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v-test.pl
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v-test.pl
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#!/usr/bin/env perl
#
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;
require "vadr.pm";
require "sqp_opts.pm";
require "sqp_ofile.pm";
require "sqp_utils.pm";
#########################################################
# 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 ','
# "incompatible": 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 = ();
# 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{"1"} = "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, 1, undef, undef, "forcing directory overwrite", "force; if dir <output directory> exists, overwrite it", \%opt_HH, \@opt_order_A);
opt_Add("-v", "boolean", 0, 1, undef, undef, "be verbose", "be verbose; output commands to stdout as they're run", \%opt_HH, \@opt_order_A);
opt_Add("-s", "boolean", 0, 1, undef, "--rmout", "skip commands, they were already run, just compare files", "skip commands, they were already run, just compare files", \%opt_HH, \@opt_order_A);
opt_Add("-m", "boolean", 0, 1,"--noteamcity", undef, "benchmark mode: compare certain fields, do not diff", "benchmark mode: compare certain fields, do not diff files", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{"2"} = "options for defining variables in testing files";
# option type default group requires incompat preamble-output help-output
#opt_Add("--dirbuild", "string", undef, 2, undef, undef, "build directory, replaces !dirbuild! in test file with <s>", "build directory, replaces !dirbuild! in test file with <s>", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{"3"} = "other options";
opt_Add("--rmout", "boolean", 0, 3, undef, "-s", "if output files listed in testin file already exist, remove them", "if output files listed in testin file already exist, remove them", \%opt_HH, \@opt_order_A);
opt_Add("--keep", "boolean", 0, 3, undef, undef, "leaving intermediate files on disk", "do not remove intermediate files, keep them all on disk", \%opt_HH, \@opt_order_A);
opt_Add("--noteamcity", "boolean", 0, 3, undef, undef, "do not output teamcity test info", "do not output teamcity test info", \%opt_HH, \@opt_order_A);
opt_Add("--skipmsg", "boolean", 0, 3, undef, undef, "do not compare errors and warnings", "do not compare errors and warning lines", \%opt_HH, \@opt_order_A);
$opt_group_desc_H{"4"} = "other expert options";
# option type default group requires incompat preamble-output help-output
opt_Add("--execname", "string", undef, 4, undef, undef, "define executable name of this script as <s>", "define executable name of this script as <s>", \%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"},
'v' => \$GetOptions_H{"-v"},
'f' => \$GetOptions_H{"-f"},
's' => \$GetOptions_H{"-s"},
'm' => \$GetOptions_H{"-m"},
# 'dirbuild=s' => \$GetOptions_H{"--dirbuild"},
'rmout' => \$GetOptions_H{"--rmout"},
'keep' => \$GetOptions_H{"--keep"},
'noteamcity' => \$GetOptions_H{"--noteamcity"},
'skipmsg' => \$GetOptions_H{"--skipmsg"},
'execname=s' => \$GetOptions_H{"--execname"});
my $total_seconds = -1 * ofile_SecondsSinceEpoch(); # by multiplying by -1, we can just add another secondsSinceEpoch call at end to get total time
my $execname_opt = $GetOptions_H{"--execname"};
my $executable = (defined $execname_opt) ? $execname_opt : "v-test.pl";
my $usage = "Usage: $executable [-options] <input test file e.g. testfiles/testin.1> <output directory to create>\n";
my $synopsis = "$executable :: test VADR scripts [TEST SCRIPT]";
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
}
# set options in opt_HH
opt_SetFromUserHash(\%GetOptions_H, \%opt_HH);
# validate options (check for conflicts)
opt_ValidateSet(\%opt_HH, \@opt_order_A);
# 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 $executable -h\n\n";
exit(1);
}
my ($test_file, $dir) = (@ARGV);
#############################
# 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 . "/" . $dir_tail . ".vadr";
#############################################
# output program banner and open output files
#############################################
# output preamble
my @arg_desc_A = ("test file", "output directory");
my @arg_A = ($test_file, $dir);
ofile_OutputBanner(*STDOUT, $pkgname, $version, $releasedate, $synopsis, $date, undef);
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 (at least initially)
# "log": log file of what's output to stdout
# "cmd": command file with list of all commands executed
# "list": file with list of all output files created
# 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 . ".list", 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 = $ofile_info_HH{"FH"};
# output files are all open, if we exit after this point, we'll need
# to close these first.
# now we have the log file open, output the banner there too
ofile_OutputBanner($log_FH, $pkgname, $version, $releasedate, $synopsis, $date, undef);
opt_OutputPreamble($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";
}
# are we running in 'benchmark' mode?
my $do_mark = opt_Get("-m", \%opt_HH);
# read in the test file
my $progress_w = 50; # the width of the left hand column in our progress output, hard-coded
my $start_secs = ofile_OutputProgressPrior("Parsing test file", $progress_w, $log_FH, *STDOUT);
my @cmd_A = (); # array of the commands to run
my @desc_A = (); # array of the descriptions for the commands
my @outfile_AA = (); # array of arrays of output files to compare for each command
my @expfile_AA = (); # array of arrays of expected files to compare output to for each command
my @cmpstr_AA = (); # array of arrays of 'compare' strings, to compare output to for each command, used only in benchmark mode (-m)
my @rmdir_AA = (); # array of directories to remove after each command is completed
my $do_teamcity = opt_Get("--noteamcity", \%opt_HH) ? 0 : 1;
my $ncmd = parse_test_or_mark_file($test_file, \@cmd_A, \@desc_A, \@outfile_AA, \@expfile_AA, \@cmpstr_AA, \@rmdir_AA, \%opt_HH, $ofile_info_HH{"FH"});
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
my $npass = 0;
my $nfail = 0;
my $w_cmpcat = 20;
my @data_pertest_AA = (); # pertest file data, only used if -m
my @data_perline_AA = (); # perline file data, only used if -m
my @data_perval_AA = (); # perval file data, only used if -m
for(my $i = 1; $i <= $ncmd; $i++) {
my $cmd = $cmd_A[($i-1)];
my $desc = $desc_A[($i-1)];
if($do_teamcity) {
ofile_OutputString($log_FH, 1, sprintf("##teamcity[testStarted name='$desc' captureStandardOutput='true']\n"));
}
my $outfile_AR = \@{$outfile_AA[($i-1)]};
my $expfile_AR = ($do_mark) ? undef : \@{$expfile_AA[($i-1)]};
my $cmpstr_AR = ($do_mark) ? \@{$cmpstr_AA[($i-1)]} : undef;
my $rmdir_AR = \@{$rmdir_AA[($i-1)]};
my $npass_i = 0; # number of tests that passed for current cmd
my $nfail_i = 0; # number of tests that failed for current cmd
if((opt_IsUsed("-s", \%opt_HH)) && (opt_Get("-s", \%opt_HH))) {
# -s used, we aren't running commands, just comparing files
$start_secs = ofile_OutputProgressPrior(sprintf("Skipping command %2d [%20s]", $i, $desc_A[($i-1)]), $progress_w, $log_FH, *STDOUT);
}
else {
# -s not used, run command
$start_secs = ofile_OutputProgressPrior(sprintf("Running command %2d [%20s]", $i, $desc_A[($i-1)]), $progress_w, $log_FH, *STDOUT);
utl_RunCommand($cmd, opt_Get("-v", \%opt_HH), 1, $ofile_info_HH{"FH"}); # 1: do not fail if command fails
}
ofile_OutputProgressComplete($start_secs, undef, $log_FH, *STDOUT);
my $nout = scalar(@{$outfile_AR});
for(my $j = 0; $j < $nout; $j++) {
if($do_mark) {
my @outfields_A = ();
my @cmpfields_A = ();
my ($cmpcat, $cmpfile) = parse_cmpstr($cmpstr_AR->[$j], \@outfields_A, \@cmpfields_A, $ofile_info_HH{"FH"});
my $desccat = $desc . ":" . $cmpcat;
my ($nlines, $nidentical, $ndifferent) = compare_two_files($desccat, $i.".".($j+1), $outfile_AR->[$j], $cmpfile, \@outfields_A, \@cmpfields_A, \@data_perline_AA, \@data_perval_AA, $ofile_info_HH{"FH"});
my $idx = $i . "." . ($j+1);
push(@data_pertest_AA, [$idx, $cmpcat, $nlines, $nidentical, $ndifferent,
sprintf("%7.5f", ($nidentical / $nlines)),
sprintf("%7.5f", ($ndifferent / $nlines))]);
}
else { # default -m not enabled
my $diff_file = $out_root . "." . $i . "." . ($j+1) . ".diff";
my $pass = diff_two_files($outfile_AR->[$j], $expfile_AR->[$j], $diff_file, \%opt_HH, $ofile_info_HH{"FH"});
if($pass) { $npass++; $npass_i++; }
else { $nfail++; $nfail_i++; }
}
}
if(($nfail_i == 0) && (! opt_Get("--keep", \%opt_HH))) { # only remove dir if no tests failed
my $nrmdir = (defined $rmdir_AR) ? scalar(@{$rmdir_AR}) : 0;
for(my $k = 0; $k < $nrmdir; $k++) {
ofile_OutputString($log_FH, 1, sprintf("#\t%-60s ... ", "removing directory $rmdir_AR->[$k]"));
utl_RunCommand("rm -rf $rmdir_AR->[$k]", opt_Get("-v", \%opt_HH), 0, $ofile_info_HH{"FH"});
ofile_OutputString($log_FH, 1, "done\n");
}
}
if($do_teamcity) {
if($nfail_i > 0) {
ofile_OutputString($log_FH, 1, sprintf("##teamcity[testFailed name='$desc' message='v-test.pl failure']\n"));
}
ofile_OutputString($log_FH, 1, sprintf("##teamcity[testFinished name='$desc']\n"));
}
}
##########
# Conclude
##########
if(! $do_mark) {
# summarize number of files checked and passed
my $overall_pass = ($nfail == 0) ? 1 : 0;
ofile_OutputString($log_FH, 1, "#\n#\n");
if($overall_pass) {
ofile_OutputString($log_FH, 1, "# PASS: all $npass files were created correctly.\n");
$total_seconds += ofile_SecondsSinceEpoch();
ofile_OutputConclusionAndCloseFilesOk($total_seconds, $dir, \%ofile_info_HH);
}
else {
ofile_OutputString($log_FH, 1, sprintf("# FAIL: %d of %d files were not created correctly.\n", $nfail, $npass+$nfail));
$total_seconds += ofile_SecondsSinceEpoch();
ofile_OutputConclusionAndCloseFilesFail($total_seconds, $dir, \%ofile_info_HH);
ofile_FAIL("ERROR, at least one test FAILed", 1, undef);
}
}
else {
# -m enabled, output summary files
my @head_pertest_AA = ();
@{$head_pertest_AA[0]} = ("test", "", "number", "number", "number", "fraction", "fraction");
@{$head_pertest_AA[1]} = ("index", "category", "comparisons", "identical", "different", "identical", "different");
my @clj_pertest_A = (1, 1, 0, 0, 0, 0, 0);
# data already added to @data_pertest_AA above
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "pertest", $out_root . ".pertest", 1, 1, "per-test tabular summary file");
ofile_TableHumanOutput(\@data_pertest_AA, \@head_pertest_AA, \@clj_pertest_A, undef, undef, " ", "-", "#", "#", "", 1, $FH_HR->{"pertest"}, undef, $FH_HR);
close($ofile_info_HH{"FH"}{"pertest"});
my @head_perline_AA = ();
@{$head_perline_AA[0]} = ("line", "description+", "anchor", "expected", "observed", "identical/");
@{$head_perline_AA[1]} = ("index", "category", "data", "data", "data", "different");
my @clj_perline_A = (1, 1, 1, 1, 1, 1);
# data already added to @data_perline_AA above
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "perline", $out_root . ".perline", 1, 1, "per-line tabular summary file");
ofile_TableHumanOutput(\@data_perline_AA, \@head_perline_AA, \@clj_perline_A, undef, undef, " ", "-", "#", "#", "", 0, $FH_HR->{"perline"}, undef, $FH_HR);
close($ofile_info_HH{"FH"}{"perline"});
my @head_perval_AA = ();
@{$head_perval_AA[0]} = ("value", "description+", "", "number", "number", "number", "fraction", "fraction");
@{$head_perval_AA[1]} = ("index", "category", "value", "comparisons", "identical", "different", "identical", "different");
my @clj_perval_A = (1, 1, 1, 0, 0, 0, 0, 0);
# data already added to @data_perval_AA above
ofile_OpenAndAddFileToOutputInfo(\%ofile_info_HH, "perval", $out_root . ".perval", 1, 1, "per-value tabular summary file");
ofile_TableHumanOutput(\@data_perval_AA, \@head_perval_AA, \@clj_perval_A, undef, undef, " ", "-", "#", "#", "", 0, $FH_HR->{"perval"}, undef, $FH_HR);
close($ofile_info_HH{"FH"}{"perval"});
my @conclude_A = ();
push(@conclude_A, "#");
push(@conclude_A, "# Summary of comparison tests:");
push(@conclude_A, "#");
my @file_A = ();
utl_FileLinesToArray($ofile_info_HH{"fullpath"}{"pertest"}, 1, \@file_A, $FH_HR);
push(@conclude_A, @file_A);
push(@conclude_A, "#");
foreach my $line (@conclude_A) {
ofile_OutputString($log_FH, 1, $line . "\n");
}
}
exit 0;
#################################################################
# Subroutine: parse_test_or_mark_file()
# Incept: EPN, Wed May 16 16:03:40 2018
#
# Purpose: Parse an input test or mark file and store the relevant
# information in passed in array references.
#
# Arguments:
# $testfile: name of file to parse
# $cmd_AR: ref to array of commands to fill here
# $desc_AR: ref to array of descriptions to fill here
# $outfile_AAR: ref to 2D array of output files to fill here
# $expfile_AAR: ref to 2D array of expected files to fill here
# $cmpstr_AAR: ref to 2D array of compare strings to fill here, only if -m
# $rmdir_AAR: ref to 2D array of directories to remove after calling each command
# $opt_HHR: ref to 2D hash of option values, see top of sqp_opts.pm for description
# $FH_HR: ref to hash of file handles, including "log" and "cmd"
#
# Returns: number of commands read in $testfile
#
# Dies: - if any of the expected files do not exist
# - if number of expected files is not equal to number of output files
# for any command
# - if there are 0 output files for a given command
# - if output file already exists
# - if any desc values are duplicates
#################################################################
sub parse_test_or_mark_file {
my $sub_name = "parse_test_or_mark_file";
my $nargs_expected = 9;
if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
my ($testfile, $cmd_AR, $desc_AR, $outfile_AAR, $expfile_AAR, $cmpstr_AAR, $rmdir_AAR, $opt_HHR, $FH_HR) = @_;
my $do_mark = opt_Get("-m", $opt_HHR);
open(IN, $testfile) || ofile_FileOpenFailure($testfile, $sub_name, $!, "reading", $FH_HR);
my $ncmd = 0;
my $ndesc = 0;
my $outfile;
my $expfile;
my $rmdir;
my %desc_H = (); # used to prevent two desc from being identical
while(my $line = <IN>) {
if(($line !~ m/^\#/) && ($line =~ m/\w/)) {
# example input file:
# # comment line (ignored)
#command: perl $VADRSCRIPTSDIR/v-annotate.pl -f $VADRSCRIPTSDIR/testfiles/dengue.r5.fa va-dengue.r5 > va-dengue.r5.out
#desc: annotate-dengue-5-local
#out: va-dengue.r5/va-dengue.r5.vadr.pass.ft
#exp: @VADRSCRIPTSDIR@/testfiles/expected-files/va-dengue.r5/va-dengue.r5.vadr.pass.ft
chomp $line;
if($line =~ m/\r$/) { chop $line; } # remove ^M if it exists
if($line =~ s/^command\:\s+//) {
my $cmd = $line;
if($ncmd > 0) {
# make sure we have read >= 1 outfiles and expfiles for previous command
if(! (@{$outfile_AAR->[($ncmd-1)]})) { ofile_FAIL("ERROR did not read any out: lines for command " . ($ncmd+1), 1, $FH_HR); }
my $nout_prv = scalar(@{$outfile_AAR->[($ncmd-1)]});
if($do_mark) {
if(! (@{$cmpstr_AAR->[($ncmd-1)]})) { ofile_FAIL("ERROR did not read any cmp: lines for command " . ($ncmd+1), 1, $FH_HR); }
my $ncmp_prv = scalar(@{$cmpstr_AAR->[($ncmd-1)]});
if($nout_prv != $ncmp_prv) {
ofile_FAIL("ERROR different number of output and compare lines for command " . ($ncmd+1), 1, $FH_HR);
}
}
else {
if(! (@{$expfile_AAR->[($ncmd-1)]})) { ofile_FAIL("ERROR did not read any exp: lines for command " . ($ncmd+1), 1, $FH_HR); }
my $nexp_prv = scalar(@{$expfile_AAR->[($ncmd-1)]});
if($nout_prv != $nexp_prv) {
ofile_FAIL("ERROR different number of output and expected lines for command " . ($ncmd+1), 1, $FH_HR);
}
}
}
# replace !<s>! with value of --<s> from options, die if it wasn't set or doesn't exist
while($cmd =~ /\!(\w+)\!/) {
my $var = $1;
my $varopt = "--" . $var;
if(! opt_Exists($varopt, $opt_HHR)) {
ofile_FAIL("ERROR trying to replace !$var! in test file but option --$var does not exist in command line options", 1, $FH_HR);
}
if(! opt_IsUsed($varopt, $opt_HHR)) {
ofile_FAIL("ERROR trying to replace !$var! in test file but option --$var was not specified on the command line, please rerun with --$var", 1, $FH_HR);
}
my $replacevalue = opt_Get($varopt, $opt_HHR);
$cmd =~ s/\!$var\!/$replacevalue/g;
}
push(@{$cmd_AR}, $cmd);
$ncmd++;
}
elsif($line =~ s/^desc\:\s+//) {
my $desc = $line;
if(defined $desc_H{$desc}) {
ofile_FAIL("ERROR read desc $desc twice in $testfile", 1, $FH_HR);
}
push(@{$desc_AR}, $desc);
$desc_H{$desc} = 1;
$ndesc++;
}
elsif($line =~ s/^out\:\s+//) {
$outfile = $line;
$outfile =~ s/^\s+//;
$outfile =~ s/\s+$//;
if($outfile =~ m/\s/) { ofile_FAIL("ERROR output file has spaces: $outfile", 1, $FH_HR); }
if(scalar(@{$outfile_AAR}) < $ncmd) {
@{$outfile_AAR->[($ncmd-1)]} = ();
}
push(@{$outfile_AAR->[($ncmd-1)]}, $outfile);
if((opt_IsUsed("-s", $opt_HHR)) && (opt_Get("-s", $opt_HHR))) {
# -s used, we aren't running commands, just comparing files, output files must already exist
if(! -e $outfile) { ofile_FAIL("ERROR, output file $outfile does not already exist (and -s used)", 1, $FH_HR); }
}
elsif((opt_IsUsed("--rmout", $opt_HHR)) && (opt_Get("--rmout", $opt_HHR))) {
# --rmout used, remove any file that already exists
if(-e $outfile) { utl_FileRemoveUsingSystemRm($outfile, "v-test.pl", $opt_HHR, $FH_HR); }
}
else { # -s not used, --rmout not used
if(-e $outfile) { ofile_FAIL("ERROR, output file $outfile already exists (and -s/--rmout not used)", 1, $FH_HR); }
}
}
elsif($line =~ s/^exp\:\s+//) {
if($do_mark) { ofile_FAIL("ERROR, read exp line but -m enabled", 1, $FH_HR); }
$expfile = $line;
$expfile =~ s/^\s+//;
$expfile =~ s/\s+$//;
# replace @<s>@ with value of $ENV{'<s>'}
while($expfile =~ /\@(\w+)\@/) {
my $envvar = $1;
my $replacevalue = $ENV{"$envvar"};
$expfile =~ s/\@$envvar\@/$replacevalue/g;
}
if($expfile =~ m/\s/) { ofile_FAIL("ERROR expected file has spaces: $expfile", 1, $FH_HR) }
if(scalar(@{$expfile_AAR}) < $ncmd) {
@{$expfile_AAR->[($ncmd-1)]} = ();
}
push(@{$expfile_AAR->[($ncmd-1)]}, $expfile);
if(! -e $expfile) { ofile_FAIL("ERROR, expected file $expfile does not exist", 1, $FH_HR); }
}
elsif($line =~ s/^cmp\:\s+//) {
if(! $do_mark) { ofile_FAIL("ERROR, read cmp line but -m not enabled", 1, $FH_HR); }
# expect 4 tokens:
# cmp: <category>:<comma-separated-out-fields>:<comma-separated-cmp-fields>:<cmp-file-path>
my $cmpstr = $line;
$cmpstr =~ s/^\s+//;
$cmpstr =~ s/\s+$//;
# replace @<s>@ with value of $ENV{'<s>'}
while($cmpstr =~ /\@(\w+)\@/) {
my $envvar = $1;
my $replacevalue = $ENV{"$envvar"};
$cmpstr =~ s/\@$envvar\@/$replacevalue/g;
}
if($cmpstr =~ m/\s/) { ofile_FAIL("ERROR compare string has spaces: $expfile", 1, $FH_HR) }
if(scalar(@{$cmpstr_AAR}) < $ncmd) {
@{$cmpstr_AAR->[($ncmd-1)]} = ();
}
push(@{$cmpstr_AAR->[($ncmd-1)]}, $cmpstr);
# validate the line, we don't store this info, we reparse it when needed
my ($cmpcat, $cmpfile) = parse_cmpstr($line, undef, undef, $FH_HR);
}
elsif($line =~ s/^rmdir\:\s+//) {
$rmdir = $line;
$rmdir =~ s/^\s+//;
$rmdir =~ s/\s+$//;
if(scalar(@{$rmdir_AAR}) < $ncmd) {
@{$rmdir_AAR->[($ncmd-1)]} = ();
}
push(@{$rmdir_AAR->[($ncmd-1)]}, $rmdir);
}
else {
ofile_FAIL("ERROR unable to parse line $line in $testfile", 1, $FH_HR);
}
}
}
close(IN);
if($ndesc != $ncmd) { ofile_FAIL("ERROR did not read same number of descriptions and commands", 1, $FH_HR); }
# for final command, check that number of exp and out files is equal
if(! (@{$outfile_AAR->[($ncmd-1)]})) { ofile_FAIL("ERROR did not read any out: lines for command " . ($ncmd+1), 1, $FH_HR); }
my $nout_prv = scalar(@{$outfile_AAR->[($ncmd-1)]});
if($do_mark) {
if(! (@{$cmpstr_AAR->[($ncmd-1)]})) { ofile_FAIL("ERROR did not read any cmp: lines for command " . ($ncmd+1), 1, $FH_HR); }
my $ncmp_prv = scalar(@{$cmpstr_AAR->[($ncmd-1)]});
if($nout_prv != $ncmp_prv) {
ofile_FAIL("ERROR different number of output and compare lines for command " . ($ncmd+1), 1, $FH_HR);
}
}
else {
if(! (@{$expfile_AAR->[($ncmd-1)]})) { ofile_FAIL("ERROR did not read any exp: lines for command " . ($ncmd+1), 1, $FH_HR); }
my $nexp_prv = scalar(@{$expfile_AAR->[($ncmd-1)]});
if($nout_prv != $nexp_prv) {
ofile_FAIL("ERROR different number of output and expected lines for command " . ($ncmd+1), 1, $FH_HR);
}
}
return $ncmd;
}
#################################################################
# Subroutine: diff_two_files()
# Incept: EPN, Thu May 17 14:24:06 2018
#
# Purpose: Diff two files, and output whether they are identical or not.
#
# Arguments:
# $out_file: name of output file
# $exp_file: name of expected file
# $diff_file: output file for diff command
# $opt_HHR: REF to 2D hash of option values, see top of sqp_opts.pm for description
# $FH_HR: REF to hash of file handles, including "log" and "cmd"
#
# Returns: '1' if $outfile is identical to $expfile as determined by diff
#
# Dies: If an expected file does not exist or is empty.
#
#################################################################
sub diff_two_files {
my $sub_name = "diff_two_files";
my $nargs_expected = 5;
if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
my ($out_file, $exp_file, $diff_file, $opt_HHR, $FH_HR) = @_;
my $out_file_exists = (-e $out_file) ? 1 : 0;
my $exp_file_exists = (-e $exp_file) ? 1 : 0;
my $out_file_nonempty = (-s $out_file) ? 1 : 0;
my $exp_file_nonempty = (-s $exp_file) ? 1 : 0;
my $conclusion = "";
my $pass = 0;
if(! $exp_file_exists) {
ofile_FAIL("ERROR in $sub_name, expected file $exp_file does not exist", 1, $FH_HR) ;
}
ofile_OutputString($FH_HR->{"log"}, 1, sprintf("#\tchecking %-100s ... ", $out_file));
if($out_file_exists) {
utl_RunCommand("diff -U 0 $out_file $exp_file > $diff_file", opt_Get("-v", $opt_HHR), 1, $FH_HR); # 1: don't die if command fails
if(-s $diff_file) {
# copy the two files here:
my $copy_of_out_file = $diff_file . ".out";
my $copy_of_exp_file = $diff_file . ".exp";
utl_RunCommand("cp $out_file $copy_of_out_file", opt_Get("-v", $opt_HHR), 0, $FH_HR);
utl_RunCommand("cp $exp_file $copy_of_exp_file", opt_Get("-v", $opt_HHR), 0, $FH_HR);
# analyze the diff file and print out how many lines
if($out_file =~ m/\.sqtable/ && $exp_file =~ m/\.sqtable/) {
if($out_file_nonempty && $exp_file_nonempty) {
my $sqtable_diff_file = $diff_file . ".man";
compare_two_sqtable_files($out_file, $exp_file, $sqtable_diff_file, \%opt_HH, $FH_HR);
$conclusion = "FAIL [files differ, see $sqtable_diff_file]";
}
else {
if(! $exp_file_nonempty) {
$conclusion = "FAIL [files differ, expected file is empty, but output file is not (see $diff_file)]";
}
elsif(! $out_file_nonempty) {
$conclusion = "FAIL [files differ, output file is empty, but expected file is not (see $diff_file)]";
}
else {
ofile_FAIL("ERROR in $sub_name, unexpected case exp_file_nonempty: $exp_file_nonempty out_file_nonempty: $out_file_nonempty", 1, $FH_HR) ;
}
}
}
else {
$conclusion = "FAIL [files differ, see $diff_file]";
}
}
else {
$conclusion = "pass";
$pass = 1;
}
}
else {
$conclusion = "FAIL [output file does not exist]";
}
ofile_OutputString($FH_HR->{"log"}, 1, "$conclusion\n");
return $pass;
}
#################################################################
# Subroutine: compare_two_files()
# Incept: EPN, Tue Jul 7 11:20:56 2020
#
# Purpose: Compares ceratin fields of two files
#
# Arguments:
# $desccat: description and category concatenated together, to push
# to @{$data_perline_AAR}.
# $prefix: index prefix
# $out_file: name of output file
# $cmp_file: name of compare file
# $outfields_AR: ref to array of fields from out file to compare
# $cmpfields_AR: ref to array of fields from cmp file to compare
# $data_perline_AAR: ref to 2D array of perline data
# $data_perval_AAR: ref to 2D array of perval data
# $FH_HR: ref to hash of file handles, including "log" and "cmd"
#
# Returns: '1' if $outfile is identical to $expfile as determined by diff
#
# Dies: If an expected file does not exist or is empty.
#
#################################################################
sub compare_two_files {
my $sub_name = "compare_two_files";
my $nargs_expected = 9;
if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
my ($desccat, $prefix, $out_file, $cmp_file, $outfields_AR, $cmpfields_AR, $data_perline_AAR, $data_perval_AAR, $FH_HR) = @_;
if(! -s $cmp_file) {
ofile_FAIL("ERROR in $sub_name, compare file $cmp_file does not exist or is empty", 1, $FH_HR) ;
}
if(! -s $out_file) {
ofile_FAIL("ERROR in $sub_name, output file $out_file does not exist or is empty", 1, $FH_HR) ;
}
# ofile_OutputString($FH_HR->{"log"}, 1, sprintf("#\tchecking %-100s ... ", $out_file));
# read in fields of out file
my @outdata0_A = (); # value from field 0 from outfile
my @outdataN_A = (); # values from fields 1->N from outfile, concatenated and separated by ';'
my @cmpdata0_A = (); # value from field 0 from cmpfile
my @cmpdataN_A = (); # values from fields 1->N from cmpfile, concatenated and separated by ';'
get_field_data_from_file($out_file, $outfields_AR, \@outdata0_A, \@outdataN_A);
get_field_data_from_file($cmp_file, $cmpfields_AR, \@cmpdata0_A, \@cmpdataN_A);
my $noutlines = scalar(@outdata0_A);
my $ncmplines = scalar(@cmpdata0_A);
if($noutlines ne $ncmplines) {
ofile_FAIL(sprintf("ERROR in $sub_name, when trying to compare $out_file and $cmp_file, number of lines differ: out: %d != cmp: %d\n", scalar(@outdata0_A), scalar(@cmpdata0_A)), 1, $FH_HR);
}
my $nidentical = 0;
my $ndifferent = 0;
my $id_or_df = "";
my %nidentical_perval_H = (); # key is a outdataN_A[$i] value, value is number of identities with $cmpdataN_A[$i]
my %ndifferent_perval_H = (); # key is a outdataN_A[$i] value, value is number of differents with $cmpdataN_A[$i]
my %ntotal_perval_H = (); # key is a outdataN_A[$i] value, value is number of comparisons with $cmpdataN_A[$i]
for (my $i = 0; $i < $noutlines; $i++) {
# first field should always be identical
if($outdata0_A[$i] ne $cmpdata0_A[$i]) {
ofile_FAIL(sprintf("ERROR in $sub_name, when trying to compare $out_file and $cmp_file, line %d, first token differs: out: %s != cmp: %s\n", $i+1, $outdata0_A[$i], $cmpdata0_A[$i]), 1, $FH_HR);
}
# remaining fields (which were concatenated together (after separating by ;) by get_field_data_from_file, may be different
my $perval_key = $cmpdataN_A[$i];
if($outdataN_A[$i] eq $cmpdataN_A[$i]) {
$nidentical++;
if(! defined $ntotal_perval_H{$perval_key}) {
$nidentical_perval_H{$perval_key} = 1;
$ndifferent_perval_H{$perval_key} = 0;
$ntotal_perval_H{$perval_key} = 1;
}
else {
$nidentical_perval_H{$perval_key}++;
$ntotal_perval_H{$perval_key}++;
}
$id_or_df = "identical";
}
else {
$ndifferent++;
if(! defined $ndifferent_perval_H{$perval_key}) {
$ndifferent_perval_H{$perval_key} = 1;
$nidentical_perval_H{$perval_key} = 0;
$ntotal_perval_H{$perval_key} = 1;
}
else {
$ndifferent_perval_H{$perval_key}++;
$ntotal_perval_H{$perval_key}++;
}
$id_or_df = "different";
}
push(@{$data_perline_AAR}, [sprintf("%s.%d", $prefix, ($i+1)), $desccat, $cmpdata0_A[$i], $cmpdataN_A[$i], $outdataN_A[$i], $id_or_df]);
}
push(@{$data_perline_AAR}, []); # empty array -> blank line
# add perval data
my $i = 1;
foreach my $val (sort { $ntotal_perval_H{$b} <=> $ntotal_perval_H{$a} } keys %ntotal_perval_H) {
push(@{$data_perval_AAR}, [sprintf("%s.%d", $prefix, $i), $desccat, $val, $ntotal_perval_H{$val},
$nidentical_perval_H{$val}, $ndifferent_perval_H{$val},
sprintf("%7.5f", $nidentical_perval_H{$val} / $ntotal_perval_H{$val}),
sprintf("%7.5f", $ndifferent_perval_H{$val} / $ntotal_perval_H{$val})]);
$i++;
}
push(@{$data_perval_AAR}, []); # empty array -> blank line
return ($noutlines, $nidentical, $ndifferent);
}
#################################################################
# Subroutine: get_field_data_from_file()
# Incept: EPN, Tue Jul 7 11:52:33 2020
#
# Purpose: Fill arrays with data from specific fields from a file
#
# Arguments:
# $in_file: name of output file
# $fields_AR: ref to array with field indices
# $data0_AR: REF to array to fill with per-line data from $fields_AR[0]
# $dataN_AR: REF to array to fill with per-line data from all fields $fields_AR[$i] with $i>0,
#
# Returns: void, fills @{$data0_AR} and @{$dataN_AR}
#
# Dies: If a non-# comment line of the file does not have enough fields
#
#################################################################
sub get_field_data_from_file {
my $sub_name = "get_field_data_from_file";
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_file, $fields_AR, $data0_AR, $dataN_AR) = @_;
if(! -s $in_file) {
ofile_FAIL("ERROR in $sub_name, file $in_file does not exist or is empty", 1, $FH_HR) ;
}
open(IN, $in_file) || ofile_FileOpenFailure($in_file, $sub_name, $!, "reading", $FH_HR);
while(my $line = <IN>) {
if($line !~ m/^\#/) {
chomp $line;
my @el_A = split(/\s+/, $line);
my $nfields = scalar(@el_A);
my $data0 = "";
my $dataN = "";
for(my $i = 0; $i < scalar(@{$fields_AR}); $i++) {
my $act_field = $fields_AR->[$i]-1;
if($act_field >= $nfields) {
ofile_FAIL("ERROR in $sub_name, trying to get token $fields_AR->[$i] but only read $nfields on line $line of $in_file", 1, $FH_HR);
}
if($i == 0) {
$data0 = $el_A[$act_field];
}
else {
if($dataN ne "") { $dataN .= ";"; }
$dataN .= $el_A[$act_field];
}
}
push(@{$data0_AR}, $data0);
push(@{$dataN_AR}, $dataN);
}
}
close(IN);
return;
}
#################################################################
# Subroutine: parse_cmpstr()
# Incept: EPN, Tue Jul 7 09:57:23 2020
#
# Purpose: Validate and parse a 'compare string'.
# Format should be 4 ':' delimited tokens:
# <category>:<comma-separated-out-fields>:<comma-separated-cmp-fields>:<cmp-file-path>
# Checks that <comma-separated-out-fields> and
# <comma-separated-cmp-fields> have the same number
# of fields. Validates that the file <cmp-file-path>
# exists and is non empty.
# Fill @{$outfields_AR} with field indices from
# <comma-separated-out-fields> [0..nfields-1]
# Fill @{$cmpfields_AR} with field indices from
# <comma-separated-cmp-fields> [0..nfields-1]
#
#
# Arguments:
# $cmpstr: name of output sqtable file
# $outfields_AR: ref to array of out file field indices
# $cmpfields_AR: ref to array of cmp file field indices
# $FH_HR: REF to hash of file handles, including "log" and "cmd"
#
# Returns: Two values:
# <category>: first ':'-delimited token from $cmpstr
# <cmp-file-path>: path to cmpfile
#
# Dies: If cmpstr is not parseable or invalid
# If <cmp-file-path> file does not exist or is empty.
#
#################################################################
sub parse_cmpstr {
my $sub_name = "parse_cmpstr";
my $nargs_expected = 4;
if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
my ($cmpstr, $outfields_AR, $cmpfields_AR, $FH_HR) = @_;
my @el_A = split(":", $cmpstr);
if(scalar(@el_A) != 4) {
ofile_FAIL(sprintf("ERROR unable to parse cmp: string $cmpstr, expected 4 ':' delimited tokens got: %d", scalar(@el_A)), 1, $FH_HR);
}
my ($category, $outfields_str, $cmpfields_str, $cmpfile) = (@el_A);
my @outfields_A = split(",", $outfields_str);
my @cmpfields_A = split(",", $cmpfields_str);
my $nout = scalar(@outfields_A);
my $ncmp = scalar(@cmpfields_A);
if($nout == 1) {
ofile_FAIL("ERROR unable to parse cmp: string $cmpstr, read only 1 field in outfields str $outfields_str, must be at least 2", 1, $FH_HR);
}
if($ncmp == 1) {
ofile_FAIL("ERROR unable to parse cmp: string $cmpstr, read only 1 field in cmpfields str $cmpfields_str, must be at least 2", 1, $FH_HR);
}
if($nout != $ncmp) {
ofile_FAIL("ERROR unable to parse cmp: string $cmpstr, different numbers of comma-delimited tokens in outfields str $outfields_str and cmpfields str $cmpfields_str", 1, $FH_HR);
}
for(my $i = 0; $i < $nout; $i++) {
if($outfields_A[$i] !~ m/^\d+$/) {
ofile_FAIL("ERROR unable to parse cmp: string $cmpstr, found non-positive-integer in outfields str $outfields_str: $outfields_A[$i]", 1, $FH_HR);
}
if($cmpfields_A[$i] !~ m/^\d+$/) {
ofile_FAIL("ERROR unable to parse cmp: string $cmpstr, found non-positive-integer in cmpfields str $cmpfields_str: $cmpfields_A[$i]", 1, $FH_HR);
}
}
if(defined $outfields_AR) { @{$outfields_AR} = @outfields_A; }
if(defined $cmpfields_AR) { @{$cmpfields_AR} = @cmpfields_A; }
if(! -e $cmpfile) { ofile_FAIL("ERROR, problem with cmp: string $cmpstr, expected file $cmpfile does not exist", 1, $FH_HR); }
return ($category, $cmpfile);
}
#################################################################
# Subroutine: compare_two_sqtable_files()
# Incept: EPN, Mon Jun 11 09:42:11 2018
#
# Purpose: Compare two sqtable files outputting the number of
# lost, added, and changed features.
#
# Arguments:
# $out_file: name of output sqtable file
# $exp_file: name of expected sqtable file
# $diff_file: name of file to create with differences
# $opt_HHR: ref to 2D hash of option values, see top of sqp_opts.pm for description
# $FH_HR: REF to hash of file handles, including "log" and "cmd"
#
# Returns: void
#
# Dies: If sequences are not in the same order in the two files
#
#################################################################
sub compare_two_sqtable_files {
my $sub_name = "compare_two_sqtable_files";
my $nargs_expected = 5;
if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
my ($out_file, $exp_file, $diff_file, $opt_HHR, $FH_HR) = @_;
my $out_file_exists = (-e $out_file) ? 1 : 0;
my $exp_file_exists = (-e $exp_file) ? 1 : 0;
my $out_file_nonempty = (-s $out_file) ? 1 : 0;
my $exp_file_nonempty = (-s $exp_file) ? 1 : 0;
my $conclusion = "";
my $pass = 0;
my $skip_msg_lines = opt_Get("--skipmsg", $opt_HHR) ? 1 : 0;
if(! $exp_file_exists) {
ofile_FAIL("ERROR in $sub_name, expected file $exp_file does not exist", 1, $FH_HR) ;
}
if(! $exp_file_nonempty) {
ofile_FAIL("ERROR in $sub_name, expected file $exp_file exists but is empty", 1, $FH_HR);
}
if(! $out_file_exists) {
ofile_FAIL("ERROR in $sub_name, output file $out_file does not exist", 1, $FH_HR) ;
}
if(! $out_file_nonempty) {
ofile_FAIL("ERROR in $sub_name, output file $out_file exists but is empty", 1, $FH_HR);
}
my @out_line_A = (); # array of all lines in out file
my @exp_line_A = (); # array of all lines in exp file
my $out_line; # single line from out file
my $exp_line; # single line from exp file
my %exp_seq_lidx_H = (); # key: sequence name, value line index where sequence annotation starts for key in $exp_file
my @exp_seq_A = (); # array of all sequence name keys in order in %exp_seq_lidx_H
my %out_seq_lidx_H = (); # key: sequence name, value line index where sequence annotation starts for key in $out_file
my @out_seq_A = (); # array of all sequence name keys in order in %out_seq_lidx_H
my %seq_exists_H = (); # key is a sequence name, value is '1' if sequence exists in either @exp_seq_A or @out_seq_A
my $lidx = 0; # line index
my $seq; # a sequence name
my $nseq = 0; # total number of sequences
my $tot_nseq_ftr_identical = 0; # number of sequences with all features identically annotated between output and expected
my $tot_nseq_ftr_diff = 0; # number of sequences with >=1 feature differently annotated between output and expected
my $tot_nseq_ftr_out_only = 0; # number of sequences with >=1 feature only in the output file (not in the expected file)
my $tot_nseq_ftr_exp_only = 0; # number of sequences with >=1 feature only in the expected file (not in the output file)
my $tot_nseq_note_identical = 0; # number of sequences with all notes identically annotated between output and expected
my $tot_nseq_note_diff = 0; # number of sequences with >=1 note differently annotated between output and expected
my $tot_nseq_note_out_only = 0; # number of sequences with >=1 note only in the output file (not in the expected file)
my $tot_nseq_note_exp_only = 0; # number of sequences with >=1 note only in the expected file (not in the output file)
if($out_file_nonempty && $exp_file_nonempty) {
open(DIFFOUT, ">", $diff_file) || ofile_FileOpenFailure($diff_file, $sub_name, $!, "writing", $FH_HR);
my %seq_H = (); # key is sequence name, 1 is if sequence exists in @seq_A or not
my @seq_A = (); # array of sequence names in order
my %seq_ftr_HH = (); # key1: sequence, key2: feature, value always 1
my %seq_ftr_HA = (); # key1: sequence, array of features in both out and exp for this sequence
my @file_A = ($out_file, $exp_file);
my %file_seq_ftr_HHH = (); # key 1: "out" or "exp", key 2: sequence name, key 3: a single feature for that sequence in output file, value: always 1
my @filekey_A = ("out", "exp");
my ($line, $file, $seq, $ftr, $filekey);
for(my $f = 0; $f < 2; $f++) { # loop over out and exp files
$file = $file_A[$f];
$filekey = $filekey_A[$f];
$seq = undef;
$ftr = ""; # current feature string (multiple lines)
my $prv_line_seq = 0;
%{$file_seq_ftr_HHH{$filekey}} = ();
open(IN, $file) || ofile_FileOpenFailure($file, $sub_name, $!, "reading", $FH_HR);
while(my $line = <IN>) {
if($line !~ m/\S+/) { # skip blank lines
; # do nothing
}
elsif($skip_msg_lines && ($line =~ m/^Additional/)) {
; # do nothing
}
elsif($skip_msg_lines && ($line =~ m/^ERROR/)) {
; # do nothing
}
elsif($skip_msg_lines && ($line =~ m/^WARNING/)) {
; # do nothing
}
elsif($line =~ m/^\>/) { # sequence line
if(defined $seq) { # if this isn't our first sequence
# store final feature string from previous sequence
$file_seq_ftr_HHH{$filekey}{$seq}{$ftr} = 1;
if(! exists $seq_ftr_HH{$seq}{$ftr}) {
push(@{$seq_ftr_HA{$seq}}, $ftr);
$seq_ftr_HH{$seq}{$ftr} = 1;
}
}
$ftr = "";
$seq = $line;
chomp $seq;
if(! exists $seq_H{$seq}) {
push(@seq_A, $seq);
$seq_H{$seq} = 1;
}
$prv_line_seq = 1;
%{$file_seq_ftr_HHH{$filekey}{$seq}} = ();
if(! exists $seq_ftr_HA{$seq}) {
@{$seq_ftr_HA{$seq}} = ();
}
}
elsif($line =~ m/^\<?\d+\s+\d+\s+\S+/) { # coordinate plus feature line
if(! $prv_line_seq) { # previous line was not a sequence line so
# we know we just ended a feature, store it
$file_seq_ftr_HHH{$filekey}{$seq}{$ftr} = 1;
if(! exists $seq_ftr_HH{$seq}{$ftr}) {
push(@{$seq_ftr_HA{$seq}}, $ftr);
$seq_ftr_HH{$seq}{$ftr} = 1;
}
$ftr = $line; # reset this to new coordinate line
}
else { # previous line was a sequence line, this will be first part of $ftr
$ftr .= $line
}