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af5b95f60a445c5f9512cb3bad33126e0f99863b5f16003e05d4f22c0c4e6843
Perl
1,807
72
#!/usr/bin/env perl # Copyright 2017 John Morgan # Apache 2.0. #usma_native_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/native"; # input wav file list my $w = "$tmpdir/wav_list.txt"; #...
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Perl
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75
#!/usr/bin/perl # Converts one PHN file to FST, in a format similar to what # create_hmmnets.pl generates. # Input: PH-file PHN-file use Hmm; use Fsm; use strict; my $eps = ","; $Hmm::verbose = 0; my $hmmfile = shift @ARGV; my $hmms = Hmm::read($hmmfile); my $first = 1; my $fsm = Fsm->new; $fsm->set_initial($fs...
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Perl
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72
#!/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...
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Perl
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76
#!/usr/bin/perl use warnings; use strict; use Getopt::Std; die "Please specify (1)fasta file\n" unless(@ARGV==1); my $fastafile = $ARGV[0]; my $outfile="$fastafile\.largestIsoform"; #open(my $fastahandle, "<", $fastafile) or die "Could not open $fastafile \n"; no need to open here for bioperl #open(my $fastafile,...
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Perl
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90
#!/usr/bin/env perl use warnings; # Copyright 2015 Tokyo Institute of Technology (Authors: Takafumi Moriya and Takahiro Shinozaki) # 2015 Mitsubishi Electric Research Laboratories (Author: Shinji Watanabe) # Apache 2.0 # Acknowledgement This work was supported by JSPS KAKENHI Grant Number 26280055. # Con...
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Perl
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49
#!/usr/bin/env perl use warnings; #sed replacement for -w perl parameter use strict; # 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...
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Perl
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49
#!/usr/bin/env perl use warnings; #sed replacement for -w perl parameter use strict; # 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...
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Perl
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57
#!/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...
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Perl
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54
#!/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...
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Perl
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#Copyright (c) 2010 LUQMAN HAKIM BIN ABDUL HADI (csilhah@nus.edu.sg) # #Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files #(the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, ...
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Perl
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54
#!/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...
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Perl
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74
#!/usr/bin/env perl # # Copyright 2015 University of Sheffield (Author: Ning Ma) # Apache 2.0. # # Prepare a simple grammar G.fst for the GRID corpus (CHiME 1/2) # with silence at the beginning and the end of each utterance. # use strict; use warnings; # GRID has the following grammar: # verb=bin|lay|place|set # col...
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Perl
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77
#!/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...
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Perl
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113
#!/usr/bin/perl use warnings; use strict; use Data::Dumper; die "Need to give an input file name: DEGs file (1) and a number of permutations (2)\n" unless (@ARGV==2); my $info= $ARGV[0]; my $user_option = $ARGV[1]; open(my $input, "<", $info) or die "Could not open $info\n"; my $outfile="Permutation_data.txt"; open(...
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Perl
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54
#!/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 I...
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Perl
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#!/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 I...
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Perl
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54
#!/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...
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Perl
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54
#!/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 I...
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Perl
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82
#!/usr/bin/perl my $boundary = "#"; my $eps = ","; use Hmm; use Fsm; use strict 'vars'; my $max_boundary_id = 0; if (open(FILE, "boundaries")) { $max_boundary_id = <FILE>; chomp $max_boundary_id; close(FILE); } $Hmm::verbose = 0; my $hmmfile = shift @ARGV; my $hmms = Hmm::read($hmmfile); my @accept = @ARGV;...
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Perl
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63
#!/usr/bin/perl # # Copyright 2015 David Snyder # Apache 2.0. # Usage: make_sre.pl <path-to-data> <name-of-source> <sre-ref> <output-dir> if (@ARGV != 4) { print STDERR "Usage: $0 <path-to-data> <name-of-source> <sre-ref> <output-dir>\n"; print STDERR "e.g. $0 /export/corpora5/LDC/LDC2006S44 sre2004 sre_ref data...
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Perl
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#!/usr/bin/env perl # Copyright 2010-2011 Microsoft Corporation # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # THIS CODE IS PROVIDED *AS I...
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Perl
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52
#!/usr/bin/env perl # Modified from swbd_map_words.pl in Kaldi s5 recipe to make pattern # matches case-insensitive --Arnab (Jan 2013) if ($ARGV[0] eq "-f") { shift @ARGV; $field_spec = shift @ARGV; if ($field_spec =~ m/^\d+$/) { $field_begin = $field_spec - 1; $field_end = $field_spec - 1; } if ($fie...
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Perl
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65
#!/usr/bin/env perl # The test script is written in Perl. It runs the voigt_fit program with 3 planes for pseudo-3D fitting 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 ...
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Perl
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#!/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...
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Perl
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71
#!/usr/bin/perl use strict; use warnings; use File::Basename; =head for i in `ls *features.tab`; do j=`echo $i | sed 's/features/scores/'`; paste $i $j ; done | cut -d$'\t' -f1-10,16-20,56- > WHESS F="WHESS.txt" head -1 WHESS | cut -f 2- | awk '{ print "#chr\tstart\tend\t"$0 }' > $F cat WHESS | grep -v transcri...
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Perl
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65
#!/usr/bin/env perl # The test script is written in Perl. It runs the voigt_fit program with 3 planes for pseudo-3D fitting 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 ...
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Perl
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64
#!/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...
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Perl
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93
#!/usr/bin/perl use strict; use warnings; use YAML qw(DumpFile); use Cwd; my $dir = getcwd; my $zip = $ARGV[0]; my $list = $ARGV[1]; my $out = $ARGV[2]; my $zip_fasta = $ARGV[3]; $list =~s/NZ_//g; my @list_ids = split(/,/,$list); my %data = (); # case list of accessions if ($list ne 'None'){ foreach my $id(@list...
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Perl
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62
#!/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...
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Perl
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91
#!/usr/bin/env perl # Copyright 2013 Karlsruhe Institute of Technology (Author: Jonas Gehring) # Apache 2.0. # # Concatenates random subsets of a list of pfiles # use Getopt::Long; use List::Util qw(shuffle); use File::Basename; # Prints usage information sub usage() { print STDERR << "EOF"; Usage: pfile_rconcat <...
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Perl
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64
#!/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...
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Perl
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64
#!/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...
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Perl
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80
#!/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...
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Perl
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89
#!/usr/bin/env perl # Copyright 2012 Johns Hopkins University (Author: Guoguo Chen, Jan Trmal) # Apache 2.0. # use strict; use warnings; use Getopt::Long; use XML::Simple; use Data::Dumper; use File::Basename; sub mysort { if ($a->{kwid} =~ m/[0-9]+$/ and $b->{kwid} =~ m/[0-9]+$/) { ($a->{kwid} =~ /([0-9]*)$/...
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Perl
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89
#!/usr/bin/env perl # Copyright 2012 Johns Hopkins University (Author: Guoguo Chen, Jan Trmal) # Apache 2.0. # use strict; use warnings; use Getopt::Long; use XML::Simple; use Data::Dumper; use File::Basename; sub mysort { if ($a->{kwid} =~ m/[0-9]+$/ and $b->{kwid} =~ m/[0-9]+$/) { ($a->{kwid} =~ /([0-9]*)$/...
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Perl
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60
#!/usr/bin/perl # # Copyright 2015 David Snyder # 2017 Radboud University (Author: Emre Yilmaz) # Apache 2.0. # Usage: make_fame_train.pl corpus/SV/ data/ complete 3sec eval. if (@ARGV != 5) { print STDERR "Usage: $0 <path-to-FAME corpus> <path-to-output> <task-name> <subtask-name> <dataset-name>\n"; ...
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Perl
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65
#!/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...
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Perl
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87
#!/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 $c...
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Perl
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60
#!/usr/bin/perl # # Copyright 2015 David Snyder # 2017 Radboud University (Author: Emre Yilmaz) # Apache 2.0. # Usage: make_fame_train_year.pl corpus/SV/ data/ complete 3sec eval 1t3. if (@ARGV != 5) { print STDERR "Usage: $0 <path-to-FAME corpus> <path-to-output> <task-name> <subtask-name> <dataset-na...
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Perl
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64
#!/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...
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Perl
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88
#!/usr/bin/perl ​ use strict; use warnings; ## Script that reads a PHYLIP alignment and a text file ## with the species names to be subset. It outputs a new ## alignment with the species listed in this text file. ## ## Usage: ## <path_to_script>/Get_partitions.pl <path_to_aln1> <path_to_text_file> <num_bp> ## ## Co...
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Perl
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70
#!/usr/bin/perl # # Copyright 2018 Ewald Enzinger # # Usage: make_voxceleb2.pl /export/voxceleb2 dev data/dev # # Note: This script requires ffmpeg to be installed and its location included in $PATH. if (@ARGV != 3) { print STDERR "Usage: $0 <path-to-voxceleb2> <dataset> <path-to-data-dir>\n"; print STDERR "e.g. ...
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Perl
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65
#!/usr/bin/env perl use warnings; #sed replacement for -w perl parameter # Copyright 2012 Milos Janda # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICE...
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Perl
2,290
73
#!/usr/bin/env perl #This reads in rules, of the form put out by get_rules.pl, e.g.: # ERT,,ER0 T, # MENT,ING,M AH0 N T,IH0 NG # S,TON,Z,T AH0 N # ,ER,IH0 NG,IH0 NG ER0 # ,'S,M AH0 N,M AH0 N Z #TIONS,TIVE,SH AH0 N Z,T IH0 V # and it works out a hierarchy that says which rules are sub-cases # of which rules: it output...
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Perl
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80
#!/usr/bin/perl use strict; use warnings; use Data::Dumper; use List::Util qw/shuffle/; my ($dataid, $testclass, $maxreads) = @ARGV; my %seqcounts = ( "Coronaviridae.genomes.fasta" => 12, "Homo_sapiens.GRCh38.cdna.e99.canonicaltranscripts.fasta" => 22499, "Influenza.genomes.fasta" => 1024, "Metapneumovirus.genome...
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Perl
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73
#!/usr/bin/perl use strict; use warnings; use Data::Dumper; our %INX = ('ML25997a' => 'INXB', 'ML25999a' => 'INXD', 'ML25993a' => 'INXA', 'ML25998a' => 'INXC', 'ML32831a' => 'INXG.1', 'ML218922a' => 'INXH', 'ML07312a' => 'INXL', ...
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Perl
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94
#!/usr/bin/env perl # Copyright 2012 Johns Hopkins University (Author: Guoguo Chen) # Apache 2.0. # use strict; use warnings; use Getopt::Long; my $Usage = <<EOU; Usage: count_to_logprob.pl <confusing_in|-> <counfusing_out|-> This script takes in the confusion phone pair counts and converts t...
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Perl
2,439
73
#!/usr/bin/env perl # Copyright 2019 Junbo Zhang # 2020 Xiaomi Corporation (Author: Junbo Zhang) # 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...
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Perl
2,441
108
#!/usr/bin/perl my $eps = ","; my $boundary = "#"; my $final_symbol = $eps; # "-2" my $sentence_end = "</s>"; my %boundary_hash = (); my $max_boundary_id = -1; my $morphs = 0; # If true, does not generate word breaks automatically use Fsm; use strict; use warnings; # Open input # my $fh; my $lexfile = shift @ARGV...
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Perl
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108
#!/usr/bin/perl use strict; use warnings; use Getopt::Long; my $Usage = <<EOU; Usage: txt2rttm.pl [options] <txt_in|-> <rttm_out|-> Allowed options: --flen : Frame length (float, default = 0.1) --symtab : Symbol table (string, default = "") --segment ...
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Perl
2,450
65
#!/usr/bin/perl # # Copyright 2017 Ewald Enzinger # Apache 2.0 # # Usage: data_prep.pl /export/data/cv_corpus_v1/cv-valid-train valid_train if (@ARGV != 3) { print STDERR "Usage: $0 <path-to-commonvoice-corpus> <dataset> <valid-train|valid-dev|valid-test>\n"; print STDERR "e.g. $0 /export/data/cv_corpus_v1 cv-va...
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Perl
2,452
85
#!/usr/bin/env perl # # Johns Hopkins University (Author : Gaurav Kumar) # # This script should be run from one directory above the current one # # Rough partitions that are needed are : # # ASR Train : 120k utterances # ASR tune : 20k utterances # ASR eval : 20k utterances # MT train : 105k utterances # MT tune : Same...
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Perl
2,463
76
#!/usr/bin/perl use strict; use Cwd; use File::Spec; use File::Basename; =head Download both COSMIC CosmicCodingMuts.vcf.gz and CosmicNonCodingVariants.vcf.gz files from http://cancer.sanger.ac.uk/cosmic/download. An account is needed to download COSMIC VCF files - see https://cancer.sanger.ac.uk/cosmic/register sf...
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Perl
2,471
71
#!/usr/bin/env perl # # Copyright 2015 University of Sheffield (Author: Ning Ma) # Apache 2.0. # # Create transcriptions for the CHIME/GRID corpus from a list of # file names (used as UTTERANCE-ID, e.g. s1_bgab3n) # It outputs lines containing UTTERANCE-ID TRANSCRIPTIONS, e.g. # s1_bgab3n BIN GREEN AT B THREE NOW #...
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Perl
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83
#!/usr/bin/perl use warnings; #sed replacement for -w perl parameter # # Copyright 2013 Daniel Povey # Apache 2.0 if (@ARGV != 2) { print STDERR "Usage: $0 <path-to-LDC2001S13> <path-to-output>\n"; print STDERR "e.g. $0 /export/corpora5/LDC/LDC2001S13 data/swbd_cellular1_train\n"; exit(1); } ($db_base, $out_...
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Perl
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62
#!/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...
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Perl
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83
#!/usr/bin/perl use warnings; #sed replacement for -w perl parameter # # Copyright 2013 Daniel Povey # Apache 2.0 if (@ARGV != 2) { print STDERR "Usage: $0 <path-to-LDC2004S07> <path-to-output>\n"; print STDERR "e.g. $0 /export/corpora5/LDC/LDC2004S07 data/swbd_cellular2_train\n"; exit(1); } ($db_base, $out_...
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Perl
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62
#!/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...
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Perl
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147
#!/usr/bin/env perl use warnings; use strict; use Data::Dump qw(pp dumpf); use List::Util qw(reduce); sub cartesian_product { reduce { [ map { my $item = $_; map [ @$_, $item ], @$a } @$b ] } [[]], @_ } sub gen_range { (my $begin, my $step, my $end) = split(':', $_[0]); my @range = (...
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Perl
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128
#!/usr/bin/perl my $DNA= $ARGV[0]; @dna = $DNA; print "@dna[0]\t\t-> DNA\n"; for ($i = 0 ; $i < length(@dna[0]); $i++ ) { @c[$i] = substr( @dna[0], $i, 1); #print "@c[$i]"; if(@c[$i] eq 'A') { $counterpart=$counterpart."T"; $rna=$rna."A"; } elsif(@c[...
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Perl
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147
#!/usr/bin/env perl use warnings; use strict; use Data::Dump qw(pp dumpf); use List::Util qw(reduce); sub cartesian_product { reduce { [ map { my $item = $_; map [ @$_, $item ], @$a } @$b ] } [[]], @_ } sub gen_range { (my $begin, my $step, my $end) = split(':', $_[0]); my @range = (...
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Perl
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72
#!/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...
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Perl
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62
#!/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...
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Perl
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98
#!/usr/bin/perl use strict; my $chrom_focus = $ARGV[0]; for (my $i=37; $i >= 1; $i--){print "NL$i;";}exit; print "[\n"; my %gene_positions; open(G,"Map_annotation_ID_NFGwada.gff3.gff3"); while(<G>){ my $line = $_; $line =~s/\n//g;$line =~s/\r//g; my @infos = split("\t",$line); if ($infos[2] eq "mRNA" && /ID=([^...
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Perl
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81
#!/usr/bin/env perl # Copyright 2014 Gaurav Kumar. Apache 2.0 use utf8; use File::Basename; ($tmpdir)=@ARGV; #$tmpdir='../data/local/tmp'; $trans="$tmpdir/train_transcripts.flist"; $reco="$tmpdir/reco2file_and_channel"; open(T, "<", "$trans") || die "Can't open transcripts file"; open(R, "|sort >$reco") || die "Can...
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Perl
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113
#!/usr/bin/env perl # Copyright 2017 John Morgan # Apache 2.0. # heroico_answers_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/heroico"; system "mkdir -p $tmpdir/answers"; # input wav file li...
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Perl
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82
#!/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...
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Perl
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106
#!/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...
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Perl
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86
#!/usr/bin/perl # check_spaces.pl : Check source files for tabs and trailing spaces # # Author : Rob Davies <rmd@sanger.ac.uk> # # Copyright (C) 2018-2019 Genome Research Ltd. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (...
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Perl
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84
#!/usr/bin/env perl # This takes the output of e.g. get_candidate_prons.pl or limit_candidate_prons.pl # or reverse_candidates.pl, which is 7-tuples, one per line, of the form: # # word;pron;base-word;base-pron;rule-name;de-stress;rule-score # # and selects the most likely prons for the words based on rule # score. I...
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Perl
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90
#!/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...
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Perl
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89
#!/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...
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Perl
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124
#!/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...
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Perl
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94
#!/usr/bin/env perl use warnings; #sed replacement for -w perl parameter # Copyright 2012-2014 Johns Hopkins University (Author: Daniel Povey) # Apache 2.0. # This program is a bit like ./sym2int.pl in that it applies a map # to things in a file, but it's a bit more general in that it doesn't # assume the things be...
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Perl
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94
#!/usr/bin/env perl use warnings; #sed replacement for -w perl parameter # Copyright 2012-2014 Johns Hopkins University (Author: Daniel Povey) # Apache 2.0. # This program is a bit like ./sym2int.pl in that it applies a map # to things in a file, but it's a bit more general in that it doesn't # assume the things be...
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Perl
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69
#!/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...
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Perl
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162
#!/usr/bin/perl # Transforms a BLASTP output into a flat MA file containing in the first line # the number of alignments and the sequences in the following lines # $filen=$ARGV[0]; $fileo=$ARGV[1]; $fasta=$ARGV[2]; open(fast,"<$fasta"); @testo_temp=<fast>; shift(@testo_temp); while (@testo_temp) { chomp(@testo_tem...
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Perl
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119
#!/usr/bin/env perl # Copyright 2010-2011 Yanmin Qian 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 P...
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Perl
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92
#!/usr/bin/env perl # Copyright 2015 University of Sheffield (Author: Ning Ma) # Apache 2.0. # # Computes keyword recognition accuracy (letter+digit) for the CHiME/GRID # corpus from a transcription file containing: # s01_bgaa9a_0dB BIN GREEN IN R NINE AGAIN # s01_bgaa9a_3dB BIN GREEN AT A NINE AGAIN # # Us...
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Perl
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85
#!/usr/bin/perl # # Copyright 2015 David Snyder # 2017 Radboud University (Author: Emre Yilmaz) # Apache 2.0. # Usage: make_fame_test.pl corpus/SV/ data/ complete 3sec eval. if (@ARGV != 5) { print STDERR "Usage: $0 <path-to-FAME corpus> <path-to-output> <task-name> <subtask-name> <dataset-name>\n"; ...
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Perl
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95
#!/usr/bin/env perl # Reads a dictionary, and prints out a list of words that seem to be pronounced # as acronyms (not including plurals of acronyms, just acronyms). Uses # the prons of the individual letters (A., B. and so on) to judge this. # Note: this is somewhat dependent on the convention used in CMUduct, that ...
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Perl
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60
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; # bioperl module to handle sequence input/output use Bio::Seq; # bioperl module to handle sequences with features use Bio::SeqUtils; # bioperl module with additional methods (including features) for Bio::Seq objects my $usage = "\n". "\t####################...
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Perl
2,879
130
#!/usr/bin/env perl # Copyright Hong Kong University of Science and Technology (Author: Ricky Chan) 2013. # # A script for dictionary generation with an input dict and a wordlist # # example of dict format as follow: # WORD1 ph1 ph2 # WORD2 ph1 ph2 ph3 # WORDX ph4 # WORDY ph4 ph5 # WORDZ ph3 ph1 # # example of wordli...
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Perl
2,882
85
#!/usr/bin/perl # # Copyright 2015 David Snyder # 2017 Radboud University (Author: Emre Yilmaz) # Apache 2.0. # Usage: make_fame_test_year.pl corpus/SV/ data/ complete 3sec eval 1t3. if (@ARGV != 5) { print STDERR "Usage: $0 <path-to-FAME corpus> <path-to-output> <task-name> <subtask-name> <dataset-nam...
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Perl
2,889
102
#!/usr/bin/perl use warnings; #sed replacement for -w perl parameter # # Copyright 2013 Daniel Povey # Apache 2.0 if (@ARGV != 2) { print STDERR "Usage: $0 <path-to-LDC2002S06> <path-to-output>\n"; print STDERR "e.g. $0 /export/corpora5/LDC/LDC2002S06 data/swbd2_phase3_train\n"; exit(1); } ($db_base, $out_di...
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Perl
2,890
73
#!/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...
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Perl
2,908
80
#!/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 ...
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Perl
2,909
129
#!/usr/bin/perl #merge_bams_in_tophat_folder.pl use warnings; use strict; die "Please give 1. Orthogroups.csv 2. Number of groups you wish to merge\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 $o...
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Perl
2,911
83
#!/usr/bin/env perl use warnings; #sed replacement for -w perl parameter # Copyright 2013 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...
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Perl
2,914
115
#!/usr/bin/env perl use warnings; #sed replacement for -w perl parameter # Author: Peng Qi (pengqi@cs.stanford.edu) # This script maps Switchboard speaker IDs to the true physical speakers # and fixes the utterances IDs accordingly. Expected to be run one level of # directory above. sub trim { (my $s = $_[0]) =~ ...
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Perl
2,926
84
#!/usr/bin/env perl use warnings; #sed replacement for -w perl parameter # Copyright 2013 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...
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Perl
2,934
87
#!/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...
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Perl
2,942
106
#!/usr/bin/perl use warnings; #sed replacement for -w perl parameter # # Copyright 2017 David Snyder # Apache 2.0 if (@ARGV != 2) { print STDERR "Usage: $0 <path-to-LDC98S75> <path-to-output>\n"; print STDERR "e.g. $0 /export/corpora3/LDC/LDC98S75 data/swbd2_phase1_train\n"; exit(1); } ($db_base, $out_dir) =...
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Perl
2,961
120
#!/usr/bin/env perl # Copyright 2017 John Morgan # Apache 2.0. # subs_prepare_data.pl - condition subs data for lm training use strict; use warnings; use Carp; use Encode; # set lower and upper bounds my $low_bound = 8; # only segments with at least $low_bound words will be written my $up_bound = 16; # only segme...
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Perl
2,966
125
#!/usr/bin/perl use strict; my $indir = $ARGV[0]; my $matrix = $ARGV[1]; my $out = $ARGV[2]; my $strain_names = $ARGV[3]; my $gene_info_dir = $ARGV[4]; my %strains_of_gb; open(F,$strain_names); while(<F>){ my $line = $_; $line =~s/\n//g;$line =~s/\r//g; my ($gb,$strain) = split(/\t/,$line); $strains_of_gb{$gb} =...
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Perl
2,969
155
#!/usr/bin/perl # Copyright 2020 Ivan Medennikov (STC-innovations Ltd) # Apache 2.0. # This script creates 3 negative utt2spk files with speakers from the same session. ($filein,$fileout,$fileout2,$fileout3)=@ARGV; $Nspk=4; %id2time2utt={}; %utt2spk={}; %utt2P={}; %sid2spk={}; open(fidin, "<$filein") or die "...
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Perl
2,972
112
#!/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...
7d5064363308fa485ab7efd2e5310619d0cd41ca10379b0f5e6a3fbcae634ef2
Perl
2,989
135
#!/usr/bin/env perl use warnings; # Copyright 2015 Tokyo Institute of Technology (Authors: Takafumi Moriya and Takahiro Shinozaki) # 2015 Mitsubishi Electric Research Laboratories (Author: Shinji Watanabe) # Apache 2.0 # Acknowledgement This work was supported by JSPS KAKENHI Grant Number 26280055. # Thi...
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Perl
2,996
101
#!/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...
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Perl
3,013
121
#!/usr/bin/env perl # Copyright 2012 Johns Hopkins University (Author: Daniel Povey). Apache 2.0. #scalar(@ARGV) >= 1 && print STDERR "Usage: summarize_warnings.pl <log-dir>\n" && exit 1; sub split_hundreds { # split list of filenames into groups of 100. my $names = shift @_; my @A = split(" ", $names); my @a...