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v-build.pl
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v-build.pl
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#!/usr/bin/env perl
# EPN, Wed May 1 10:48:51 2019 [renamed to vadr-build.pl]
# EPN, Mon Feb 1 15:07:43 2016 [dnaorg_build.pl split off from dnaorg_annotate_genomes.pl]
# EPN, Mon Aug 10 10:39:33 2015 [development began on dnaorg_annotate_genomes.pl]
#
use strict;
use warnings;
use Getopt::Long qw(:config no_auto_abbrev);
use Time::HiRes qw(gettimeofday);
use Bio::Easel::MSA;
use Bio::Easel::SqFile;
use LWP::Simple;
use LWP::Protocol::https;
require "vadr.pm";
require "sqp_opts.pm";
require "sqp_ofile.pm";
require "sqp_seq.pm";
require "sqp_seqfile.pm";
require "sqp_utils.pm";
#######################################################################################
# What this script does:
#
# - Preliminaries:
# o processes options
# o creates the output directory
# o outputs program banner
# o makes sure the required executables are executable
#
# - Fetches GenBank file (if ! --gb)
# - Parses GenBank file
# - Prunes data read from GenBank file
# - Parses input stockholm file (if --stk)
# - Fills in feature and segment info
# - Translates CDS (if any) and creates BLAST db
# - Builds CM
# - Presses CM
# - Writes model info file
# - Writes optional output files
#
#######################################################################################
# make sure required environment variables are set
my $env_vadr_scripts_dir = utl_DirEnvVarValid("VADRSCRIPTSDIR");
my $env_vadr_blast_dir = utl_DirEnvVarValid("VADRBLASTDIR");
my $env_vadr_infernal_dir = utl_DirEnvVarValid("VADRINFERNALDIR");
my $env_vadr_hmmer_dir = utl_DirEnvVarValid("VADRHMMERDIR");
my $env_vadr_easel_dir = utl_DirEnvVarValid("VADREASELDIR");
# make sure the required executables exist and are executable
my %execs_H = (); # hash with paths to all required executables
$execs_H{"cmbuild"} = $env_vadr_infernal_dir . "/cmbuild";
$execs_H{"cmfetch"} = $env_vadr_infernal_dir . "/cmfetch";
$execs_H{"cmpress"} = $env_vadr_infernal_dir . "/cmpress";
$execs_H{"hmmbuild"} = $env_vadr_hmmer_dir . "/hmmbuild";
$execs_H{"hmmpress"} = $env_vadr_hmmer_dir . "/hmmpress";
$execs_H{"esl-reformat"} = $env_vadr_easel_dir . "/esl-reformat";
$execs_H{"esl-sfetch"} = $env_vadr_easel_dir . "/esl-sfetch";
$execs_H{"esl-translate"} = $env_vadr_easel_dir . "/esl-translate";
$execs_H{"makeblastdb"} = $env_vadr_blast_dir . "/makeblastdb";
utl_ExecHValidate(\%execs_H, undef);
#########################################################
# Command line and option processing using sqp_opts.pm
#
# opt_HH: 2D hash:
# 1D key: option name (e.g. "-h")
# 2D key: string denoting type of information
# (one of "type", "default", "group", "requires", "incompatible", "preamble", "help")
# value: string explaining 2D key:
# "type": "boolean", "string", "int" or "real"
# "default": default value for option
# "group": integer denoting group number this option belongs to
# "requires": string of 0 or more other options this option requires to work, each separated by a ','
# "incompatiable": string of 0 or more other options this option is incompatible with, each separated by a ','
# "preamble": string describing option for preamble section (beginning of output from script)
# "help": string describing option for help section (printed if -h used)
# "setby": '1' if option set by user, else 'undef'
# "value": value for option, can be undef if default is undef
#
# opt_order_A: array of options in the order they should be processed
#
# opt_group_desc_H: key: group number (integer), value: description of group for help output
my %opt_HH = ();
my @opt_order_A = ();
my %opt_group_desc_H = ();
my $g = 0; # option group
# Add all options to %opt_HH and @opt_order_A.
# This section needs to be kept in sync (manually) with the &GetOptions call below
$opt_group_desc_H{++$g} = "basic options";
# option type default group requires incompat preamble-output help-output
opt_Add("-h", "boolean", 0, 0, undef, undef, undef, "display this help", \%opt_HH, \@opt_order_A);
opt_Add("-f", "boolean", 0, $g, undef, undef, "forcing directory overwrite", "force; if dir <output directory> exists, overwrite it", \%opt_HH, \@opt_order_A);
opt_Add("-v", "boolean", 0, $g, undef, undef, "be verbose", "be verbose; output commands to stdout as they're run", \%opt_HH, \@opt_order_A);
opt_Add("--stk", "string", undef, $g, undef, undef, "read single sequence stockholm 'alignment' from <s>", "read single sequence stockholm 'alignment' from <s>", \%opt_HH, \@opt_order_A);
opt_Add("--infa", "string", undef, $g, undef, undef, "read single sequence fasta file from <s>, don't fetch it", "read single sequence fasta file from <s>, don't fetch it", \%opt_HH, \@opt_order_A);
opt_Add("--inft", "string", undef, $g, "--inft", "--gb", "read feature table file from <s>, don't fetch it", "read feature table file from <s>, don't fetch it", \%opt_HH, \@opt_order_A);
opt_Add("--ftfetch1", "boolean", 0, $g, undef, "--inft,--gb,--ftfetch2", "fetch feature table with efetch -format ft", "fetch feature table with efetch -format ft", \%opt_HH, \@opt_order_A);
opt_Add("--ftfetch2", "boolean", 0, $g, undef, "--inft,--gb,--ftfetch1", "fetch feature table with efetch -format gbc | xml2tbl", "fetch feature table with efetch -format gbc | xml2tbl", \%opt_HH, \@opt_order_A);
opt_Add("--gb", "boolean", 0, $g, undef, undef, "parse a genbank file, not a feature table file", "parse a genbank file, not a feature table file", \%opt_HH, \@opt_order_A);
opt_Add("--ingb", "string", undef, $g, "--gb", undef, "read genbank file from <s>, don't fetch it", "read genbank file from <s>, don't fetch it", \%opt_HH, \@opt_order_A);
opt_Add("--addminfo", "string", undef, $g, undef, undef, "add feature info from model info file <s>", "add feature info from model info file <s>", \%opt_HH, \@opt_order_A);
opt_Add("--forcelong", "boolean", 0, $g, undef, undef, "allow long models > 25Kb in length", "allow long models > 25Kb in length", \%opt_HH, \@opt_order_A);
opt_Add("--keep", "boolean", 0, $g, undef, undef, "leave intermediate files on disk", "do not remove intermediate files, keep them all on disk", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{++$g} = "options for controlling what feature types are stored in model info file\n[default set is: CDS,gene,mat_peptide,sig_peptide]";
# option type default group requires incompat preamble-output help-output
opt_Add("--fall", "boolean", 0, $g, undef, undef, "store info for all feature types (except those in --fskip)", "store info for all feature types (except those in --fskip)", \%opt_HH, \@opt_order_A);
opt_Add("--fadd", "string", undef, $g, undef,"--fall", "also store features types in comma separated string <s>", "also store feature types in comma separated string <s>", \%opt_HH, \@opt_order_A);
opt_Add("--fskip", "string", undef, $g, undef, undef, "do not store info for feature types in comma separated string <s>", "do not store info for feature types in comma separated string <s>", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{++$g} = "options for controlling what qualifiers are stored in model info file\n[default set is:product,gene,exception]";
# option type default group requires incompat preamble-output help-output
opt_Add("--qall", "boolean", 0, $g, undef, undef, "store info for all qualifiers (except those in --qskip)", "store info for all qualifiers (except those in --qskip)", \%opt_HH, \@opt_order_A);
opt_Add("--qadd", "string", undef, $g, undef,"--qall", "also store info for qualifiers in comma separated string <s>", "also store info for qualifiers in comma separated string <s>", \%opt_HH, \@opt_order_A);
opt_Add("--qftradd", "string", undef, $g,"--qadd", undef, "--qadd <s2> only applies for feature types in comma separated string <s>", "--qadd <s2> only applies for feature types in comma separated string <s>", \%opt_HH, \@opt_order_A);
opt_Add("--qskip", "string", undef, $g, undef, undef, "do not store info for qualifiers in comma separated string <s>", "do not store info for qualifiers in comma separated string <s>", \%opt_HH, \@opt_order_A);
opt_Add("--noaddgene", "boolean", 0, $g, undef, undef, "do not add gene qualifiers from gene features to overlapping features", "do not add gene qualifiers from gene features to overlapping features", \%opt_HH, \@opt_order_A);
opt_Add("--nosplice", "boolean", 0, $g, undef, undef, "do not check and add valid splice sites qualifiers for CDS", "do not check and add valid splice sites qualifiers for CDS", \%opt_HH, \@opt_order_A);
opt_Add("--ssplice", "boolean", 0, $g, undef,"--nosplice", "exit if any noncanonical splice sites exist in any CDS", "exit if any noncanonical splice sites exist in any CDS", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{++$g} = "options for including additional model attributes";
# option type default group requires incompat preamble-output help-output
opt_Add("--group", "string", undef, $g, undef, undef, "specify model group is <s>", "specify model group is <s>", \%opt_HH, \@opt_order_A);
opt_Add("--subgroup", "string", undef, $g, "--group", undef, "specify model subgroup is <s>", "specify model subgroup is <s>", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{++$g} = "options for controlling CDS translation step";
# option type default group requires incompat preamble-output help-output
opt_Add("--ttbl", "integer", 1, $g, undef, undef, "use NCBI translation table <n> to translate CDS", "use NCBI translation table <n> to translate CDS", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{++$g} = "options for controlling cmbuild step";
# option type default group requires incompat preamble-output help-output
opt_Add("--cmn", "integer", undef, $g, undef, "--skipbuild,--cminfile", "set number of seqs for glocal fwd HMM calibration to <n>", "set number of seqs for glocal fwd HMM calibration to <n>", \%opt_HH, \@opt_order_A);
opt_Add("--cmp7ml", "boolean", 0, $g, undef, "--skipbuild,--cminfile", "set CM's filter p7 HMM as the ML p7 HMM", "set CM's filter p7 HMM as the ML p7 HMM", \%opt_HH, \@opt_order_A);
opt_Add("--cmere", "real", undef, $g, undef, "--skipbuild,--cminfile", "set CM relative entropy target to <x>", "set CM relative entropy target to <x>", \%opt_HH, \@opt_order_A);
opt_Add("--cmeset", "real", undef, $g, undef, "--skipbuild,--cminfile", "set CM eff seq # for CM to <x>", "set CM eff seq # for CM to <x>", \%opt_HH, \@opt_order_A);
opt_Add("--cmemaxseq","real", undef, $g, undef, "--skipbuild,--cminfile", "set CM maximum allowed eff seq # for CM to <x>", "set CM maximum alowed eff seq # for CM to <x>", \%opt_HH, \@opt_order_A);
opt_Add("--cmnoh3pri","boolean", 0, $g, undef, "--skipbuild,--cminfile", "do not use --noh3pri option with cmbuild", "do not use --noh3pri option with cmbuild", \%opt_HH, \@opt_order_A);
opt_Add("--cminfile", "string", undef, $g, undef, "--skipbuild", "read cmbuild options from file <s>, one per line", "read cmbuild options from file <s>, one per line", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{++$g} = "options for skipping stages";
# option type default group requires incompat preamble-output help-output
opt_Add("--skipbuild", "boolean", 0, $g, undef, undef, "skip the cmbuild step", "skip the cmbuild and blastn db creation steps", \%opt_HH, \@opt_order_A);
opt_Add("--onlyurl", "boolean", 0, $g, undef,"--stk,--ingb,--inft", "output genbank file url for accession and exit", "output genbank file url for accession and exit", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{++$g} = "optional output files";
# option type default group requires incompat preamble-output help-output
opt_Add("--ftrinfo", "boolean", 0, $g, undef, undef, "output internal feature information", "create file with internal feature information", \%opt_HH, \@opt_order_A);
opt_Add("--sgminfo", "boolean", 0, $g, undef, undef, "output internal segment information", "create file with internal segment information", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{++$g} = "other expert options";
# option type default group requires incompat preamble-output help-output
opt_Add("--execname", "string", undef, $g, undef, undef, "define executable name of this script as <s>", "define executable name of this script as <s>", \%opt_HH, \@opt_order_A);
opt_Add("--nosig2mat", "boolean", 0, $g, undef, undef, "do not treat sig_peptide as mat_peptide", "do not treat sig_peptide as mat_peptide", \%opt_HH, \@opt_order_A);
opt_Add("--intlen", "integer", 40, $g, undef,"--nosplice", "set min length of intron to check for splice sites to <n>", "set min length of intron to check for splice sites to <n>", \%opt_HH, \@opt_order_A);
# This section needs to be kept in sync (manually) with the opt_Add() section above
my %GetOptions_H = ();
my $options_okay =
&GetOptions('h' => \$GetOptions_H{"-h"},
# basic options
'f' => \$GetOptions_H{"-f"},
'v' => \$GetOptions_H{"-v"},
'stk=s' => \$GetOptions_H{"--stk"},
'infa=s' => \$GetOptions_H{"--infa"},
'inft=s' => \$GetOptions_H{"--inft"},
'ftfetch1' => \$GetOptions_H{"--ftfetch1"},
'ftfetch2' => \$GetOptions_H{"--ftfetch2"},
'gb' => \$GetOptions_H{"--gb"},
'ingb=s' => \$GetOptions_H{"--ingb"},
'addminfo=s' => \$GetOptions_H{"--addminfo"},
'forcelong' => \$GetOptions_H{"--forcelong"},
'keep' => \$GetOptions_H{"--keep"},
# options for controlling what feature types are stored in model info file
'fall' => \$GetOptions_H{"--fall"},
'fadd=s' => \$GetOptions_H{"--fadd"},
'fskip=s' => \$GetOptions_H{"--fskip"},
# options for controlling what qualifiers are stored in model info file
'qall' => \$GetOptions_H{"--qall"},
'qadd=s' => \$GetOptions_H{"--qadd"},
'qftradd=s' => \$GetOptions_H{"--qftradd"},
'qskip=s' => \$GetOptions_H{"--qskip"},
'noaddgene' => \$GetOptions_H{"--noaddgene"},
'nosplice' => \$GetOptions_H{"--nosplice"},
'ssplice' => \$GetOptions_H{"--ssplice"},
# options for including additional model attributes
'group=s' => \$GetOptions_H{"--group"},
'subgroup=s' => \$GetOptions_H{"--subgroup"},
# options for controlling CDS translation step
'ttbl=s' => \$GetOptions_H{"--ttbl"},
# options for controlling cmbuild step
'cmn=s' => \$GetOptions_H{"--cmn"},
'cmp7ml' => \$GetOptions_H{"--cmp7ml"},
'cmere=s' => \$GetOptions_H{"--cmere"},
'cmeset=s' => \$GetOptions_H{"--cmeset"},
'cmemaxseq=s' => \$GetOptions_H{"--cmemaxseq"},
'cmnoh3pr' => \$GetOptions_H{"--cmnoh3pri"},
'cminfile=s' => \$GetOptions_H{"--cminfile"},
# options for skipping stages
'skipbuild' => \$GetOptions_H{"--skipbuild"},
'onlyurl' => \$GetOptions_H{"--onlyurl"},
# optional output files
'sgminfo' => \$GetOptions_H{"--sgminfo"},
'ftrinfo' => \$GetOptions_H{"--ftrinfo"},
# other expert options
'execname=s' => \$GetOptions_H{"--execname"},
'nosig2mat' => \$GetOptions_H{"--nosig2mat"},
'intlen=s' => \$GetOptions_H{"--intlen"});
my $total_seconds = -1 * ofile_SecondsSinceEpoch(); # by multiplying by -1, we can just add another ofile_SecondsSinceEpoch call at end to get total time
my $execname_opt = $GetOptions_H{"--execname"};
my $executable = (defined $execname_opt) ? $execname_opt : "v-build.pl";
my $usage = "Usage: $executable [-options] <accession> <path to output directory to create>\n";
my $synopsis = "$executable :: build homology model of a single sequence for feature annotation";
my $date = scalar localtime();
my $version = "1.6.3";
my $releasedate = "Dec 2023";
my $pkgname = "VADR";
# print help and exit if necessary
if((! $options_okay) || ($GetOptions_H{"-h"})) {
ofile_OutputBanner(*STDOUT, $pkgname, $version, $releasedate, $synopsis, $date, undef);
opt_OutputHelp(*STDOUT, $usage, \%opt_HH, \@opt_order_A, \%opt_group_desc_H);
if(! $options_okay) { die "ERROR, unrecognized option;"; }
else { exit 0; } # -h, exit with 0 status
}
# check that number of command line args is correct
if(scalar(@ARGV) != 2) {
print "Incorrect number of command line arguments.\n";
print $usage;
print "\nTo see more help on available options, do $executable -h\n\n";
exit(1);
}
my ($mdl_name, $dir) = (@ARGV);
if($mdl_name =~ /[\(\)]/) {
die "ERROR, accession cannot contain '(' or ')'";
}
# set options in opt_HH
opt_SetFromUserHash(\%GetOptions_H, \%opt_HH);
# validate options (check for conflicts)
opt_ValidateSet(\%opt_HH, \@opt_order_A);
############################################
# if --onlyurl used, output the url and exit
############################################
if(opt_Get("--onlyurl", \%opt_HH)) {
if(opt_Get("--gb", \%opt_HH)) {
print vdr_EutilsFetchUrl($mdl_name, "nuccore", "gb") . "\n";
}
else {
print vdr_EutilsFetchUrl($mdl_name, "nuccore", "ft") . "\n";
}
exit 0;
}
#############################
# create the output directory
#############################
my $cmd; # a command to run with utl_RunCommand()
my @early_cmd_A = (); # array of commands we run before our log file is opened
if($dir =~ m/\/$/) {
$dir =~ s/\/$//; # remove final '/' if it exists
}
if(-d $dir) {
$cmd = "rm -rf $dir";
if(opt_Get("-f", \%opt_HH)) { utl_RunCommand($cmd, opt_Get("-v", \%opt_HH), 0, undef); push(@early_cmd_A, $cmd); }
else { die "ERROR directory named $dir already exists. Remove it, or use -f to overwrite it."; }
}
if(-e $dir) {
$cmd = "rm $dir";
if(opt_Get("-f", \%opt_HH)) { utl_RunCommand($cmd, opt_Get("-v", \%opt_HH), 0, undef); push(@early_cmd_A, $cmd); }
else { die "ERROR a file named $dir already exists. Remove it, or use -f to overwrite it."; }
}
# create the dir
$cmd = "mkdir $dir";
utl_RunCommand($cmd, opt_Get("-v", \%opt_HH), 0, undef);
push(@early_cmd_A, $cmd);
my $dir_tail = $dir;
$dir_tail =~ s/^.+\///; # remove all but last dir
my $out_root = $dir . "/" . $dir_tail . ".vadr";
#######################
# output program banner
#######################
# output preamble
my @arg_desc_A = ("accession/model name", "output directory");
my @arg_A = ($mdl_name, $dir);
my %extra_H = ();
$extra_H{"\$VADRSCRIPTSDIR"} = $env_vadr_scripts_dir;
$extra_H{"\$VADRINFERNALDIR"} = $env_vadr_infernal_dir;
$extra_H{"\$VADREASELDIR"} = $env_vadr_easel_dir;
$extra_H{"\$VADRBLASTDIR"} = $env_vadr_blast_dir;
ofile_OutputBanner(*STDOUT, $pkgname, $version, $releasedate, $synopsis, $date, \%extra_H);
opt_OutputPreamble(*STDOUT, \@arg_desc_A, \@arg_A, \%opt_HH, \@opt_order_A);
# open the log and command files:
# set output file names and file handles, and open those file handles
my %ofile_info_HH = (); # hash of information on output files we created,
# 1D keys:
# "fullpath": full path to the file
# "nodirpath": file name, full path minus all directories
# "desc": short description of the file
# "FH": file handle to output to for this file, maybe undef
# 2D keys:
# "log": log file of what's output to stdout
# "cmd": command file with list of all commands executed
# open the log and command files
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "log", $out_root . ".log", 1, 1, "Output printed to screen");
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "cmd", $out_root . ".cmd", 1, 1, "List of executed commands");
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "list", $out_root . ".filelist", 1, 1, "List and description of all output files");
my $log_FH = $ofile_info_HH{"FH"}{"log"};
my $cmd_FH = $ofile_info_HH{"FH"}{"cmd"};
my $FH_HR = $ofile_info_HH{"FH"};
# output files are all open, if we exit after this point, we'll need
# to close these first.
# open optional output files
if(opt_Get("--ftrinfo", \%opt_HH)) {
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "ftrinfo", $out_root . ".ftrinfo", 1, 1, "Feature information (created due to --ftrinfo)");
}
if(opt_Get("--sgminfo", \%opt_HH)) {
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "sgminfo", $out_root . ".sgminfo", 1, 1, "Segment information (created due to --sgminfo)");
}
# now we have the log file open, output the banner there too
ofile_OutputBanner($log_FH, $pkgname, $version, $releasedate, $synopsis, $date, \%extra_H);
opt_OutputPreamble($log_FH, \@arg_desc_A, \@arg_A, \%opt_HH, \@opt_order_A);
# output any commands we already executed to $log_FH
foreach $cmd (@early_cmd_A) {
print $cmd_FH $cmd . "\n";
}
#######################################################
# Parse the input minfo file if --addminfo file is used
#######################################################
my $progress_w = 60; # the width of the left hand column in our progress output, hard-coded
my $start_secs;
my $addminfo_file = opt_Get("--addminfo", \%opt_HH);
my @add_mdl_info_AH = ();
my %add_ftr_info_HAH = ();
if(defined $addminfo_file) {
$start_secs = ofile_OutputProgressPrior("Processing --addminfo option", $progress_w, $log_FH, *STDOUT);
my @reqd_mdl_keys_A = ("name");
my @reqd_ftr_keys_A = ("type");
utl_FileValidateExistsAndNonEmpty($addminfo_file, "--addminfo file", undef, 1, $FH_HR);
vdr_ModelInfoFileParse($addminfo_file, \@reqd_mdl_keys_A, \@reqd_ftr_keys_A, \@add_mdl_info_AH, \%add_ftr_info_HAH, $FH_HR);
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
}
###################################################
# Fetch the fasta file (if necessary) and parse it
###################################################
my $fa_file = $out_root . ".fa";
my %seq_H = ();
if(opt_IsUsed("--infa", \%opt_HH)) {
utl_RunCommand("cp " . opt_Get("--infa", \%opt_HH) . " $fa_file", opt_Get("-v", \%opt_HH), 0, $FH_HR);
}
else {
$start_secs = ofile_OutputProgressPrior("Fetching FASTA file", $progress_w, $log_FH, *STDOUT);
vdr_EutilsFetchToFile($fa_file, $mdl_name, "nuccore", "fasta", 5, $ofile_info_HH{"FH"}); # number of attempts to fetch to make before dying
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "fasta", $fa_file, 1, 1, "fasta file for $mdl_name");
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
}
$start_secs = ofile_OutputProgressPrior("Parsing FASTA file", $progress_w, $log_FH, *STDOUT);
vdr_ParseSeqFileToSeqHash($fa_file, \%seq_H, $FH_HR);
my @fetched_seq_A = (sort keys %seq_H);
if(scalar(@fetched_seq_A) != 1) {
ofile_FAIL("ERROR did not fetch exactly 1 sequence from fasta file $fa_file\n", 1, $FH_HR);
}
my $mdl_name_ver = $fetched_seq_A[0];
# make sure it's the right sequence
if($mdl_name_ver =~ /(\S+)\.\d+/) {
if($1 ne $mdl_name) {
ofile_FAIL("ERROR did not fetch correct sequence from fasta file $fa_file (expected accession.version starting with $mdl_name, got $mdl_name_ver)\n", 1, $FH_HR);
}
}
else {
ofile_FAIL("ERROR did not fetch correct sequence from fasta file $fa_file (expected accession.version starting with $mdl_name, got $mdl_name_ver)\n", 1, $FH_HR);
}
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
#######################################################################
# Verify our sequence is not longer than our hard-coded maximum of 25Kb
#######################################################################
# allow any length if --forcelong
my $maxlen = 25000;
my $mdllen = length($seq_H{$mdl_name_ver});
if(! opt_Get("--forcelong", \%opt_HH)) {
if($mdllen > 25000) {
ofile_FAIL("ERROR, model length ($mdllen) exceeds maximum allowed length of $maxlen.\nYou can use --forcelong to bypass this at your own risk.\nUse of VADR on models > 25Kb is not recommended.\nModel building will be very slow and\ndownstream v-annotate.pl annotation will have large memory requirements.", 1, $FH_HR);
}
}
###################################################################
# Fetch the feature table (ft) or GenBank (gb) file (if necessary)
# and parse it.
###################################################################
my $ft_file = undef;
my $gb_file = undef;
my %ftr_info_HAH = (); # the feature info
if(! opt_IsUsed("--gb", \%opt_HH)) {
if(opt_IsUsed("--inft", \%opt_HH)) {
$ft_file = opt_Get("--inft", \%opt_HH);
}
else {
# --inft not used, create ft file by fetching using eutils
$start_secs = ofile_OutputProgressPrior("Fetching feature table file", $progress_w, $log_FH, *STDOUT);
$ft_file = $out_root . ".tbl";
if(opt_Get("--ftfetch1", \%opt_HH)) {
utl_RunCommand("efetch -db nuccore -id $mdl_name -format ft > $ft_file", opt_Get("-v", \%opt_HH), 0, $FH_HR);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "ft", $ft_file, 1, 1, "feature table format file for $mdl_name (--ftfetch1)");
}
elsif(opt_Get("--ftfetch2", \%opt_HH)) {
utl_RunCommand("efetch -db nuccore -id $mdl_name -format gbc | xml2tbl > $ft_file", opt_Get("-v", \%opt_HH), 0, $FH_HR);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "ft", $ft_file, 1, 1, "feature table format file for $mdl_name (--ftfetch2)");
}
else { # default way of fetching a feature table
vdr_EutilsFetchToFile($ft_file, $mdl_name, "nuccore", "ft", 5, $ofile_info_HH{"FH"}); # number of attempts to fetch to make before dying
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "ft", $ft_file, 1, 1, "feature table format file for $mdl_name");
}
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
}
# parse the feature table file
$start_secs = ofile_OutputProgressPrior("Parsing feature table file", $progress_w, $log_FH, *STDOUT);
sqf_FeatureTableParse($ft_file, \%ftr_info_HAH, $FH_HR);
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
# if we have any CDS features with protein_id qualifiers, fetch and parse those
$start_secs = ofile_OutputProgressPrior("Fetching and parsing protein feature table file(s)", $progress_w, $log_FH, *STDOUT);
fetch_and_parse_cds_protein_feature_tables(\@{$ftr_info_HAH{$mdl_name}}, $out_root, $FH_HR);
if(! exists $ftr_info_HAH{$mdl_name}) {
ofile_FAIL("ERROR parsing GenBank file $gb_file, did not read info for reference accession $mdl_name\n", 1, $FH_HR);
}
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
} # end of 'if(! opt_IsUsed("--gb", \%opt_HH))' {
else {
# If --gb (and not --ingb) used: fetch the genbank file
if(opt_IsUsed("--ingb", \%opt_HH)) {
$gb_file = opt_Get("--ingb", \%opt_HH);
}
else {
# --ingb not used, create gb file by fetching using eutils
$start_secs = ofile_OutputProgressPrior("Fetching GenBank file", $progress_w, $log_FH, *STDOUT);
$gb_file = $out_root . ".gb";
vdr_EutilsFetchToFile($gb_file, $mdl_name, "nuccore", "gb", 5, $ofile_info_HH{"FH"}); # number of attempts to fetch to make before dying
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "gb", $gb_file, 1, 1, "GenBank format file for $mdl_name");
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
}
# parse the genbank file
$start_secs = ofile_OutputProgressPrior("Parsing GenBank file", $progress_w, $log_FH, *STDOUT);
sqf_GenbankParse($gb_file, undef, \%ftr_info_HAH, $FH_HR);
if(! exists $ftr_info_HAH{$mdl_name}) {
ofile_FAIL("ERROR parsing GenBank file $gb_file, did not read info for reference accession $mdl_name\n", 1, $FH_HR);
}
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
}
if(exists $ofile_info_HH{"FH"}{"ftrinfo"}) {
utl_AHDump("Feature information", \@{$ftr_info_HAH{$mdl_name}}, $ofile_info_HH{"FH"}{"ftrinfo"});
}
#######################################################
# Prune data read from %ftr_info_HAH, only keeping what
# we want to output to the eventual model info file
#######################################################
$start_secs = ofile_OutputProgressPrior("Pruning data read from GenBank", $progress_w, $log_FH, *STDOUT);
# determine what types of features we will store based on cmdline options
# --fall is incompatible with --fadd
my %fdf_H = (); # default feature types to keep
my %fadd_H = (); # feature types to add
my %fskip_H = (); # feature types to skip
process_add_and_skip_options("CDS,gene,mat_peptide,sig_peptide", "--fadd", "--fskip", undef, \%fdf_H, \%fadd_H, \%fskip_H, undef, \%opt_HH, $FH_HR);
# determine what qualifiers we will store based on cmdline options
# --qall is incompatible with --qadd
my %qdf_H = (); # default qualifiers to keep
my %qadd_H = (); # qualifiers to add
my %qskip_H = (); # qualifiers to skip
my %qftr_add_H = (); # if --qftradd, subset of features to add qualifiers in --qadd option for
process_add_and_skip_options("type,coords,location,product,gene,exception,parent_idx_str,5p_trunc,3p_trunc", "--qadd", "--qskip", "--qftradd", \%qdf_H, \%qadd_H, \%qskip_H, \%qftr_add_H, \%opt_HH, $FH_HR);
# we only need ribosomal_slippage above so we can get the exception:ribosomal slippage
# qualifier, if we switch to parsing feature tables instead of GenBank files, then
# "ribosomal_slippage" should be removed from the list.
# remove all features types we don't want
my $ftr_idx;
for($ftr_idx = 0; $ftr_idx < scalar(@{$ftr_info_HAH{$mdl_name}}); $ftr_idx++) {
my $ftype = $ftr_info_HAH{$mdl_name}[$ftr_idx]{"type"};
# we skip this type and remove it from ftr_info_HAH
# if all three of A1, A2, A3 OR B is satisfied
# (A1) it's not a default feature type AND
# (A2) it's not listed in --fadd AND
# (A3) --fall not used
# OR
# (B) it is listed in --fskip string
if(((! defined $fdf_H{$ftype}) && # (A1)
(! defined $fadd_H{$ftype}) && # (A2)
(! opt_Get("--fall", \%opt_HH))) # (A3)
|| (defined $fskip_H{$ftype})) { # (B)
splice(@{$ftr_info_HAH{$mdl_name}}, $ftr_idx, 1);
$ftr_idx--; # this is about to be incremented
}
}
# deal with special case: remove any CDS features that have "trunc5"
# or "trunc3" keys set as 1 we can't deal with these because we
# don't know how to translate them in v-build.pl and (even if we did
# handle that based on codon_start) v-annotate.pl can't deal with
# these because a start/stop codon is not expected and all complete
# CDS are validated by looking for a start/stop
for($ftr_idx = 0; $ftr_idx < scalar(@{$ftr_info_HAH{$mdl_name}}); $ftr_idx++) {
my $ftype = $ftr_info_HAH{$mdl_name}[$ftr_idx]{"type"};
if(($ftype eq "CDS") &&
(((defined $ftr_info_HAH{$mdl_name}[$ftr_idx]{"trunc5"}) &&
($ftr_info_HAH{$mdl_name}[$ftr_idx]{"trunc5"} == 1)) ||
((defined $ftr_info_HAH{$mdl_name}[$ftr_idx]{"trunc3"}) &&
($ftr_info_HAH{$mdl_name}[$ftr_idx]{"trunc3"} == 1)))) {
ofile_OutputString($log_FH, 1, "\n# WARNING: not modelling CDS feature with coords " . $ftr_info_HAH{$mdl_name}[$ftr_idx]{"coords"} . " because it is 5' and/or 3' truncated\n# (e.g. incomplete, with a \"<\" or \">\" in its coordinates in the feature table.\n#\n# ");
splice(@{$ftr_info_HAH{$mdl_name}}, $ftr_idx, 1);
$ftr_idx--; # this is about to be incremented
}
}
# remove any qualifier key/value pairs with keys not in %qual_H, unless --qall used
for($ftr_idx = 0; $ftr_idx < scalar(@{$ftr_info_HAH{$mdl_name}}); $ftr_idx++) {
my $ftype = $ftr_info_HAH{$mdl_name}[$ftr_idx]{"type"};
foreach my $qual (sort keys %{$ftr_info_HAH{$mdl_name}[$ftr_idx]}) {
# we skip this qualifier and remove it from ftr_info_HAH
# if all three of A1, A2, A3 OR B is satisfied
# (A1) it's not a default qualifier AND
# (A2) (it's not listed in --qadd OR
# (--qftradd is used AND $ftype is not listed in --qftradd)) AND
# (A3) --qall not used
# OR
# (B) it is listed in --qskip string
if(((! defined $qdf_H{$qual}) && # (A1)
((! defined $qadd_H{$qual}) ||
((opt_IsUsed("--qftradd", \%opt_HH)) &&
(! defined $qftr_add_H{$ftype}))) && # (A2)
(! opt_Get("--qall", \%opt_HH))) # (A3)
|| (defined $qskip_H{$qual})) { # (B)
delete $ftr_info_HAH{$mdl_name}[$ftr_idx]{$qual};
}
}
}
if(opt_Get("--gb", \%opt_HH)) {
# Deal with special case: we purposefully added 'ribosomal_slippage' qualifiers if they
# existed just so we could now add 'exception' qualifiers with 'ribosomal slippage' values
# at this stage. This is ONLY to get around problem that GenBank format includes 'ribosomal_slippage'
# qualifiers but not 'exception' qualifiers with 'ribosomal slippage' values, but
# only 'exception:ribosomal slippage' qualifier/values are desired in the
# output feature table. If we switch to parsing Entrez feature tables as input then
# the need for this should go away because 'exception:ribosomal slippage' is in that
# feature table file (along with the unwanted 'ribosomal_slippage' qualifier which
# we can just ignore).
#
# If ribosomal_slippage qualifier exists: create a new "exception"
# qualifier with value of "ribosomal slippage"
#
for($ftr_idx = 0; $ftr_idx < scalar(@{$ftr_info_HAH{$mdl_name}}); $ftr_idx++) {
if((defined $ftr_info_HAH{$mdl_name}[$ftr_idx]) &&
(defined $ftr_info_HAH{$mdl_name}[$ftr_idx]{"ribosomal_slippage"})) {
if(defined $ftr_info_HAH{$mdl_name}[$ftr_idx]{"exception"}) {
$ftr_info_HAH{$mdl_name}[$ftr_idx]{"exception"} .= ":GBSEP:" . "ribosomal slippage";
}
else {
$ftr_info_HAH{$mdl_name}[$ftr_idx]{"exception"} = "ribosomal slippage";
}
# now remove the "ribosomal_slippage" qualifier UNLESS --qall used or $qadd_H{"ribosomal_slippage"} exists
if((! opt_Get("--qall", \%opt_HH)) &&
(! defined $qadd_H{"ribosomal_slippage"})) {
delete $ftr_info_HAH{$mdl_name}[$ftr_idx]{"ribosomal_slippage"};
}
}
}
}
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
####################################################################################
# Change 'type' value for sig_peptide features to 'mat_peptide' (unless --nosig2mat)
####################################################################################
if(! opt_Get("--nosig2mat", \%opt_HH)) {
for($ftr_idx = 0; $ftr_idx < scalar(@{$ftr_info_HAH{$mdl_name}}); $ftr_idx++) {
if((defined $ftr_info_HAH{$mdl_name}[$ftr_idx]) &&
(defined $ftr_info_HAH{$mdl_name}[$ftr_idx]{"type"}) &&
($ftr_info_HAH{$mdl_name}[$ftr_idx]{"type"} eq "sig_peptide")) {
$ftr_info_HAH{$mdl_name}[$ftr_idx]{"type"} = "mat_peptide";
$ftr_info_HAH{$mdl_name}[$ftr_idx]{"out_type"} = "sig_peptide";
}
}
}
###############################################
# Add in features read from --addminfo if used
###############################################
# if --addminfo was used, add the feature info read from that file
if(defined $addminfo_file) {
$start_secs = ofile_OutputProgressPrior("Adding feature info read from --addminfo file", $progress_w, $log_FH, *STDOUT);
if(! defined $add_ftr_info_HAH{$mdl_name}) {
ofile_FAIL("ERROR with --addminfo <s>, <s> must include model $mdl_name, but it does not", 1, $FH_HR);
}
vdr_FeatureInfoMerge(\@{$add_ftr_info_HAH{$mdl_name}}, \@{$ftr_info_HAH{$mdl_name}}, $FH_HR);
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
}
#####################################################################
# Parse the input stockholm file (if --stk) or create it (if ! --stk)
#####################################################################
my $stk_file = $out_root . ".stk";
my $stk_has_ss = undef;
my $in_stk_file = opt_Get("--stk", \%opt_HH);
if(defined $in_stk_file) {
$start_secs = ofile_OutputProgressPrior("Validating input Stockholm file", $progress_w, $log_FH, *STDOUT);
$stk_has_ss = stockholm_validate_single_sequence_input($in_stk_file, $seq_H{$mdl_name_ver}, \%opt_HH, $FH_HR);
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
utl_RunCommand("cp $in_stk_file $stk_file", opt_Get("-v", \%opt_HH), 0, $FH_HR);
}
else {
# --stk not used, we create it from the fasta file we read
$start_secs = ofile_OutputProgressPrior("Reformatting FASTA file to Stockholm file", $progress_w, $log_FH, *STDOUT);
sqf_EslReformatRun($execs_H{"esl-reformat"}, undef, $fa_file, $stk_file, "afa", "stockholm", \%opt_HH, $FH_HR);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "stk", $stk_file, 1, 1, "Stockholm alignment file for $mdl_name");
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
}
###########################
# Build the blastn database
###########################
$start_secs = ofile_OutputProgressPrior("Building BLAST nucleotide database ", $progress_w, $log_FH, *STDOUT);
my $tmp_blastn_fa_file = $out_root . ".fa.tmp";
my $blastn_fa_file = $out_root . ".fa";
sqf_EslReformatRun($execs_H{"esl-reformat"}, "-d -u", $fa_file, $tmp_blastn_fa_file, "fasta", "fasta", \%opt_HH, $FH_HR);
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "blastn-fa", $blastn_fa_file, 1, 1, "nucleotide blastn db fasta sequence file for $mdl_name");
my $nt_sqfile = Bio::Easel::SqFile->new({ fileLocation => $tmp_blastn_fa_file });
my $tmp_seq_name = $nt_sqfile->fetch_seq_name_given_ssi_number(0);
my $tmp_sqstring = $nt_sqfile->fetch_seq_to_sqstring($tmp_seq_name);
printf { $ofile_info_HH{"FH"}{"blastn-fa"} } ">" . $mdl_name . "\n" . seq_SqstringAddNewlines($tmp_sqstring, 60);
close $ofile_info_HH{"FH"}{"blastn-fa"};
# run makeblastdb
sqf_BlastDbCreate($execs_H{"makeblastdb"}, "nucl", $blastn_fa_file, \%opt_HH, $FH_HR);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-nhr", $blastn_fa_file . ".nhr", 1, 1, "BLAST db .nhr file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-nin", $blastn_fa_file . ".nin", 1, 1, "BLAST db .nin file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-nsq", $blastn_fa_file . ".nsq", 1, 1, "BLAST db .nsq file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-ndb", $blastn_fa_file . ".ndb", 1, 1, "BLAST db .ndb file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-not", $blastn_fa_file . ".not", 1, 1, "BLAST db .not file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-ntf", $blastn_fa_file . ".ntf", 1, 1, "BLAST db .ntf file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-nto", $blastn_fa_file . ".nto", 1, 1, "BLAST db .nto file for $mdl_name");
if(! opt_Get("--keep", \%opt_HH)) {
utl_FileRemoveUsingSystemRm($tmp_blastn_fa_file, "v-build.pl main", \%opt_HH, $FH_HR);
if(-e $tmp_blastn_fa_file . ".ssi") {
utl_FileRemoveUsingSystemRm($tmp_blastn_fa_file . ".ssi", "v-build.pl main", \%opt_HH, $FH_HR);
}
}
# index the new file
my $sfetch_cmd = $execs_H{"esl-sfetch"} . " --index $blastn_fa_file > /dev/null";
utl_RunCommand($sfetch_cmd, opt_Get("-v", \%opt_HH), 0, $FH_HR);
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
######################################################################
# Finish populating @{$ftr_info_HAH{$mdl_name} and create @sgm_info_AH
######################################################################
$start_secs = ofile_OutputProgressPrior("Finalizing feature information", $progress_w, $log_FH, *STDOUT);
if(opt_Get("--gb", \%opt_HH)) { # we only need to derive 'coords' if we parsed the GenBank file
vdr_FeatureInfoImputeCoords(\@{$ftr_info_HAH{$mdl_name}}, $FH_HR);
}
vdr_FeatureInfoImputeLength(\@{$ftr_info_HAH{$mdl_name}}, $FH_HR);
vdr_FeatureInfoInitializeParentIndexStrings(\@{$ftr_info_HAH{$mdl_name}}, $FH_HR);
# A special step only needed in v-build.pl (not needed in v-annotate.pl):
# Convert parent_index_str values from the strings they were set to in
# fetch_and_parse_cds_protein_feature_tables to integers, now that all
# feature pruning is complete
integerize_parent_index_strings(\@{$ftr_info_HAH{$mdl_name}}, $FH_HR);
vdr_FeatureInfoImputeOutname(\@{$ftr_info_HAH{$mdl_name}});
# add 'gene' qualifiers to 'CDS' features
if((! opt_Get("--noaddgene", \%opt_HH)) && (! defined $qskip_H{"gene"})) {
vdr_FeatureInfoImputeByOverlap(\@{$ftr_info_HAH{$mdl_name}}, "gene", "gene", "CDS", "gene", $FH_HR);
vdr_FeatureInfoImputeByOverlap(\@{$ftr_info_HAH{$mdl_name}}, "gene", "gene", "mRNA", "gene", $FH_HR);
vdr_FeatureInfoImputeByOverlap(\@{$ftr_info_HAH{$mdl_name}}, "gene", "gene", "regulatory", "gene", $FH_HR);
}
my @sgm_info_AH = (); # segment info, inferred from feature info
vdr_SegmentInfoPopulate(\@sgm_info_AH, \@{$ftr_info_HAH{$mdl_name}}, $FH_HR);
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
###################################
# If any CDS:
# - translate the CDS
# - build BLAST DB
# - build HMMER DB
# - check for valid splice sites
###################################
my $ncds = vdr_FeatureInfoCountType(\@{$ftr_info_HAH{$mdl_name}}, "CDS");
my $cds_fa_file = undef;
my $protein_fa_file = undef;
my $hmm_file = undef;
my $hmmbuild_file = undef;
if($ncds > 0) {
# translate CDS
$start_secs = ofile_OutputProgressPrior("Translating CDS ", $progress_w, $log_FH, *STDOUT);
$cds_fa_file = $out_root . ".cds.fa";
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "cdsfasta", $cds_fa_file, 1, 1, "fasta sequence file for CDS from $mdl_name");
vdr_CdsFetchStockholmToFasta($ofile_info_HH{"FH"}{"cdsfasta"}, $stk_file, \@{$ftr_info_HAH{$mdl_name}}, $FH_HR);
close $ofile_info_HH{"FH"}{"cdsfasta"};
$protein_fa_file = $out_root . ".protein.fa";
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "proteinfasta", $protein_fa_file, 1, 1, "fasta sequence file for translated CDS from $mdl_name");
sqf_EslTranslateCdsToFastaFile($ofile_info_HH{"FH"}{"proteinfasta"}, $execs_H{"esl-translate"}, $cds_fa_file,
$out_root, \@{$ftr_info_HAH{$mdl_name}}, \%opt_HH, $FH_HR);
close $ofile_info_HH{"FH"}{"proteinfasta"};
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
# build blast db
$start_secs = ofile_OutputProgressPrior("Building BLAST protein database ", $progress_w, $log_FH, *STDOUT);
sqf_BlastDbCreate($execs_H{"makeblastdb"}, "prot", $protein_fa_file, \%opt_HH, $FH_HR);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-phr", $protein_fa_file . ".phr", 1, 1, "BLAST db .phr file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-pin", $protein_fa_file . ".pin", 1, 1, "BLAST db .pin file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-psq", $protein_fa_file . ".psq", 1, 1, "BLAST db .psq file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-pdb", $protein_fa_file . ".pdb", 1, 1, "BLAST db .pdb file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-pot", $protein_fa_file . ".pot", 1, 1, "BLAST db .pot file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-ptf", $protein_fa_file . ".ptf", 1, 1, "BLAST db .ptf file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "blastdb-pto", $protein_fa_file . ".pto", 1, 1, "BLAST db .pto file for $mdl_name");
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
# build hmmer db, need to build one HMM per CDS and concatenate them
$start_secs = ofile_OutputProgressPrior("Building HMMER protein database ", $progress_w, $log_FH, *STDOUT);
# run esl-seqstat and parse it
my $protein_sqfile = Bio::Easel::SqFile->new({ fileLocation => $protein_fa_file });
my $nhmm = 0;
my @hmm_file_A = (); # array of names of individual HMM files to be concatenated to make the library
my @hmmbuild_file_A = (); # array of names of individual hmmbuild output files to be concatenated to make the library
for(my $i = 0; $i < $ncds; $i++) {
my $seq_name = $protein_sqfile->fetch_seq_name_given_ssi_number($i);
my $hmm_name = undef;
# remove version from $hmm_name
if($seq_name =~ /^(.+)\.\d+(\/[^\/]+)$/) {
$hmm_name = $1 . $2;
if($hmm_name =~ /[\(\)]/) {
ofile_FAIL("ERROR, illegal sequence name in $protein_fa_file, sequence names can't have ')' or '(' in them", 1, $FH_HR);
}
}
else {
ofile_FAIL("ERROR, unable to parse protein sequence name $seq_name to make HMM model name", 1, $FH_HR);
}
my $tmp_hmm_file = $out_root . "." . ($nhmm+1) . ".hmm";
my $tmp_hmmbuild_file = $out_root . "." . ($nhmm+1) . ".hmmbuild";
my $sfetch_to_hmmbuild_cmd = $execs_H{"esl-sfetch"} . " $protein_fa_file $seq_name | ";
$sfetch_to_hmmbuild_cmd .= $execs_H{"hmmbuild"} . " -n $hmm_name --informat afa $tmp_hmm_file - > $tmp_hmmbuild_file";
utl_RunCommand($sfetch_to_hmmbuild_cmd, opt_Get("-v", \%opt_HH), 0, $FH_HR);
push(@hmm_file_A, $tmp_hmm_file);
push(@hmmbuild_file_A, $tmp_hmmbuild_file);
$nhmm++;
}
$hmm_file = $out_root . ".protein.hmm";
$hmmbuild_file = $out_root . ".protein.hmmbuild";
utl_ConcatenateListOfFiles(\@hmm_file_A, $hmm_file, "v-build.pl main()", \%opt_HH, $FH_HR);
utl_ConcatenateListOfFiles(\@hmmbuild_file_A, $hmmbuild_file, "v-build.pl main()", \%opt_HH, $FH_HR);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "proteinindex", $protein_fa_file . ".ssi", 0, 1, "esl-sfetch index file for $protein_sqfile");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "hmmdb", $hmm_file, 1, 1, "HMMER model db file for $mdl_name");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "hmmbuild", $hmmbuild_file, 1, 1, "hmmbuild build output (concatenated)");
# run hmmpress on it
my $hmmpress_file = $out_root . ".hmmpress";
my $hmmpress_cmd = $execs_H{"hmmpress"} . " $hmm_file > $hmmpress_file";
utl_RunCommand($hmmpress_cmd, opt_Get("-v", \%opt_HH), 0, $FH_HR);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "h3m", $hmm_file . ".h3m", 1, 1, "binary HMM and p7 HMM filter file");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "h3i", $hmm_file . ".h3i", 1, 1, "SSI index for binary HMM file");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "h3f", $hmm_file . ".h3f", 1, 1, "optimized p7 HMM filters (MSV part)");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "h3p", $hmm_file . ".h3p", 1, 1, "optimized p7 HMM filters (remainder)");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "hmmpress", $hmmpress_file, 1, 1, "hmmpress output file");
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
# check splice sites and add canon_splice_sites:"1" if all are valid
if(! opt_Get("--nosplice", \%opt_HH)) {
$start_secs = ofile_OutputProgressPrior("Checking intron splice sites, if any", $progress_w, $log_FH, *STDOUT);
check_and_add_cds_splice_sites($stk_file, \@{$ftr_info_HAH{$mdl_name}}, \@sgm_info_AH, \%opt_HH, $FH_HR);
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
}
}
##############
# Build the CM
##############
my $cm_file = undef;
if(! opt_Get("--skipbuild", \%opt_HH)) {
my $cmbuild_str = undef;
my $clen_times_cmn = length($seq_H{$mdl_name_ver}) * 200;
if(opt_IsUsed("--cmn", \%opt_HH)) {
$clen_times_cmn *= (opt_Get("--cmn", \%opt_HH) / 200);
}
if ($clen_times_cmn > 4000000) { $cmbuild_str = "(may take more than an hour)"; }
elsif($clen_times_cmn > 3000000) { $cmbuild_str = "(should take roughly an hour)"; }
elsif($clen_times_cmn > 2000000) { $cmbuild_str = "(should take roughly 20-40 minutes)"; }
elsif($clen_times_cmn > 1000000) { $cmbuild_str = "(should take roughly 10-30 minutes)"; }
elsif($clen_times_cmn > 500000) { $cmbuild_str = "(should take roughly 5-10 minutes)"; }
else { $cmbuild_str = "(shouldn't take more than a few minutes)"; }
$start_secs = ofile_OutputProgressPrior("Building CM $cmbuild_str", $progress_w, $log_FH, *STDOUT);
# my $cmbuild_occ_file = $out_root . ".cmbuild.occ";
# my $cmbuild_cp9occ_file = $out_root . ".cmbuild.cp9occ";
# my $cmbuild_fp7occ_file = $out_root . ".cmbuild.fp7occ";
# my $cmbuild_opts = "-n $mdl_name --verbose --occfile $cmbuild_occ_file --cp9occfile $cmbuild_cp9occ_file --fp7occfile $cmbuild_fp7occ_file ";
my $cmbuild_opts = "-n $mdl_name --verbose ";
if(opt_IsUsed("--cminfile", \%opt_HH)) {
my @cminfile_A = ();
utl_FileLinesToArray(opt_Get("--cminfile", \%opt_HH), 1, \@cminfile_A, $FH_HR);
foreach my $optline (@cminfile_A) {
chomp $optline;
$cmbuild_opts .= " " . $optline . " ";
}
}
else {
if((! defined $stk_has_ss) || (! $stk_has_ss)) { $cmbuild_opts .= " --noss"; }
if(opt_IsUsed("--cmn", \%opt_HH)) { $cmbuild_opts .= " --EgfN " . opt_Get("--cmn", \%opt_HH); }
if(opt_IsUsed("--cmp7ml", \%opt_HH)) { $cmbuild_opts .= " --p7ml"; }
if(opt_IsUsed("--cmere", \%opt_HH)) { $cmbuild_opts .= " --ere " . opt_Get("--cmere", \%opt_HH); }
if(opt_IsUsed("--cmeset", \%opt_HH)) { $cmbuild_opts .= " --eset " . opt_Get("--cmeset", \%opt_HH); }
if(opt_IsUsed("--cmemaxseq", \%opt_HH)) { $cmbuild_opts .= " --emaxseq " . opt_Get("--cmemaxseq", \%opt_HH); }
if(! opt_IsUsed("--cmnoh3pri", \%opt_HH)) { $cmbuild_opts .= " --noh3pri"; }
}
# if model is big > 0.5 * 25Kb (maxlen), then use the --Egcmult option
# this avoids problems and slowness with very large sequence lengths for glocal HMM calibration
if($mdllen > (0.5 * $maxlen)) {
$cmbuild_opts .= " --Egcmult " . sprintf("%.5f", ($maxlen / $mdllen));
}
my $cmbuild_file = $out_root . ".cmbuild";
$cm_file = $out_root . ".cm";
my $cmbuild_cmd = $execs_H{"cmbuild"} . " " . $cmbuild_opts . " $cm_file $stk_file > $cmbuild_file";
utl_RunCommand($cmbuild_cmd, opt_Get("-v", \%opt_HH), 0, $ofile_info_HH{"FH"});
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "cm", $cm_file, 1, 1, "CM file");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "cmbuild", $cmbuild_file, 1, 1, "cmbuild output file");
# press the file we just created
$start_secs = ofile_OutputProgressPrior("Pressing CM file", $progress_w, $log_FH, *STDOUT);
my $cmpress_file = $out_root . ".cmpress";
my $cmpress_cmd = $execs_H{"cmpress"} . " $cm_file > $cmpress_file";
utl_RunCommand($cmpress_cmd, opt_Get("-v", \%opt_HH), 0, $ofile_info_HH{"FH"});
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "i1m", $cm_file . ".i1m", 1, 1, "binary CM and p7 HMM filter file");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "i1i", $cm_file . ".i1i", 1, 1, "SSI index for binary CM file");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "i1f", $cm_file . ".i1f", 1, 1, "optimized p7 HMM filters (MSV part)");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "i1p", $cm_file . ".i1p", 1, 1, "optimized p7 HMM filters (remainder)");
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "cmpress", $cmpress_file, 1, 1, "cmpress output file");
}
########################
# Output model info file
########################
$start_secs = ofile_OutputProgressPrior("Creating model info file", $progress_w, $log_FH, *STDOUT);
# create @mdl_info_AH, and add info for our lone model
# modelInfoFileWrite() can output data for multiple models at once,
# but we use it here only for a single model.
my @mdl_info_AH = ();
%{$mdl_info_AH[0]} = ();
$mdl_info_AH[0]{"name"} = $mdl_name;
$mdl_info_AH[0]{"length"} = length($seq_H{$mdl_name_ver});
if(defined $cm_file) {
$mdl_info_AH[0]{"cmfile"} = utl_RemoveDirPath($cm_file);
}
if($ncds > 0) {
$mdl_info_AH[0]{"blastdb"} = utl_RemoveDirPath($protein_fa_file);
if((opt_IsUsed("--ttbl", \%opt_HH)) && (opt_Get("--ttbl", \%opt_HH) != 1)) {
$mdl_info_AH[0]{"transl_table"} = opt_Get("--ttbl", \%opt_HH);
}
}
if(opt_IsUsed("--group", \%opt_HH)) {
$mdl_info_AH[0]{"group"} = opt_Get("--group", \%opt_HH);
if(opt_IsUsed("--subgroup", \%opt_HH)) {
$mdl_info_AH[0]{"subgroup"} = opt_Get("--subgroup", \%opt_HH);
}
}
my $modelinfo_file = $out_root . ".minfo";
vdr_ModelInfoFileWrite($modelinfo_file, \@mdl_info_AH, \%ftr_info_HAH, $FH_HR);
ofile_AddClosedFileToOutputInfo(\%ofile_info_HH, "modelinfo", $modelinfo_file, 1, 1, "VADR 'model info' format file for $mdl_name");
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
##########
# Conclude
##########
# output optional output files
if(exists $ofile_info_HH{"FH"}{"ftrinfo"}) {
utl_AHDump("Feature information", \@{$ftr_info_HAH{$mdl_name}}, $ofile_info_HH{"FH"}{"ftrinfo"});
}
if(exists $ofile_info_HH{"FH"}{"sgminfo"}) {
utl_AHDump("Segment information", \@sgm_info_AH, $ofile_info_HH{"FH"}{"sgminfo"});
}
$total_seconds += ofile_SecondsSinceEpoch();
ofile_OutputConclusionAndCloseFilesOk($total_seconds, $dir, \%ofile_info_HH);
exit 0;
###############
# SUBROUTINES #
###############
#################################################################
# Subroutine: stockholm_validate_single_sequence_input()
# Incept: EPN, Fri Mar 15 13:19:32 2019
#
# Synopsis: Validate an input Stockholm file is in the correct
# format, has exactly 1 sequence and no gaps.
#
# Arguments:
# $in_stk_file: input stockholm file to validate
# $exp_sqstring: sequence we expect to be in the stockholm alignment
# $opt_HHR: REF to 2D hash of option values, see top of sqp_opts.pm for description, PRE-FILLED
# $FH_HR: REF to hash of file handles, including "log" and "cmd"
#
# Returns: '1' if Stockholm file has SS_cons annotation, else '0'
#
# Dies: if there's a problem parsing the file or
# a requirement is not met
#################################################################
sub stockholm_validate_single_sequence_input {
my $sub_name = "stockholm_validate_single_sequence_input";
my $nargs_expected = 4;
if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
my ($in_stk_file, $exp_sqstring, $opt_HHR, $FH_HR) = @_;
if(! -e $in_stk_file) { ofile_FAIL("ERROR, --stk enabled, stockholm file $in_stk_file does not exist", 1, $FH_HR); }
if(! -s $in_stk_file) { ofile_FAIL("ERROR, --stk enabled, stockholm file $in_stk_file exists but is empty", 1, $FH_HR); }
if( -d $in_stk_file) { ofile_FAIL("ERROR, --stk enabled, stockholm file $in_stk_file is actually a directory", 1, $FH_HR); }
my $msa = Bio::Easel::MSA->new({ fileLocation => $in_stk_file, isDna => 1});
my $nseq = $msa->nseq;
if($nseq == 1) {
# single sequence, make sure there are no gaps
if($msa->any_allgap_columns) {
ofile_FAIL("ERROR, read 1 sequence in --stk file $in_stk_file, but it has gaps, this is not allowed for single sequence 'alignments' (remove gaps with 'esl-reformat --mingap')", 1, $FH_HR);
}
# validate it matches $exp_sqstring
my $fetched_sqstring = $msa->get_sqstring_unaligned(0);
seq_SqstringCapitalize(\$fetched_sqstring);
seq_SqstringCapitalize(\$exp_sqstring);
seq_SqstringDnaize(\$fetched_sqstring);
seq_SqstringDnaize(\$exp_sqstring);
if($fetched_sqstring ne $exp_sqstring) {
my $summary_sqstring_diff_str = seq_SqstringDiffSummary($fetched_sqstring, $exp_sqstring);
ofile_FAIL("ERROR, read 1 sequence in --stk file $in_stk_file, but it does not match sequence read from GenBank file $gb_file:\n$summary_sqstring_diff_str", 1, $FH_HR);
}
}
else { # nseq != 1
ofile_FAIL("ERROR, did not read exactly 1 sequence in --stk file $in_stk_file.\nTo use VADR with models built from alignments of multiple sequences,\nyou will have to build the CM with cmbuild and create the model info file manually.\n", 1, $FH_HR);
}
return $msa->has_ss_cons;
}
#################################################################
# Subroutine: process_add_and_skip_options()
# Incept: EPN, Mon Mar 18 06:29:21 2019
#
# Synopsis: Process cmdline --{f,q}add and --{f,q}skip options
# for features or qualifiers.
#
# Arguments:
# $df_string: comma separated string of default values (e.g. "CDS,gene,mat_peptide,sig_peptide")
# $add_opt: name of add option (e.g. "--fadd")