sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9ae0c326b9301fc2a0fb74e531a6cb69972f4e0ee4b751f647dac75f0e070ab1 | Perl | 211 | 17 | #!/usr/bin/perl
use strict;
my @c;
my $node = 0;
while (<>) {
chomp;
@c = split;
while ($#c >= 0) {
my $w = shift @c;
print $node." ".($node+1)." ".$w."\n";
$node++;
}
}
print $node."\n";
|
3e25e7b691d5adbda4e4b0ab7c3f5a9ff3c82cd09f133fe6e8610e21c71ccfea | Perl | 248 | 10 | #!/usr/bin/env perl
# This script just takes VCF without header from STDIN
# and puts same VCF with REF and ALT swapped to STDOUT
while (<>) {
s/\tFail\(REF\=\=ALT\)//;
@f = split;
print join("\t", @f[0..2], @f[4,3], @f[5..9])."\n"
}
|
b8380694e65597807896c5a8e8c7eb577c4894a4f429482a817fcffcecdbdd0d | Perl | 255 | 19 | #!/usr/bin/perl
use strict;
my @c;
my $node = 0;
print "#FSTBasic MaxPlus\nI 0\n";
while (<>) {
chomp;
@c = split;
while ($#c >= 0) {
my $w = shift @c;
print "T ".$node." ".($node+1)." $w $w\n";
$node++;
}
}
print "F ".$node."\n";
|
aa178cbe05ecad8d01188cae6fd60b205731809146ba6b5ef4be06aa55c475bf | Perl | 324 | 22 | #!/usr/bin/perl
use strict;
my @c;
my $node = 0;
print "#FSTBasic MaxPlus\nI 0\n";
while (<>) {
chomp;
s/^\s*//;
s/\s*$//;
@c = split(//);
while ($#c >= 0) {
my $w = shift @c;
$w = "<w>" if ($w eq " ");
print "T ".$node." ".($node+1)." ".$w." ".$w." 0\n";
$node++;
}
}
print "F ".$node."\... |
ba8fa09b7ccaf267828d107ab2570d6023ac37c0f0bb674ad75c43ac8302e996 | Perl | 353 | 26 | #!/usr/bin/perl
open(A, $ARGV[0])
or die("could not open");
open(B, $ARGV[1])
or die("could not open");
@a = <A>;
@b = <B>;
close(A);
close(B);
die("length mismatch") if ($#a != $#b);
$max = 0;
for $i (0..$#a) {
$diff = abs($a[i] - $b[i]);
if ($diff > $max) {
$max = $diff;
}
}
print "$#a lin... |
ff02c7bfa6400609c65f724c1fe1732d78a45c972ca5673acae37768d41f3c7d | Perl | 372 | 14 | #!/usr/bin/env perl
# Used in conjunction with get_rules.pl
# example input line: XANTHE Z AE1 N DH
# example output line: EHTNAX DH N AE1 Z
while(<>){
@A = split(" ", $_);
$word = shift @A;
$word = join("", reverse(split("", $word))); # Reverse letters of word.
@A = reverse(@A); # Reverse phones in pron.
... |
9a35314b6105f149ae11de5a036056def154b1247d048b00012bc4fa444b3701 | Perl | 415 | 23 | #!/usr/bin/perl
use strict;
my $in = $ARGV[0];
my $out = $ARGV[1];
open(IN,$in);
open(OUT,">$out");
my $id = "";
my $n = 0;
while(<IN>){
my $line = $_;
$line =~s/\n//g;$line =~s/\r//g;
if ($line =~/Sequence: (.*)$/){$id=$1;}
elsif ($line =~/^(\d+) (\d+)/){
$n++;
my @infos = split(/ /,$line);
print OUT "$id... |
7bfdd8d6468aa0a3611088cdec5bb9f763bdb19e3636d39d9984b3a7edb65b99 | Perl | 461 | 27 | #!/usr/bin/perl
use strict;
use File::Basename;
my $dirname = dirname(__FILE__);
my $out = $ARGV[1];
my $in = $ARGV[0];
open(F,$in);
open(O,">$out");
while(<F>){
if (/>(.*)/){
print O $_;
}
else{
my $dna = $_;
my $DNA = uc($dna);
$DNA =~s/\n//g;$DNA =~s/\r//g;
system("perl $dirname/DNA_Transcription_Tr... |
e30b5ab774c159959d1c76a1555c17164e3e7dd3740bd816ff3cf999c012745e | Perl | 462 | 21 | #!/usr/bin/env perl
#Finds unique phones from the basic rules file
use utf8;
($b)=$ARGV[0];
($tmpdir)=$ARGV[1];
open(BB, "<", "$b/basic_rules") || die "Can't open basic rules";
open(O, ">$tmpdir/phones") || die "Can't open text file for writing";
binmode(O, ":utf8");
my %phones = qw();
while (<BB>) {
chomp;
my @s... |
d0546b2b4eade8d0992faac2b3db61574d702834c6115306fc57556d88eb6e74 | Perl | 526 | 31 | #!/usr/bin/perl
print "#FSTBasic MaxPlus\n";
while (<>) {
if (/start=(\d+)/) {
$initial = $1;
print "I $initial\n";
}
if (/end=(\d+)/) {
$final = $1;
print "F $final\n";
}
if (/^J=/) {
$s = $1 if (/S=(\d+)/);
$e = $1 if (/E=(\d+)/);
$w = $1 if (/W=(\S+)/);
$l = $1 if ... |
fc416a656dc3dff6d67bc16f4bb9a25649094043e4380ff677ac26345c90649c | Perl | 553 | 23 | #!/usr/bin/perl
# Fixes word boundary labels and removes unnecessary out labels.
# The resulting FST should be optimized after this operation.
while (<>) {
if (/(T\s+\d+\s+\d+\s+)#\d+/) { # Word boundary input symbol
if (!/#\d+\s+(\S+)/) {
print STDERR "Invalid word boundary: $_";
exit 1;
}
... |
4ca823171528a8e9aec7264bcf73cec775628b8f261654e02233ce90e2c5bed3 | Perl | 555 | 19 | #!/usr/bin/env perl
# This program reads and writes either a dictionary or just a list
# of words, and it removes any words containing ";" or "," as these
# are used in these programs. It will warn about these.
# It will die if the pronunciations have these symbols in.
while(<>) {
chop;
@A = split(" ", $_);
$w... |
14e3d4bbbf32f4844d1dcb8275d62d2250a5ffeabe887b11c4fc187f05469dba | Perl | 565 | 39 | #!/usr/bin/perl
use strict;
use warnings;
use File::Basename;
#
#
#
#
#
if ( @ARGV != 1 ) {
print "\n";
print "\nremove entries from NORMAL samples";
print "\n\nusage: perl " . basename($0) . " [ INPUT_FILE ] ";
print "\n\n";
exit (0);
}
my $INPUT_FILE = $ARGV[0];
my $line;
open (FHI, "<" , $INPUT... |
adf78975f8535b8204ca50f1176a4be86a6ae4d90912181cf42103de29129ef3 | Perl | 581 | 33 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University
# Apache 2.0.
#
use strict;
use warnings;
use XML::Simple;
use Data::Dumper;
binmode STDOUT, ":utf8";
my %seen;
while (my $keyword = <STDIN>) {
chomp $keyword;
$seen{$keyword} = 1;
}
my $data = XMLin($ARGV[0], ForceArray => 1);
#print Dumper($data... |
f297637b670fee7b69e73911a2c5b36d3ce0c5a945dafdfa77120316d099f133 | Perl | 582 | 33 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University
# Apache 2.0.
#
use strict;
use warnings;
use XML::Simple;
use Data::Dumper;
binmode STDOUT, ":utf8";
my %seen;
while (my $keyword = <STDIN>) {
chomp $keyword;
$seen{$keyword} = 1;
}
my $data = XMLin($ARGV[0], ForceArray => 1);
#print Dumper($data... |
06d00f8644e3884bb8df311ca2c0ee1fd040f1d878d19a37e8b1294f04749d2a | Perl | 589 | 25 | #!/usr/bin/env perl
#Finds unique phones from the basic rules file
# Copyright 2014 Gaurav Kumar. Apache 2.0
use utf8;
($b)=$ARGV[0];
($tmpdir)=$ARGV[1];
open(BB, "<", "$b/basic_rules") || die "Can't open basic rules";
binmode(BB, ":iso88591");
open(O, ">$tmpdir/phones") || die "Can't open text file for writing";
... |
b92d4496dd1c961c47fb39d048107d4ce4ab51a00d9b739f9c1b3cb3e3394b31 | Perl | 611 | 35 | #!/usr/bin/perl
# Convert (triphone) phn to transcript
use locale;
use POSIX;
my $cur_word = "";
while (<>)
{
my $l = "";
chomp;
@c = split;
if ($#c > 0) {
if (!($c[2] =~ /[^\.]+\.(\d+)$/) || $1 == 0) {
if ($c[2] =~ /.\-(.)\+./) {
$l = $1;
} else {
$l = $c[2]; # Monophone
... |
1018a0986685909e94e370f267811e858d417d352efbe5d2a31af6d1e9942cf5 | Perl | 615 | 41 | #!/usr/bin/perl
use strict;
my $in = $ARGV[0];
my $out = $ARGV[1];
my $ref = $ARGV[2];
open(I,$in);
open(O,">$out");
while(<I>){
if (!/^#/){
my $line = $_;
$line =~s/\n//g;$line =~s/\r//g;
my @infos = split(/\t/,$line);
print O "ref";
for (my $i = 1; $i <= $#infos; $i++){
my $val = $infos[$i];
if ($... |
8bc2102e4aaeef79ceeb7439740ac0e29c3687cda557cce9ebd2f1e386ef880e | Perl | 638 | 33 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University
# Apache 2.0.
#
use strict;
use warnings;
use XML::Simple;
use Data::Dumper;
binmode STDOUT, ":utf8";
my @keywords;
while (my $line = <STDIN>) {
chomp $line;
push @keywords, $line;
}
#print "Will retain ", scalar(@keywords), " keywords\n";
my $data... |
f15015ecc521dd5dd8ff2c3108d86a11f4f72d1a7f4a81766e60973b8e659897 | Perl | 643 | 33 | #!/usr/bin/perl
# Creates all paths needed for one type of files in training
# Input: recipe-file recipe-key
# Example: To create all paths needed for alignment files:
# ./make_recipe_paths.pl train.recipe alignment
use locale;
use strict;
use File::Path;
my $recipe = shift;
my $key = shift;
my $fh;
die "... |
71eecf84f785ae74914ce6dfcb8e0ca95f53894ec5983f84300b9345f826d664 | Perl | 680 | 31 | #!/usr/bin/env perl
# Add counts to an oovlist.
# Reads in counts as output by uniq -c, and
# an oovlist, and prints out the counts of the oovlist.
(@ARGV == 1 || @ARGV == 2) || die "Usage: add_counts.pl count_file [oovlist]\n";
$counts = shift @ARGV;
open(C, "<$counts") || die "Opening counts file $counts";
whil... |
ef2aabb6c164c28ae174b4e3489c6d120bfbd938859a1b5e0c337359931a182b | Perl | 682 | 28 | #!/usr/bin/env perl
# This script takes VCF with header on the STDIN and filters out:
# - chrM
# - indels (Selene can't parse them currently)
# - non-AGTC alleles (probably these are just Ns after conversion to hg19)
# Filtered stuff goes to STDERR, good stuff to STDOUT, both headered
while (<>) {
if (not $x) {
... |
55dbceb86fccea08a425bb8b76b1b0f3dcc58598c17c31ebd7666ac2db6bd100 | Perl | 705 | 32 | #!/usr/bin/perl
my $eps = ",";
my @num_incoming = ();
my @incoming_label = ();
use Fsm;
use strict;
# Load FST
my $fsm = Fsm->new;
$fsm->read_fst(shift);
# Find the word arcs and count incoming arcs
my @word_arcs = ();
for my $s (@{$fsm->{"V"}}) { # Iterate over each state
for my $a (@$s) { # Iterate over each a... |
7cb968c3d0878198e37ce9c0de3ef0ee7baadcd4408ce1b7931bac4553561a99 | Perl | 743 | 47 | #!/usr/bin/perl
while (<>) {
chomp;
if (/^\d+$/) {
if ($final ne undef) {
print STDERR "ERROR: multiple final states\n";
exit 1;
}
$final = $&;
next;
}
if (!/^(\d+)\s+(\d+)\s+(\S+)\s*$/) {
print STDERR "ERROR: weird line: $_\n";
exit 1;
}
$src = $1;
$tgt = $2;
$sym = ... |
6ca4012f54be87a4dc0aeae0b4fd18593484e86d0d5d6539e0bcccfb69533216 | Perl | 751 | 48 | #!/usr/bin/env perl
# The test script is written in Perl. It runs the peak_match program to compare the output file with the expected peak coordinates.
use strict;
my $expected_result="K169N-HN
M001N-HN
E168N-HN
T002N-HN
V109N-HN
R123N-HN
S136N-HN
K167N-HN
E063N-HN
K165N-HN
D108N-HN
Q061N-HN
G060N-HN
E049N-HN
... |
a06b8589b720491ee7b7ed3c74e6dac7db53d869fc400742585b9762f41f8d6c | Perl | 777 | 35 | #!/usr/bin/perl
# Usage: copy_recipe_files.pl RECIPE source-key target-key
use locale;
use strict;
my $recipe_file = shift;
my $source_key = shift;
my $target_key = shift;
die "Usage: copy_recipe_files.pl RECIPE source-key target-key" if (!defined($target_key));
open REC, "< $recipe_file" || die "Could not open $re... |
7565b325ad7951ce75bd8a8a02028faddade05aa57bb929ed4266296191d8d25 | Perl | 823 | 25 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright Chao Weng
# normalizations for hkust trascript
# see the docs/trans-guidelines.pdf for details
while (<STDIN>) {
@A = split(" ", $_);
print "$A[0] ";
for ($n = 1; $n < @A; $n++) {
$a = $A[$n];
if (($a eq "{breath}")||... |
3662c14c32bd016a7c609451386f627a1074f849647745f13ba02e74ef887d8c | Perl | 825 | 23 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
500b3413591c326586aa17b520e5d7ee3fe731c6671a448e0ee47d647c4da17c | Perl | 831 | 51 | #!/usr/bin/perl
# Copyright 2020 Ivan Medennikov (STC-innovations Ltd)
# Apache 2.0.
# This script creates utt2uniq file for the CHiME-6 utterances.
($filein,$fileout)=@ARGV;
open(fidout, ">$fileout") or die "can't open $fileout : $!";
open(fidin, "<$filein") or die "can't open $filein : $!";
while ($line=<fidi... |
952312455ad0f7b7749556fc7b660949552e406c49f6b928c8a7d6d5840f965a | Perl | 854 | 27 | #!/usr/bin/env perl
# If the command-line argument is 4, this script prints "0 1 2 3";
# If the command-line argument is 20, it prints 10 through 29.
# These numbers are used to allocate the names of split-up data
# directories. We make the names this way so that when we use globs
# to represent filenames with these... |
81c25f4c90b7a95d133df2f672e4e09ddcf733f506cf338fadca4a88e24b67de | Perl | 857 | 28 | #!/usr/bin/env perl
#
# If the command-line argument is 4, this script prints "0 1 2 3";
# If the command-line argument is 20, it prints 10 through 29.
# These numbers are used to allocate the names of split-up data
# directories. We make the names this way so that when we use globs
# to represent filenames with th... |
5870b6c7077ce33c9bbfbff4cb8e2828616dee55d52d937d8f199f833f878f20 | Perl | 875 | 45 | #!/usr/bin/perl
# Copyright 2020 Ivan Medennikov (STC-innovations Ltd)
# Apache 2.0.
# This script splits speakers in utt2spk file,
# leaving $ups utterances for each sub-speaker.
($filein,$ups,$fileout)=@ARGV;
open(fidin, "<$filein") or die "can't open $filein : $!";
open(fidout, ">$fileout") or die "can't op... |
38552712b506f66740f273368527741cd16a974a500e6a0be5ce1628ec50b227 | Perl | 897 | 51 | #!/usr/bin/perl
use strict;
use warnings;
my $BLASTResult=$ARGV[0];
my $SEQFile=$ARGV[1];
my $coverage=$ARGV[2];
my $identity=$ARGV[3]*100;#percents
my $score=$ARGV[4];
my %hash;
my @row;
my $line;
#my $coverage=0.5;
#my $identity=50;#percents
#my $score=50;
&ReadSeqLength("$SEQFile",\%hash);
open(F,$BLASTResult);... |
946c8bb1d95a9205fe729776b2d0128767703914f589493a03cacdcbce86c40e | Perl | 919 | 50 | #!/usr/bin/perl
use strict;
my $file = $ARGV[0];
my $out = $ARGV[1];
my %h;
open(F,$file);
while(<F>){
my @infos = split(/\t/,$_);
if ($infos[2] eq 'CDS' && /Name=([^;]*);/){
my $id = $1;
$h{$id}++;
}
}
close(F);
my %dup;
foreach my $id(keys(%h)){
my $n = $h{$id};
if ($n > 1){
$dup{$id} = 1;
}
}
open(O,... |
2781ebdd36f2a84538185f7560f66dd57efe0021859900915a4270aa10ad44cd | Perl | 920 | 28 | #!/usr/bin/env perl
# Copyright 2017 Vimal Manohar
# Apache 2.0
@ARGV == 2 || die "usage: normalize_bn96_transcripts.pl noise_word spoken_noise_word < transcript > transcript2";
$noise_word = shift @ARGV;
$spoken_noise_word = shift @ARGV;
while(<STDIN>) {
$_ =~ m:^(\S+) (.+): || die "bad line $_";
$utt = $... |
3d0715ac5dcf1d0db6183fd72e7dd08a1cc343cd4c4845b49507899658b87f1d | Perl | 1,002 | 39 | #!/usr/bin/perl
#require "Parse_Form.lib";
#&Parse_Form;
require "./cgi-lib.pl";
my (%formdata, # The form data
%cgi_cfn, # The uploaded file(s) client-provided name(s)
%cgi_ct, # The uploaded file(s) content-type(s). These are
# set by the user's browser and may be unreliable
... |
b83f552cd508c59400bc6936b967a58381b96c4869efc8ad01bd4485c92361be | Perl | 1,009 | 27 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
5f7e0a2039c803b1a3e01c59d737807408546f451fd1512177bfe6712fe14d02 | Perl | 1,047 | 46 | #!/usr/bin/perl
use Cwd;
use File::Spec;
use File::Basename;
use strict;
my @tools = ("git", "wget", "bzip2", "java", "tabix", "weka.jar");
my $tool_path = '';
my $foundTool;
my $printHeader = 1;
print "\n\nChecking dependencies for ISOWN ... \n\n";
my $cwd = dirname($0);
foreach my $t (0 .. $#tools) {
$foundT... |
ff064aae5a3d52026db9c6fc2e04e61f1438760f9dab5644b34da180d03b6f1f | Perl | 1,063 | 45 | #!/usr/bin/perl
# Parses the segmentation output of the decoder and saves segmentations
# of different files to target directory in PHN format. New file
# names are taken from 'LNA: ' line of the decoder output and use
# .snseg suffix.
use locale;
die "Arguments: segmentation-file [target-directory]" if ($#ARGV < 0... |
2fd597c463ef47fbbda11b53a99aecc2ae3659d1ec2455694cbb7d492f4dfff0 | Perl | 1,082 | 44 | #!/usr/bin/env perl
# This program takes the output of score_prons.pl and collates
# it for each (rule, destress) pair so that we get the
# counts of right/partial/wrong for each pair.
# The input is a 7-tuple on each line, like:
# word;pron;base-word;base-pron;rule-name;de-stress;right|partial|wrong
#
# The output f... |
b881822f673a041042cc62bc2c3cd831788b3b5a2a748a0006c5fd6aecb4111d | Perl | 1,107 | 62 | #!/usr/bin/perl
use strict;
my $file = $ARGV[0];
my $metadata = $ARGV[1];
my %strains;
open(F,$metadata);
while(<F>){
my $line = $_;
$line =~s/\n//g;$line =~s/\r//g;
my ($path_genome,$strain) = split(/\t/,$line);
$strains{$path_genome} = $strain;
}
close(F);
my %ANIs;
my %genomes;
my %genome_names;
my $num_lin... |
b5a21fc579ef1334a2fbb13f1177a7a6e4dc65fc47596e5daba5d09082de2e1a | Perl | 1,113 | 55 | #!/usr/bin/env perl
# The test script is written in Perl. It runs the fid program and phase program with a test input file and checks the output file for the expected phase correction values
use strict;
my $exe1 = "./fid -process full -nus none -out test.ft2 -di no -di-indirect no -phase-in none";
my $exe2 =... |
30de878f80b11706ce370f046a03146bf5ea2a73fd4822f8e0f51db0eb3c9e05 | Perl | 1,132 | 62 | #!/usr/bin/perl
# updates the old .cfg file to the new format
# where the old fft module is split to audiofile and fft modules
# arg 1 = cfg-file
my $done=0;
open(CFGIN, "<$ARGV[0]");
while (<CFGIN>) {
$line=$_;
if ($line =~ m/module/ && !$done) {
$line = <CFGIN>;
unless ($line =~ m/\{/) {
print "E... |
667c590ca7377e5f434c87775ec83aab6189298a8f2117316d3a515e6b14fa64 | Perl | 1,137 | 36 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright Chao Weng
# normalizations for hkust trascript
# see the docs/trans-guidelines.pdf for details
while (<STDIN>) {
@A = split(" ", $_);
for ($n = 0; $n < @A; $n++) {
$a = $A[$n];
if (($a eq "{breath}")||($a eq "{cough}")|... |
687c764f0a5eac0d24e828e448761e24b3f4c88393e581a52f0e88c8ca1f7da5 | Perl | 1,144 | 51 | #!/usr/bin/perl
use strict;
use Cwd;
use File::Basename;
sub usage {
print "\nUsage: $0 [ INPUT_VCF_FILE ] [ INPUT_VCF_DATABASE_FILE ] [ INPUT_VCF_DATABASE_FILE_PREFIX ] [ OUTPUT_VCF_FILE ] [ FASTA_REFERENCE_FILE ]\n";
}
my ($inputVCFFile, $vcfDatabase, $vcfDatabasePrefix, $outputVCFFile, $referenceFile) = @ARGV... |
44490a2f2c3ff5919b65538d313089db4b5c267ffb44fc79c43c227c4905cd24 | Perl | 1,148 | 47 | #!/usr/bin/perl
use strict;
use Cwd;
use File::Spec;
use File::Basename;
use Cwd 'abs_path';
=head
=cut
# directory of where this script is called
my $cwd = dirname($0);
sub usage {
print "\nUsage: " . basename($0) . " [ INPUT-DIR ] [ OUTPUT-FILE ] ";
}
if ( @ARGV != 2 ) {
usage;
print "\n\n\tPlease ensure... |
167a578f0b5c17cf2fb13cd35cb6bb5ac81e0293a02ad2b273856d6fc8dc1aea | Perl | 1,155 | 51 | #!/usr/bin/perl
my $in = $ARGV[0];
my $out = $ARGV[1];
my $rowmetadata = $ARGV[2];
my $colmetadata = $ARGV[3];
my %hash;
my %hash2;
my $n = 0;
open(M,$rowmetadata);
while(<M>){
my $line = $_;
$line =~s/\n//g;$line =~s/\r//g;
$n++;
my @infos = split(/\t/,$line);
my $genus = $infos[1];
my $country = $infos[2];
m... |
4a80b62a5f34205dff89a6c90e2762b2ba724334d6465cdabf173353c81c07c5 | Perl | 1,172 | 48 | #!/usr/bin/env perl
# Copyright 2016 Alibaba Robotics Corp. (Author: Xingyu Na)
#
# A script for char-based Chinese OOV lexicon generation.
#
# Input 1: char-based dictionary, example
# CHAR1 ph1 ph2
# CHAR2 ph3
# CHAR3 ph2 ph4
#
# Input 2: OOV word list, example
# WORD1
# WORD2
# WORD3
#
# where WORD1 is in the format... |
1547e1c751d0f009590b236c4bd8ef359195b205a50fa0b9824ab1e30f2db27d | Perl | 1,184 | 31 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
710a80bdeaafaca711fdcf1d04826f2ad3bc5fb7311151951aa3deeaf9378115 | Perl | 1,186 | 50 | #!/usr/bin/env perl
# Copyright 2013 Karlsruhe Institute of Technology (Author: Jonas Gehring)
# Apache 2.0.
#
# Bursts a pfile into equally-sized parts
#
use Getopt::Std;
use List::Util qw/min/;
# Prints usage information
sub usage() {
print STDERR << "EOF";
Usage: pfile_burst <options>
Where <options> include:
-... |
4ec380ebe80477e88b5f9e6a378b21bbe0e2f187939b09366c875a983210d824 | Perl | 1,187 | 31 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
95e699f9dee24addefce10a2d6bb9d4ac66c1c46aa3926077f1b41d95addbb3f | Perl | 1,189 | 53 | #!/usr/bin/perl
use strict;
use Cwd;
use File::Spec;
use File::Basename;
=head
# need to add 'chr' in front of chromosome column
# change chrMT to chrM
zcat 00-All.vcf.gz | head -500 | grep ^# > 00-All.modified.vcf
zcat 00-All.vcf.gz | grep -v ^# | awk '{ print "chr"$0 }' | sed 's/chrMT/chrM/' >> 00-All.modified.vc... |
63b5d482a42d2eefe4d327b8d2558e4fdaba1495dfa62d371926a21916926e50 | Perl | 1,196 | 41 | #!/usr/bin/perl
use strict;
use Cwd;
use File::Basename;
sub usage {
print "\nUsage: $0 [ INPUT_VCF_FILE ] [ OUTPUT_VCF_FILE ] \n";
}
my ($inputVCFFile, $outputVCFFile) = @ARGV;
# dirname of where this script is
my $cwd = dirname($0);
if (not defined $inputVCFFile) {
usage;
print "\n\tPlease provide inpu... |
75aef4c7824b914319cdb90380e76987d77cc33ff390d2231080d9fd9df00dd7 | Perl | 1,211 | 37 | #!/usr/bin/perl
use strict;
use Cwd;
use File::Spec;
use File::Basename;
use Cwd 'abs_path';
# directory of where this script is called
my $cwd = dirname($0);
sub usage {
print "\nUsage: " . basename($0) . " [ INPUT-DIR ] [ OUTPUT-PREDICTED-FILE ] [ ADDITIONAL_ARG ] ";
}
if ( @ARGV != 3 ) {
usage;
print "\n\n\... |
1bedb91c9d8ce3cd6fd3611f80edf6f2114c2b3fa4cb5392b6340e730814a5ce | Perl | 1,214 | 50 | #!/usr/bin/perl
use strict;
use Cwd;
use File::Spec;
use File::Basename;
=head
wget ftp://ftp.broadinstitute.org/pub/ExAC_release/current/ExAC.r0.3.1.sites.vep.vcf.gz
zcat ExAC.r0.3.1.sites.vep.vcf.gz | head -500 | grep ^# > ExAC.r0.3.1.sites.vep.modified.vcf
zcat ExAC.r0.3.1.sites.vep.vcf.gz | grep -v ^# | aw... |
067e0e6a68fac3aa3702e58737c7ece0a33492249b31d33461cf776fe3b98545 | Perl | 1,234 | 55 | #!/usr/bin/env perl
# This script takes a VCF on STDIN
# tries to remove FILTER, QUAL, and INFO/* except for INFO/DEEPCT
# and outputs it back to STDOUT
while (<>) {
if (not $x) {
if (/^#/) {
# We're in header
if (/^#CHROM/) {
# Last header line, remove FORMAT and s... |
20add8b4eb91d88a9ac4cc55fe6fb11118fec0b11fcb81c9694a3caebd860240 | Perl | 1,238 | 39 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
d7d74f076742d2c30fae834cfdb1ce9ffc957a72bdc8997d56bf3b28d5b91200 | Perl | 1,272 | 43 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Yenda Trmal)
# Apache 2.0.
#This script takes the source STM file and generates the *.txt files which
#are usually part of the BABEL delivery
#The *.txt files are not the part of the delivery for the evalpart1 subset
#The program works as a filte... |
ceddf9c07f4c3264cffb6c677685394f0fd88d56ee673e7bfc215e23126af20f | Perl | 1,277 | 43 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Yenda Trmal)
# Apache 2.0.
#This script takes the source STM file and generates the *.txt files which
#are usually part of the BABEL delivery
#The *.txt files are not the part of the delivery for the evalpart1 subset
#The program works as a filt... |
f1839ecd28d066ef0147be9d281a320899d90200b5158b9802ecd8d27757788a | Perl | 1,282 | 57 | #!/usr/bin/perl
# Copyright 2020 Ivan Medennikov (STC-innovations Ltd)
# Apache 2.0.
# This script creates per-utterance json alignment by per-session alignment and segments.
($segments,$jsonali_scp,$jsonali_scp_perutt)=@ARGV;
%ark={};
open(fidin, "<$jsonali_scp") or die "can't open $jsonali_scp : $!";
while (... |
9af4633e0ec0deedbefe9cee842293fc8e6a320068090181bdfc64e50caeefd2 | Perl | 1,315 | 68 | #!/usr/bin/env perl
use strict;
use warnings;
use Encode;
my $Usage = <<EOU;
Usage: filter_keywords.pl <dictin> <queryin|-> <queryout|->
EOU
if(@ARGV != 3) {
die $Usage;
}
# Get parameters
my $dictin = shift @ARGV;
my $filein = shift @ARGV;
my $fileout = shift @ARGV;
# Open dictionary
if (!open(D, "<$dictin"... |
c6516d3790effdda7a9f5f7ba520a82fec2e9aeb940a8fa0616e3653967b39dd | Perl | 1,324 | 55 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Yenda Trmal)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
use XML::Simple;
my $data = XMLin(\*STDIN);
my $duptime= $ARGV[0];
#print Dumper($data);
# Filters duplicate keywords that have the same keyword and about the same time.
#... |
9547c1eb024a4ef5c27e0ebdb8313c9fa0bb9d2a435ace742ea889342a024bc1 | Perl | 1,332 | 46 | #!/usr/bin/perl
#require "Parse_Form.lib";
#&Parse_Form;
require "./cgi-lib.pl";
my (%formdata, # The form data
%cgi_cfn, # The uploaded file(s) client-provided name(s)
%cgi_ct, # The uploaded file(s) content-type(s). These are
# set by the user's browser and may be unreliable
... |
1ad166b62bd2accd4fb5614d8347716b57c0fbe280f56c98c0cccac9dcd5fcd4 | Perl | 1,342 | 65 | #!/usr/bin/perl
use strict;
my $indir = $ARGV[0];
my $matrix = $ARGV[1];
my $out = $ARGV[2];
my $strain_names = $ARGV[3];
my %strains_of_gb;
open(F,$strain_names);
while(<F>){
my $line = $_;
$line =~s/\n//g;$line =~s/\r//g;
my ($gb,$strain) = split(/\t/,$line);
$strains_of_gb{$gb} = $strain;
}
close(F);
my %co... |
f7536fd0fc1e7c68317d8dfc7a61fe01eb911470b5b167c48765d1859cd733f9 | Perl | 1,343 | 36 | #!/usr/bin/env perl
# Copyright 2017 Vimal Manohar
# Apache 2.0
@ARGV == 2 || die "usage: normalize_bn97_transcripts.pl noise_word spoken_noise_word < transcript > transcript2";
$noise_word = shift @ARGV;
$spoken_noise_word = shift @ARGV;
while(<STDIN>) {
$_ =~ m:^(\S+) (.+): || die "bad line $_";
$utt = $... |
673dfd9c85cef9bd9d402c43955f7c475dd176029eb75a20cabfb4ab7dd695b2 | Perl | 1,345 | 55 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Yenda Trmal)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
use XML::Simple;
my $data = XMLin(\*STDIN);
my $duptime= $ARGV[0];
#print Dumper($data);
# Filters duplicate keywords that have the same keyword and about the same time.
#... |
48fb2c99f905a68b22b7cf438e38b96499046e37875b10c15afdaecf520dc510 | Perl | 1,381 | 42 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/... |
e4a8ad9942e3b1c275d494ace330bed15501ef9dca34625a3c669e046e34aca9 | Perl | 1,399 | 51 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
0631f4e3529c34f34ff9c57a98dcd8dd91207214038c75a89485df49eff899b1 | Perl | 1,426 | 43 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
bb35b5e1d83f7bdca71d572d9b696902365ec93d56bd1fd4574cc1a7bd17d0c8 | Perl | 1,433 | 72 | #!/usr/bin/perl
#merge_bams_in_tophat_folder.pl
use warnings;
use strict;
die "Please give 1. Orthogroups.csv 2. Number of zeros you will allow\n" unless(@ARGV==2);
my $orthogroupscsv=$ARGV[0];
open(my $IN_b, "<", $orthogroupscsv) or die "Could not open $orthogroupscsv \n";
my $number_to_merge=$ARGV[1];
my $outfi... |
551ea61e4fbba766586e72530e23e35d1dd59644efaf6b5e472daaf40cab01b4 | Perl | 1,438 | 49 | #!/usr/bin/perl
use File::Copy;
@test_set = qw(GDF1);
$abs_dir = "/d/ls3/d/apache/dreive.cryst.bbk.ac.uk/";
$abs_html = "http://dreive.cryst.bbk.ac.uk/";
foreach $gene_name (@test_set){
while (1){
$code = int(rand 100000) + 1;
$result = "$abs_dir"."htdocs/tmp/result"."$code";
last unless (-e $result);
... |
60c94e8a40d710f29e8b2e2ff72c91bb51cff3dcb11234c6865aade4360053f8 | Perl | 1,448 | 58 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
cdaa41c004d808692d9cbee2bd7d49b4b6cece0ff003a8c75164499e44fa7b40 | Perl | 1,499 | 53 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Johns Hopkins University (author: Daniel Povey)
# makes lexicon FST -- special version only for use in keyword search
# for allowing optional silences between words. This version has
# no pron-probs involved, and
# does support... |
995796132945d0dd8e9892995d49d1b2a9a68d837d1924b570960bcab60b638a | Perl | 1,500 | 53 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Johns Hopkins University (author: Daniel Povey)
# makes lexicon FST -- special version only for use in keyword search
# for allowing optional silences between words. This version has
# no pron-probs involved, and
# does suppor... |
3db36534ead5e9a9a568b0cea825adc8398deb0ee7327d60135975e460890e58 | Perl | 1,514 | 61 | #!/usr/bin/env perl
# The test script is written in Perl. It runs the deep_picker program with a test input file and checks the output file for the expected peak coordinates. If the peak coordinates match the expected values, the test script returns a success code (0), otherwise it returns an error code (1). The test ... |
4f899b23f7a585e457687551d5f9bb51bd6c848acd207652892ef18ad2c93b27 | Perl | 1,523 | 59 | #!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
my $dataid = shift;
my %coverage = (
"Cornidoviridae.genomes.fasta" => 47.5,
"Homo_sapiens.GRCh38.cdna.e99.canonicaltranscripts.fasta" => 0.227,
"Influenza.genomes.fasta" => 9.65,
"Metapneumovirus.genomes.fasta" => 228,
"Rhinovirus.genomes.fasta" => 16.7,... |
8414a964c273b61d3ba67f64af3e22f2bc04fd43652eb01bece30bd61557644d | Perl | 1,530 | 48 | #!/usr/bin/perl
# Sets the alignment and hmmnet fields in the recipe file. These are
# the ones used for output during training, so they should be unique
# to the different model trainings (the hmmnets can be shared if the
# context phoneme tying remains the same).
# The script is given the recipe and path prefixes a... |
1965a0596bbfa2105c3d78bfe882dc57f27c7317e7cdd9af5535f4dfc10bcfa9 | Perl | 1,549 | 61 | #!/usr/bin/env perl
# The test script is written in Perl. It runs the deep_picker program with a test input file and checks the output file for the expected peak coordinates. If the peak coordinates match the expected values, the test script returns a success code (0), otherwise it returns an error code (1). The test ... |
d32bdcf3e0805b9053b22a99766f8e65b99382faf008446ab5f416aa1549bb63 | Perl | 1,551 | 59 | #!/usr/bin/perl
#require "Parse_Form.lib";
#&Parse_Form;
use SP_vert;
require "./cgi-lib.pl";
my (%formdata, # The form data
%cgi_cfn, # The uploaded file(s) client-provided name(s)
%cgi_ct, # The uploaded file(s) content-type(s). These are
# set by the user's browser and may b... |
20db1b5cc6b094f7132d01e8491beba0eb654566efc46bef4ee22cc27e438bb7 | Perl | 1,568 | 62 | #!/usr/bin/env perl
# The test script is written in Perl. It runs the voigt_fit program with a test input file and checks the output file for the expected peak coordinates.
# If the peak coordinates match the expected values, the test script returns a success code (0), otherwise it returns an error code (1).
# The t... |
2330b4aceb294ccc214f30883a8d3dda07ed586b67a05410933529f3b9f8242e | Perl | 1,570 | 62 | #!/usr/bin/env perl
# The test script is written in Perl. It runs the voigt_fit program with a test input file and checks the output file for the expected peak coordinates.
# If the peak coordinates match the expected values, the test script returns a success code (0), otherwise it returns an error code (1).
# The t... |
ca5661bf5a75a1c35d6812de4ac63ac7c8f82fb3f6f551874334fc47bd77aac4 | Perl | 1,575 | 63 | #!/usr/bin/env perl
# The test script is written in Perl. It runs the voigt_fit program with a test input file and checks the output file for the expected peak coordinates.
# If the peak coordinates match the expected values, the test script returns a success code (0), otherwise it returns an error code (1).
# The t... |
6848037ce908ce60d43c8d5e45e9b905fa1bf6b036d2257816002d218e5fd779 | Perl | 1,626 | 73 | #!/usr/bin/perl
# Copyright 2020 Ivan Medennikov (STC-innovations Ltd)
# Apache 2.0.
($filein,$utt2spk,$utt2dur,$chunk,$fileout,$fileout2,$fileout3)=@ARGV;
%utt2dur={};
open(fidin, "<$utt2dur") or die "can't open $utt2dur : $!";
while ($line=<fidin>)
{
$line=~s/\s+$//;
@items=split(/\s+/,$line);
$utt2dur{... |
e80d47071908045880518845936af004cc54d72da408a5ae067e657d4cfcb523 | Perl | 1,647 | 66 | #!/usr/bin/perl -w
#author:pcj
use Parallel::ForkManager;
use strict;
my($idmapping_file,$blast6_out_dir,$databas,$max_process);
if($#ARGV<0){
&usage;
exit;
}
$idmapping_file=shift;
$blast6_out_dir=shift;
#$databas=shift;
$max_process=shift;
$max_process||=4;
sub usage{
my $parameters=<<"USAGE";
This script is t... |
0a7e6cdcfaab379911aa392cd859fcaedd2845097db6f3c53b7053fb224efffc | Perl | 1,649 | 52 | #!/usr/bin/perl
use strict;
use warnings;
use File::Basename;
sub usage {
print "\nUsage: " . basename($0) . " [ INPUT-DIR ] [ OUTPUT-VCF-FILE ]";
}
if ( @ARGV != 2 ) {
usage;
print "\n\n\tPlease ensure to have 2 agruments:\n\tinput dir contained *features* files\n\toutput VCF file name including version number!... |
4c2b22709262d4c90f3c2c65ea75d587375dd03aeab6b6ee414288486f6aa981 | Perl | 1,650 | 61 | #!/usr/bin/env perl
#===============================================================================
# Copyright 2015 (Author: Yenda Trmal <jtrmal@gmail.com>)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy o... |
153375a6340c97633948260c3303ec7d189abb64819312911b3246354da3734d | Perl | 1,652 | 94 | #!/usr/bin/perl
### usage cat vcf | addAnnvarToVcf.pl varFuncFile exonicVarFuncFile > annovar.vcf
use strict;
use warnings;
my $varFuncFile = $ARGV[0];
my $exonicVarFuncFile = $ARGV[1];
my %varFunc;
my %exonicVarFunc;
my $l;
my @f;
# pull variant function file into hash
open (FILE, "<$varFuncFile") or die "Couldn... |
791d878af1a80f26e87daa0b9ed686a3c23c92131c989b80d80ab1abdde9521a | Perl | 1,656 | 37 | #!/usr/bin/perl
use strict;
my $directory;
if ($ARGV[0]){
$directory = $ARGV[0];
}
else{
print "You must provide as an argument a directory containing fastq.gz file for testing the presence of ITS sequences\nex: perl assignFastqByITS.pl my_fastq_dir\n";
exit;
}
my %sequences =(
"1"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTCC... |
fad389993d6374799f53870a37164040f7469c9669bf2bb0544f16e5d98e9b2b | Perl | 1,667 | 50 | #!/usr/bin/env perl
# This program takes candidate prons from "get_candidate_prons.pl" or
# "limit_candidate_prons.pl", and a reference dictionary covering those words,
# and outputs the same format but with scoring information added (so we go from
# 6 to 7 fields). The scoring information says, for each generated pr... |
9c4419f56998aba230ad00f68006b91da75a46c29db2a94d24e86f636a150e31 | Perl | 1,676 | 65 | #!/usr/bin/env perl
# Once the phonetic representation for words is generated by the LDC lexicon
# This script converts them into a KALDI compatible format
# In addition, it extends the list of phonemes to consider based on
# orthograhic representations of those words which do not have stressed vowels
use utf8;
($tm... |
0ad86296e9a9ba5c5c220131d47e78647f62941cddaa200b63fc519c6d02a51c | Perl | 1,702 | 71 | #!/usr/bin/perl
# Converts transcript from standard input to triphone phn
use locale;
use strict;
while (<>) {
triphonize($_);
}
sub triphonize {
my $sent = shift(@_);
$sent =~ s/^\s+//;
$sent =~ s/\s+$//;
$sent =~ s/\s+/ /g;
$sent =~ s/ _ /_/g;
my (@left_queue, @center_queue, @right_queue);
my ... |
df482e2757c24fb4bb19c27e29ac42e52a7b4b81e2f481f35c54c3cacea86e0d | Perl | 1,705 | 72 | #!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
use Data::Dumper;
my ($inputfasta, $maxseqlen, $depth, $strand, $outputfasta) = @ARGV;
GetOptions ("inputfasta|i=s" => \$inputfasta, # path to input fasta file for sampling
"maxseqlen|l=i" => \$maxseqlen, # numeric integer for maximum le... |
6182d806d01ae5c40e33ee6384464985a28a452ce77f8895d3cd06f07bd06390 | Perl | 1,720 | 66 | #!/usr/bin/env perl
# Copyright 2014 Gaurav Kumar. Apache 2.0
# Once the phonetic representation for words is generated by the LDC lexicon
# This script converts them into a KALDI compatible format
# In addition, it extends the list of phonemes to consider based on
# orthograhic representations of those words which ... |
a461ffee6292254c23b1caf85eac79ba2a8c835464f3d5cb35584b1548942727 | Perl | 1,758 | 52 | #!/usr/bin/env perl
# This program takes the output of count_rules.pl, which is tuples
# of the form
#
# rule;destress;right-count;partial-count;wrong-count
#
# and outputs lines of the form
#
# rule;de-stress;score
#
# where the score, between 0 and 1 (1 better), is
# equal to:
#
# It forms a score between 0 and 1, ... |
055a72450fd56e7623d1e2ca8c629676caa0aa6cf6658ce611db3340f38e28d3 | Perl | 1,767 | 74 | #!/usr/bin/perl
my $eps = ",";
my @num_incoming = ();
my @incoming_label = ();
use Fsm;
use strict;
# Load FST
my $fsm = Fsm->new;
$fsm->read_fst(shift);
# Find the word arcs and count incoming arcs
my @word_arcs = ();
for my $s (@{$fsm->{"V"}}) { # Iterate over each state
for my $a (@$s) { # Iterate over each a... |
899455b901fb10b8409a4b6b763c2a5f6db969bee74e261899c954d12d3c6cb0 | Perl | 1,772 | 71 | #!/usr/bin/env perl
# Copyright 2017 John Morgan
# Apache 2.0.
#usma_nonnative_make_lists.pl - make acoustic model training lists
use strict;
use warnings;
use Carp;
use File::Spec;
use File::Copy;
use File::Basename;
my $tmpdir = "data/local/tmp/usma/nonnative";
# input wav file list
my $w = "$tmpdir/wav_list.tx... |
2b1d02eaf268e505e8238957155ca9974137cf8972135ead75bb7666f50961fa | Perl | 1,775 | 70 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Yenda Trmal)
# Apache 2.0.
use Data::Dumper;
$Data::Dumper::Indent = 1;
binmode STDOUT, ":utf8";
binmode STDIN, ":utf8";
$ignore_oov = 0;
$ignore_first_field = 0;
for($x = 0; $x < 2; $x++) {
if ($ARGV[0] eq "-f") {
shift @ARGV;
$field_... |
f078ebd639f5c1c44ec556aaa93c4a99a69bc751362a2100d9e31aeaef06eae2 | Perl | 1,785 | 70 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Yenda Trmal)
# Apache 2.0.
use Data::Dumper;
$Data::Dumper::Indent = 1;
binmode STDOUT, ":utf8";
binmode STDIN, ":utf8";
$ignore_oov = 0;
$ignore_first_field = 0;
for($x = 0; $x < 2; $x++) {
if ($ARGV[0] eq "-f") {
shift @ARGV;
$fie... |
174fb2a4d6d443cce1aee51d1a4976617bcc282ac5541c73d1a296548f99e2e1 | Perl | 1,787 | 63 | #!/usr/bin/perl
use strict;
use warnings;
#hardip@rstudio-nci:~/pacific$ # /media/dstore/covid19/seqid.vs.genomeinfo.txt
#hardip@rstudio-nci:~/pacific$ # /media/dstore/covid19/virus.genbank.20200324.fa
#V1 V2 V3 taxid assemblyname organism lineage
#GCA_000837105.1 ViralMultiSegProj14079 L14461.1 223359 ViralMultiSegP... |
fe3314c9f697156a7d62f7085c0308890c8f494a0f937ea9ff5b87c1dc9d166f | Perl | 1,799 | 50 | #!/usr/bin/env perl
# This takes the output of e.g. get_candidate_prons.pl or limit_candidate_prons.pl,
# which is 7-tuples, one per line, of the form:
# word;pron;base-word;base-pron;rule-name;de-stress;rule-score
# (where rule-score is somtimes listed as optional, but this
# program does expect it, since we don't a... |
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