", 1, $FH_HR);
}
if($value eq "..") { # special case, no hits, silently move on
;
}
elsif(! defined $cur_H{"BITSCORE"}) { # special case, no BITSCORE lines yet seen (may be a bug in parse-blastn.pl?), silently move on
;
}
elsif($value =~ /^(\d+)..(\d+)$/) {
($cur_H{"SRANGESTART"}, $cur_H{"SRANGESTOP"}) = ($1, $2);
}
else {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, unable to parse blastn summary QRANGE line $line", 1, $FH_HR);
}
}
elsif($key eq "QRANGE") {
# we don't require all of QACC, HACC, HSP, BITSCORE and STRAND even though we should have them
# sometimes we don't (may be a bug in parse-blastn.pl), we only require QACC
if(! defined $cur_H{"QACC"}) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read $key line before QACC line (line: $line_idx)\n", 1, $FH_HR);
}
if($value eq "..") { # special case, no hits, silently move on
;
}
elsif(! defined $cur_H{"BITSCORE"}) { # special case, no BITSCORE lines yet seen (may be a bug in parse-blastn.pl?), silently move on
;
}
elsif(($value =~ /^(\d+)..(\d+)$/) && ($cur_H{"BITSCORE"} >= $min_bitsc)) {
($cur_H{"QRANGESTART"}, $cur_H{"QRANGESTOP"}) = ($1, $2);
# output data in cmscan --trmF3 format
if((! defined $cur_H{"SRANGESTART"}) || (! defined $cur_H{"SRANGESTOP"})) {
ofile_FAIL("ERROR in $sub_name, reading $blastn_summary_file, read $key line before SRANGE line (line: $line_idx)\n", 1, $FH_HR);
}
my $cur_seq_name = $cur_H{"QACC"};
my $cur_seq_len = $seq_len_HR->{$cur_seq_name}; # we checked this is defined when we read QACC line
my $cur_mdl_name = $cur_H{"HACC"};
my $cur_bit_score = $cur_H{"BITSCORE"};
my $cur_evalue = $cur_H{"EVALUE"};
my ($cur_seq_start, $cur_seq_stop, $cur_seq_strand, $cur_mdl_start, $cur_mdl_stop) = (undef, undef, undef, undef, undef);
# if subject strand is negative (and subject is the model)
# we need to revcomp both the query and subject coords, to match cmscan behavior
# which is the inverse of blastn, whereas cmscan revcomps the sequence (blastn equivalent of query)
# and searches it against the always positive model (blastn equivalent of the subject), blastn
# revcomps the subject and searches it against the always positive query
if($cur_H{"SSTRAND"} eq "+") {
$cur_seq_start = $cur_H{"QRANGESTART"};
$cur_seq_stop = $cur_H{"QRANGESTOP"};
$cur_seq_strand = "+";
$cur_mdl_start = $cur_H{"SRANGESTART"};
$cur_mdl_stop = $cur_H{"SRANGESTOP"};
}
else { # SSTRAND is -
$cur_seq_start = $cur_H{"QRANGESTOP"};
$cur_seq_stop = $cur_H{"QRANGESTART"};
$cur_seq_strand = "-";
$cur_mdl_start = $cur_H{"SRANGESTOP"};
$cur_mdl_stop = $cur_H{"SRANGESTART"};
}
if(defined $pretblout_FH) {
printf $pretblout_FH ("%-30s %-30s %8.1f %9d %9d %6s %6s %3s %11s\n",
$cur_mdl_name,
$cur_seq_name,
$cur_bit_score,
$cur_seq_start,
$cur_seq_stop,
$cur_seq_strand,
sprintf(" %s%s",
($cur_seq_start == 1) ? "[" : ".",
($cur_seq_stop == $cur_seq_len) ? "]" : "."),
"?",
$cur_seq_len);
# update summed score in %scsum_HHH for this model/seq/strand trio
if(! defined $scsum_HHH{$cur_mdl_name}) {
%{$scsum_HHH{$cur_mdl_name}} = ();
}
if(! defined $scsum_HHH{$cur_mdl_name}{$cur_seq_name}) {
%{$scsum_HHH{$cur_mdl_name}{$cur_seq_name}} = ();
}
if(! defined $scsum_HHH{$cur_mdl_name}{$cur_seq_name}{$cur_seq_strand}) {
$scsum_HHH{$cur_mdl_name}{$cur_seq_name}{$cur_seq_strand} = 0.;
}
$scsum_HHH{$cur_mdl_name}{$cur_seq_name}{$cur_seq_strand} += $cur_H{"BITSCORE"};
}
else {
# in output mode 2, but we only output if this hit is
# a <seq>/<model> pair where <seq> is classified to <model>
if((defined $seq2mdl_HR->{$cur_seq_name}) &&
($seq2mdl_HR->{$cur_seq_name} eq $cur_mdl_name)) {
#target name accession query name accession mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc description of target
if(! defined $tblout_FH_H{$cur_mdl_name}) {
ofile_FAIL("ERROR in $sub_name, read unexpected model name: $cur_mdl_name", 1, $FH_HR);
}
$cur_FH = $tblout_FH_H{$cur_mdl_name};
printf $cur_FH ("%-s - %-s - blastn %d %d %d %d %s - - - 0.0 %8.1f %s ? -\n",
$cur_seq_name,
$cur_mdl_name,
$cur_mdl_start,
$cur_mdl_stop,
$cur_seq_start,
$cur_seq_stop,
$cur_seq_strand,
$cur_bit_score,
$cur_evalue);
# and output indel info to a separate file
$cur_FH = $indel_FH_H{$cur_mdl_name};
printf $cur_FH ("%s %s %s %s %s %s %s %s\n",
$cur_mdl_name,
$cur_seq_name,
vdr_CoordsSegmentCreate($cur_mdl_start, $cur_mdl_stop, "+", $FH_HR),
$cur_H{"HLEN"},
vdr_CoordsSegmentCreate($cur_seq_start, $cur_seq_stop, $cur_seq_strand, $FH_HR),
$cur_seq_len,
(defined $cur_H{"INS"}) ? $cur_H{"INS"} : "BLASTNULL",
(defined $cur_H{"DEL"}) ? $cur_H{"DEL"} : "BLASTNULL");
}
}
} # end of 'else' entered if SRANGE is NOT ".."
# reset variables
my $save_qacc = $cur_H{"QACC"};
my $save_hacc = $cur_H{"HACC"};
%cur_H = ();
$cur_H{"QACC"} = $save_qacc; # save QACC
$cur_H{"HACC"} = $save_hacc; # save HACC
} # end of 'elsif $key eq "SRANGE"
} # end of 'if($line ne "END_MATCH")'
else { # $line eq "END_MATCH"
# reset variables
my $save_qacc = $cur_H{"QACC"};
%cur_H = ();
$cur_H{"QACC"} = $save_qacc; # save QACC
# we don't update seq_name seq_len until we see a new QACC
}
} # end of 'while($my $line = <IN>)'
close(IN);
# close files depending on output mode
if(defined $pretblout_FH) {
# output mode 1
# close the pretblout file
# then call convert it pretblout to tblout (cmscan --trmF3 format)
# which will have scores summed for each seq/mdl/strand trio
close $ofile_info_HHR->{"FH"}{"$stg_key.blastn.pretblout"};
blastn_pretblout_to_tblout($ofile_info_HHR->{"fullpath"}{"$stg_key.blastn.pretblout"},
\%scsum_HHH, $out_root, $stg_key, $opt_HHR, $ofile_info_HHR);
}
else {
# output mode 2:
# close the per model files:
foreach $mdl_name (@{$mdl_name_AR}) {
$outfile_key = "$stg_key.$mdl_name.tblout";
close $ofile_info_HHR->{"FH"}{$outfile_key};
$outfile_key = "$stg_key.$mdl_name.indel";
close $ofile_info_HHR->{"FH"}{$outfile_key};
}
}
return;
}
#################################################################
# Subroutine: blastn_pretblout_to_tblout()
# Incept: EPN, Sat Mar 28 14:04:18 2020
#
# Purpose: Given a 'pretblout' file created by parse_blastn_results
# generate the 'tblout' file that is identical to the
# 'pretblout' except that scores are summed over all hits
# for each sequence/model/strand trio for the top hit for
# each sequence/model/strand trio and 0 for all other hits
# for that trio. This unusual step is necessary so the
# highest scoring hit in the tblout file can be used to
# define the winning model (as it is for the cmscan --trmF3
# tblout file).
#
# Arguments:
# $blastn_pretblout_file: path to blastn summary file to parse
# $scsum_HHHR: ref to 3D hash,
# key 1: model/subject
# key 2: sequence/query
# key 3: strand ("+" or "-")
# value: summed bit score for all hits for this model/sequence/strand trio
# NOTE: all values in this 3D hash are set to 0. by this subroutine!
# $out_root: output root for the file names
# $stg_key: stage key, "rpn.cls" or "std.cls" for classification (cmscan) ,
# or "rpn.cdt" or "std.cdt" for coverage determination (cmsearch)
# $opt_HHR: REF to 2D hash of option values, see top of sqp_opts.pm for description
# $ofile_info_HHR: REF to 2D hash of output file information, ADDED TO HERE
#
# Returns: void
#
# Dies: if unable to parse a pretblout file
#
#################################################################
sub blastn_pretblout_to_tblout {
my $sub_name = "blastn_pretblout_to_tblout";
my $nargs_exp = 6;
if(scalar(@_) != $nargs_exp) { die "ERROR $sub_name entered with wrong number of input args"; }
my ($blastn_pretblout_file, $scsum_HHHR, $out_root, $stg_key, $opt_HHR, $ofile_info_HHR) = @_;
my $FH_HR = (defined $ofile_info_HHR->{"FH"}) ? $ofile_info_HHR->{"FH"} : undef;
my $do_keep = opt_Get("--keep", $opt_HHR);
if(($stg_key ne "rpn.cls") && ($stg_key ne "rpn.cdt") &&
($stg_key ne "std.cls") && ($stg_key ne "std.cdt")) {
ofile_FAIL("ERROR in $sub_name, unrecognized stage key: $stg_key, should be rpn.cls, rpn.cdt, std.cls, or std.cdt", 1, $FH_HR);
}
ofile_OpenAndAddFileToOutputInfo($ofile_info_HHR, "$stg_key.tblout", $out_root . ".$stg_key.tblout", 0, $do_keep, "blastn output converted to cmscan --trmF3 tblout format (summed hit scores)");
my $tblout_FH = $FH_HR->{"$stg_key.tblout"};
# open and parse input blastn summary file
utl_FileValidateExistsAndNonEmpty($blastn_pretblout_file, "blastn pretblout file", $sub_name, 1, $FH_HR);
open(IN, $blastn_pretblout_file) || ofile_FileOpenFailure($blastn_pretblout_file, $sub_name, $!, "reading", $FH_HR);
while(my $line = <IN>) {
chomp $line;
if($line !~ m/^#/) {
my @el_A = split(/\s+/, $line);
if(scalar(@el_A) != 9) {
ofile_FAIL("ERROR in $sub_name, unable to parse $blastn_pretblout_file line (wrong number of space-delimited tokens):\n$line\n", 1, $FH_HR);
}
my ($model, $seq, $bitsc, $start, $end, $strand, $bounds, $ovp, $seqlen) = (@el_A);
if(! defined $scsum_HHHR->{$model}{$seq}{$strand}) {
ofile_FAIL("ERROR in $sub_name, read model/seq/strand trio not in input scsum hash: model:$model, seq:$seq, strand:$strand on line:\n$line\n", 1, $FH_HR);
}
printf $tblout_FH ("%-30s %-30s %8.1f %9d %9d %6s %6s %3s %11s\n",
$seq, $model, $scsum_HHHR->{$model}{$seq}{$strand},
$start, $end, $strand, $bounds, $ovp, $seqlen);
# set scsum to zero for all subsequent hits to this trio
$scsum_HHHR->{$model}{$seq}{$strand} = 0.;
}
else {
print $tblout_FH ($line . "\n");
}
}
close(IN);
close $ofile_info_HHR->{"FH"}{"$stg_key.tblout"};
}
#################################################################
# Subroutine: parse_blastn_indel_strings()
# Incept: EPN, Mon Mar 30 06:53:35 2020
#
# Purpose: Given information on where insertions and deletions
# are in a blastn alignment, determine the
# seed strings and optional return the alignment
# of the sequence as a string.
#
# Arguments:
# $in_mdl_coords_sgm: vadr coords segment indicating model boundaries of alignment
# $in_seq_coords_sgm: vadr coords segment indicating sequence boundaries of alignment
# $blastn_ins_str: insert string from parse_blast.pl run on blastn output indicating
# where insertions in query (sequence) with respect to model (subject)
# are, in format:
# <instok1>...<instokn> (note: final token does not have ';' after it)
# <instok> = Q<d1>:S<d2>+<d3>
# <d1> is query (sequence) position after which insertion of length <d3> nt exists
# <d2> is subject (model) position after which insertion of length <d3> nt exists
# $blastn_del_str: delete string from parse_blast.pl indicating where deletions are
# where insertions are in format:
# <deltok1>;<deltok2>;...<deltokn> (note: final token does not have ';' after it)
# <deltok> = Q<d1>:S<d2>+<d3>
# <d1> is query (sequence) position after which insertion of length <d3> nt exists
# <d2> is subject (model) position after which insertion of length <d3> nt exists
# $ofile_info_HHR: REF to 2D hash of output file information, ADDED TO HERE
#
# Returns: Two values:
# $sda_mdl_coords: vadr coords string with all segments of ungapped alignments between
# query and subject in model (subject) coords, between model coords
# in $in_mdl_coords_sgm.
# $sda_seq_coords: vadr coords string with all segments of ungapped alignments between
# query and subject in sequence (query) coords, between sequence coords
# in $in_seq_coords_sgm.
#
# Dies: if unable to parse the indel strings
#
#################################################################
sub parse_blastn_indel_strings {
my $sub_name = "parse_blastn_indel_strings";
my $nargs_exp = 5;
if(scalar(@_) != $nargs_exp) { die "ERROR $sub_name entered with wrong number of input args"; }
my ($in_mdl_coords_sgm, $in_seq_coords_sgm, $blastn_ins_str, $blastn_del_str, $ofile_info_HHR) = @_;
my $FH_HR = (defined $ofile_info_HHR) ? $ofile_info_HHR->{"FH"} : undef; # undef helpful for tests
my @ins_tok_A = ();
if($blastn_ins_str ne "BLASTNULL") {
@ins_tok_A = split(";", $blastn_ins_str);
}
my $nins = scalar(@ins_tok_A);
my @del_tok_A = ();
if($blastn_del_str ne "BLASTNULL") {
@del_tok_A = split(";", $blastn_del_str);
}
my $ndel = scalar(@del_tok_A);
# printf("nins: $nins ndel: $ndel\n");
my ($mdl_start, $mdl_stop, $mdl_strand) = vdr_CoordsSegmentParse($in_mdl_coords_sgm, $FH_HR);
my ($seq_start, $seq_stop, $seq_strand) = vdr_CoordsSegmentParse($in_seq_coords_sgm, $FH_HR);
if($mdl_strand ne "+") { ofile_FAIL("ERROR in $sub_name, model (subject) strand in model coords: $in_mdl_coords_sgm is not +", 1, $FH_HR); }
if($seq_strand ne "+") { ofile_FAIL("ERROR in $sub_name, sequence (query) strand in model coords: $in_seq_coords_sgm is not +", 1, $FH_HR); }
# construct a vadr coords string of ungapped aligned segments, segment by segment
my $sda_mdl_coords = "";
my $sda_seq_coords = "";
my $cur_mdl_start = $mdl_start;
my $cur_seq_start = $seq_start;
my $ii = 0; # insert index in @ins_tok_A
my $di = 0; # delete index in @del_tok_A
my ($ins_seq_pos, $ins_mdl_pos, $ins_len) = (undef, undef, undef);
my ($del_seq_pos, $del_mdl_pos, $del_len) = (undef, undef, undef);
my $update_ins = 1; # flag set when we should update our insert token
my $update_del = 1; # flag set when we should update our delete token
my $ins_tok = undef;
my $del_tok = undef;
while(($ii < $nins) || ($di < $ndel)) {
my $ins_tok = ($ii < $nins) ? $ins_tok_A[$ii] : "NULL";
my $del_tok = ($di < $ndel) ? $del_tok_A[$di] : "NULL";
# printf("\tin loop ii: $ii ins_tok: $ins_tok, di: $di del_tok: $del_tok\n");
if($update_ins) {
if($ii < $nins) {
$ins_tok = $ins_tok_A[$ii];
($ins_mdl_pos, $ins_seq_pos, $ins_len) = parse_blastn_indel_token($ins_tok, "insert", $FH_HR);
}
else {
($ins_tok, $ins_mdl_pos, $ins_seq_pos, $ins_len) = (undef, undef, undef, undef);
}
}
if($update_del) {
if($di < $ndel) {
$del_tok = $del_tok_A[$di];
($del_mdl_pos, $del_seq_pos, $del_len) = parse_blastn_indel_token($del_tok, "delete", $FH_HR);
}
else {
($del_tok, $del_mdl_pos, $del_seq_pos, $del_len) = (undef, undef, undef, undef);
}
}
$update_ins = 0; # set to 1 below, if our next indel is an insert ($next_is_insert set to 1) and we need to read the next one
$update_del = 0; # set to 1 below, if our next indel is a delete ($next_is_delete set to 1) and we need to read the next one
my $next_is_insert = 0; # set to 1 below if we determine next token is insert, not delete
my $next_is_delete = 0; # set to 1 below if we determine next token is delete, not insert
if((! defined $ins_seq_pos) && (! defined $del_seq_pos)) {
# shouldn't happen
ofile_FAIL("ERROR in $sub_name, ran out of insert and delete tokens, but insert token index is $ii out of $nins and delete token index is $di out of ndel\nblastn_ins_str: $blastn_ins_str\nblastn_del_str: $blastn_del_str\n", 1, $FH_HR);
}
elsif(! defined $ins_seq_pos) {
# $del_seq_pos must be defined
$next_is_delete = 1;
}
elsif(! defined $del_seq_pos) {
# $ins_seq_pos must be defined
$next_is_insert = 1;
}
else {
# both $del_seq_pos and $ins_seq_pos are defined
# determine which comes first
if(($ins_seq_pos < $del_seq_pos) && ($ins_mdl_pos <= $del_mdl_pos)) {
# insert comes first
$next_is_insert = 1;
}
elsif(($del_seq_pos < $ins_seq_pos) && ($del_mdl_pos <= $ins_mdl_pos)) {
# delete comes first
$next_is_delete = 1;
}
elsif(($ins_seq_pos == $del_seq_pos) && ($ins_mdl_pos == $del_mdl_pos)) {
# shouldn't happen
ofile_FAIL("ERROR in $sub_name, insert and delete tokens have identical query and subject positions, " . ((defined $ins_tok) ? $ins_tok : "UNDEFINED") . " and " . ((defined $del_tok) ? $del_tok : "UNDEFINED"), 1, $FH_HR);
}
else {
# shouldn't happen, seq and mdl are not in the same order
ofile_FAIL("ERROR in $sub_name, insert and delete tokens imply query and subject coordinates out of order, " . ((defined $ins_tok) ? $ins_tok : "UNDEFINED") . " and " . ((defined $del_tok) ? $del_tok : "UNDEFINED"), 1, $FH_HR);
}
} # end of else entered if both $del_seq_pos and $ins_seq_pos are defined
if($next_is_insert) {
# sanity check that the segments we are about to add to mdl and seq
# coords are the same length (they represent a chunk of ungapped alignment)
if(($ins_mdl_pos - $cur_mdl_start + 1) != ($ins_seq_pos - $cur_seq_start + 1)) {
# print("\t\tsda_mdl_coords: $sda_mdl_coords\n");
# print("\t\tsda_seq_coords: $sda_seq_coords\n");
ofile_FAIL("ERROR in $sub_name, trying to add ungapped segments before next insert, but lengths don't match up: mdl: $cur_mdl_start .. $ins_mdl_pos, seq: $cur_seq_start .. $ins_seq_pos", 1, $FH_HR);
}
$sda_mdl_coords = vdr_CoordsAppendSegment($sda_mdl_coords, vdr_CoordsSegmentCreate($cur_mdl_start, $ins_mdl_pos, "+", $FH_HR));
$cur_mdl_start = $ins_mdl_pos + 1;
$sda_seq_coords = vdr_CoordsAppendSegment($sda_seq_coords, vdr_CoordsSegmentCreate($cur_seq_start, $ins_seq_pos, "+", $FH_HR));
$cur_seq_start = $ins_seq_pos + $ins_len + 1;
$update_ins = 1;
$ii++;
}
elsif($next_is_delete) {
# sanity check that the segments we are about to add to mdl and seq
# coords are the same length (they represent a chunk of ungapped alignment)
if(($del_mdl_pos - $cur_mdl_start + 1) != ($del_seq_pos - $cur_seq_start + 1)) {
ofile_FAIL("ERROR in $sub_name, trying to add ungapped segments before next delete, but lengths don't match up: mdl: $cur_mdl_start .. $del_mdl_pos, seq: $cur_seq_start .. $del_seq_pos", 1, $FH_HR);
}
$sda_mdl_coords = vdr_CoordsAppendSegment($sda_mdl_coords, vdr_CoordsSegmentCreate($cur_mdl_start, $del_mdl_pos, "+", $FH_HR));
$cur_mdl_start = $del_mdl_pos + $del_len + 1;
$sda_seq_coords = vdr_CoordsAppendSegment($sda_seq_coords, vdr_CoordsSegmentCreate($cur_seq_start, $del_seq_pos, "+", $FH_HR));
$cur_seq_start = $del_seq_pos + 1;
$update_del = 1;
$di++;
}
else {
# shouldn't happen, can't figure out what token is next
ofile_FAIL("ERROR in $sub_name, unable to determine which insert and delete tokens imply query and subject coordinates out of order, $ins_tok_A[$ii] and $del_tok_A[$di]", 1, $FH_HR);
}
} # end of 'while(($ii < $nins) && ($di < $ndel))'
# add the final segment
if($cur_mdl_start > $mdl_stop) {
ofile_FAIL("ERROR in $sub_name, trying to append final ungapped segment but out of model (subject) positions, trying to add $cur_mdl_start..$mdl_stop:+ to $sda_mdl_coords", 1, $FH_HR);
}
if($cur_seq_start > $seq_stop) {
ofile_FAIL("ERROR in $sub_name, trying to append final ungapped segment but out of sequence (query) positions, trying to add $cur_seq_start..$seq_stop:+ to $sda_seq_coords", 1, $FH_HR);
}
# sanity check that the segments we are about to add to mdl and seq
# coords are the same length (they represent a chunk of ungapped alignment)
if(($mdl_stop - $cur_mdl_start + 1) != ($seq_stop - $cur_seq_start + 1)) {
ofile_FAIL("ERROR in $sub_name, trying to add ungapped segments as final segment, but lengths don't match up: mdl: $cur_mdl_start .. $mdl_stop, seq: $cur_seq_start .. $seq_stop", 1, $FH_HR);
}
$sda_mdl_coords = vdr_CoordsAppendSegment($sda_mdl_coords, vdr_CoordsSegmentCreate($cur_mdl_start, $mdl_stop, "+", $FH_HR));
$sda_seq_coords = vdr_CoordsAppendSegment($sda_seq_coords, vdr_CoordsSegmentCreate($cur_seq_start, $seq_stop, "+", $FH_HR));
# print("in $sub_name, returning mdl: $sda_mdl_coords, seq: $sda_seq_coords\n");
return ($sda_mdl_coords, $sda_seq_coords);
}
#################################################################
# Subroutine: parse_blastn_indel_token()
# Incept: EPN, Mon Mar 30 10:15:05 2020
#
# Purpose: Parse a token from an INS or DEL output line created
# by parse_blast.pl --program n, and return its constituent
# parts.
#
# if $type eq "insert": = Q<d1>:S<d2>+<d3>
# if $type eq "delete": = Q<d1>:S<d2>-<d3>
#
# Arguments:
# $indel_tok: token from parse_blast.pl INS or DEL line
# $type: "insert" or "delete" (just for checking if + or - is correct)
# $FH_HR: REF to hash of file handles, including "log" and "cmd"
#
# Returns: Three values:
# $mdl_pos: model (subject) position
# $seq_pos: sequence (query) position
# $len: length of insert or delete
#
# Dies: if unable to parse the token
# if $type is "insert" and we read a - not a +
# if $type is "delete" and we read a + not a -
# if $type is not "insert" or "delete"
#
#################################################################
sub parse_blastn_indel_token {
my $sub_name = "parse_blastn_indel_token";
my $nargs_exp = 3;
if(scalar(@_) != $nargs_exp) { die "ERROR $sub_name entered with wrong number of input args"; }
my ($indel_tok, $type, $FH_HR) = @_;
if(! defined $indel_tok) {
ofile_FAIL("ERROR in $sub_name, indel_tok is undefined", 1, $FH_HR);
}
if(($type ne "insert") && ($type ne "delete")) {
ofile_FAIL("ERROR in $sub_name, type is $type but should be \"insert\" or \"delete\"", 1, $FH_HR);
}
my $exp_plus_or_minus = ($type eq "insert") ? "+" : "-";
# printf("in $sub_name indel_tok: $indel_tok\n");
if($indel_tok =~ /^Q(\d+)\:S(\d+)([\+\-])(\d+)$/) {
my ($seq_pos, $mdl_pos, $plus_or_minus, $len) = ($1, $2, $3, $4);
if($plus_or_minus ne $exp_plus_or_minus) {
ofile_FAIL("ERROR in $sub_name, type is $type, expected $exp_plus_or_minus but read $plus_or_minus in input token $indel_tok", 1, $FH_HR);
}
return ($mdl_pos, $seq_pos, $len); # yes, mdl and seq are supposed to be reversed order relative to $indel_tok
}
# if we get here we couldn't parse the token
ofile_FAIL("ERROR in $sub_name, unable to parse token $indel_tok", 1, $FH_HR);
return; # NEVER REACHED
}
#################################################################
# Subroutine: parse_blastn_indel_file_to_get_seed_info()
# Incept: EPN, Thu Sep 8 15:27:30 2022
# EPN, Tue Mar 31 07:22:48 2020 (previously parse_blastn_indel_file_to_get_subseq_info())
#
# Purpose: Parse a blastn indel file created by parse_blastn_results,
# determine blastn aligned regions (seeds) of each
# sequence that we will trust. Return information on the
# seeds in %{$sda_mdl_HR} (model coords) and %{$sda_seq_HR}
# (seq coords).
#
# Arguments:
# $indel_file: blastn indel file to parse, created by
# parse_blastn_results() for a single model
# $seq_name_AR: REF to array of sequences we want to parse indel info for
# $seq_len_HR: REF to hash of sequence lengths
# $exp_mdl_name: name of model we expect on all lines of $indel_file
# $start_codon_coords: string of start codon coords for all CDS
# $stop_codon_coords: string of stop codon coords for all CDS
# $sda_mdl_HR: REF to hash, key is <seq_name>, value is mdl coords
# segment of blast seed aln, FILLED HERE
# $sda_seq_HR: REF to hash, key is <seq_name>, value is seq coords
# segment of blast seed aln, FILLED HERE
# $opt_HHR: REF to 2D hash of option values, see top of sqp_opts.pm for description
# $ofile_info_HHR: REF to 2D hash of output file information, ADDED TO HERE
#
# Returns: void
#
# Dies: if unable to parse $indel_file
#
#################################################################
sub parse_blastn_indel_file_to_get_seed_info {
my $sub_name = "parse_blastn_indel_file_to_get_seed_info";
my $nargs_exp = 10;
if(scalar(@_) != $nargs_exp) { die "ERROR $sub_name entered with wrong number of input args"; }
my ($indel_file, $seq_name_AR, $seq_len_HR, $exp_mdl_name, $start_codon_coords, $stop_codon_coords,
$sda_mdl_HR, $sda_seq_HR, $opt_HHR, $ofile_info_HHR) = @_;
my $FH_HR = $ofile_info_HHR->{"FH"};
my $nt_overhang = opt_Get("--s_overhang", $opt_HHR);
my $min_sgm_len = opt_Get("--s_minsgmlen", $opt_HHR);
my $do_allsgm = opt_Get("--s_allsgm", $opt_HHR);
my $do_ungapsgm = opt_Get("--s_ungapsgm", $opt_HHR);
my $do_realign_startstop = ($do_allsgm || opt_Get("--s_startstop", $opt_HHR)) ? 0 : 1;
my %processed_H = (); # key: sequence name we want indel info for,
# value: 0 if we have not processed an HSP for this sequence
# 1 if we have
foreach my $seq_name (@{$seq_name_AR}) {
$processed_H{$seq_name} = 0;
}
my $nprocessed = 0;
# process $start_codon_coords and $stop_codon_coords strings into arrays
my $start_and_stop_codon_coords = $start_codon_coords;
my @codon_start_A = ();
my @codon_stop_A = ();
my @codon_strand_A = ();
if(($start_and_stop_codon_coords ne "") && ($start_and_stop_codon_coords !~ m/\,$/)) {
$start_and_stop_codon_coords .= ",";
}
$start_and_stop_codon_coords .= $stop_codon_coords;
vdr_FeatureStartStopStrandArrays($start_and_stop_codon_coords, \@codon_start_A, \@codon_stop_A, \@codon_strand_A, $FH_HR);
open(IN, $indel_file) || ofile_FileOpenFailure($indel_file, $sub_name, $!, "reading", $FH_HR);
while(my $line = <IN>) {
if($line !~ m/^#/) {
chomp $line;
#model_name seq_name mdl_coords mdl_len seq_coords seq_len ins_str del_str
#NC_039477 AB541310.1 5..7513:+ 7535 1..7509:+ 7509 Q41:S46+1;Q107:S111+1; Q37:S41-1;Q113:S116-1;
chomp $line;
my @el_A = split(/\s+/, $line);
if(scalar(@el_A) != 8) {
ofile_FAIL("ERROR in $sub_name, unable to parse indel line, unexpected number of tokens:\n$line\n", 1, $FH_HR);
}
my ($mdl_name, $seq_name, $mdl_coords, $mdl_len, $seq_coords, $seq_len, $ins_str, $del_str) = (@el_A);
if(! defined $seq_len_HR->{$seq_name}) {