sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f040e2b74452db7683c608b801e3453212293d44da0c9d0177f035c3652b1473 | MATLAB | 71,667 | 1,725 | % #ko make new ATLAS from modifed "ANO.xlx"-EXCELFILE
% #k Prerequisites: ATLAS(nifti-file) such as ANO.nii and a corresponding but modified excelfile (ANO.xls).
% #k The modified excelfile (ANO.xls) must contain two additional columns (newIDs and HemisphereType)...
% #k ...see parameter/'excelfile' (below)
% _____... |
78275590764e3ee0276d3b8dee6b90a14e714c6bcbb395a2ddb5cd4f1af1591a | MATLAB | 73,220 | 1,509 | close all
clear
clc
%%%%% master input from the user
random_seed_velocity_heatmap=1;
behavior_sort_threshold=3; %% 1=for, 2=turn, 3=rev
behavior_comparision_mode=2; %% 1:<=, 2:==, 3: >=
velocity_sort_threshold=0;
velocity_comparision_mode=1; %% 1:<=, 2:==, 3: >=
analysis_new_data=1;
%%%%%%% user input parameters %%%%... |
dff4c41e82d03f0fddd1f8547883cc743007499a7c8bf9a8e5aa69edd7449811 | MATLAB | 75,335 | 1,484 | %Copyright © 2018- Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
function [void] = zef_plot_meshes(void);
void = [];
sensors_point_like = [];
loop_movie = 1;
length_reconstruction_cell = 1;
movie_fps = evalin('base','zef.movie_fps');
submesh_num = evalin('base','z... |
357ca20848187412966302dba30257f32db5b8de2ec911ab701b4570acb2ea60 | MATLAB | 76,054 | 1,446 |
% .
%
% #yk ANTx2
%
% #b ⇒ Respository: <a href= "https://github.com/ChariteExpMri/antx2">GitHub:github.com/ChariteExpMri/antx2</a>
% #b ⇒ Tutorials: <a href= "https://chariteexpmri.github.io/antxdoc/">https://chariteexpmri.github.io/antxdoc/</a>
% #b ⇒ Templates : <a href= "https://drive... |
74f1a7b6719500d750839b4e414aaba4c9c37fb3c434de01b4845fc5e4c2c194 | MATLAB | 76,082 | 1,575 | close all
clear
clc
%%%%% master input from the user
stim_threshold_min=0.01; %%%% min stim power
stim_threshold_max=10; %%%% max stim power
ellipse_ratio_threshold=3.1; %%% use 3.6 as default value
negative_vel_threshold=-0.11;
random_seed_velocity_heatmap=1;
behavior_sort_threshold=3; %% 1=for, 2=turn, 3=rev
... |
15e092a73ec53e7d19f6b5575a3a967a7cb5dfdccdbaa8ea1520d8e73a4998af | MATLAB | 131,807 | 2,638 | %Copyright © 2018- Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
function [void] = zef_print_meshes(~);
zef = evalin('base','zef');
f_ind = 1;
if isfield(zef,[zef.current_sensors '_get_functions'])
zef = zef_fix_sensors_get_functions_array_size(zef);
sensors_get_f... |
9aba42b7aea1fde2c2576dd8ffef4e4f5f2e855f7ee22f1b7ee765409ccbcc01 | MATLAB | 132,114 | 4,914 |
% Panel is an alternative to Matlab's "subplot" function.
%
% INSTALLATION. To install panel, place the file "panel.m"
% on your Matlab path.
%
% DOCUMENTATION. Scan the introductory information in the
% folder "docs". Learn to use panel by working through the
% demonstration scripts in the folder "demo" (list the d... |
ea85dda825c4d2c6b40e9e07337695757a248f215d9516a287b1f706651c545b | MATLAB | 145,098 | 2,940 | function [handles,levels,parentIdx,listing] = findjobj(container,varargin)
%findjobj Find java objects contained within a specified java container or Matlab GUI handle
%
% Syntax:
% [handles, levels, parentIds, listing] = findjobj(container, 'PropName',PropValue(s), ...)
%
% Input parameters:
% container -... |
312396e0447b50f17065396ad5c072db34af9cc6fce0aac1878f63596fc6002e | MATLAB | 173,765 | 5,127 |
%% #b ant-callbacks
%%
% #yk EXAMPLES
% antcb('getsubjects') % get selected subjects-->only those selected from [ANT] Mouse-listbox
% ..also possible to obtain the pyratNo, animalNames and a substring from animalnames
% ->for HELP type antcb('getsubjects?') ... |
8ed555764465b34e18f86068aade11b062b647f02628e611b4884c1d90d6a3ce | MATLAB | 200,000 | 3,480 | classdef PatMap < matlab.apps.AppBase
% Properties that correspond to app components
properties (Access = public)
UIFigure matlab.ui.Figure
IOPanel matlab.ui.container.Panel
LoggingConsoleLabel matlab.ui.control.Label
... |
a47d3c1bd6c4b2a238049da0ab9080da773060f6a0eb43f90b13aa7bdb1866d7 | MATLAB | 200,002 | 3,328 | function snips_input1
snips
return
%% #################################################
% cmd
% open Antx-GUI and load project
ant;
antcb('load', fullfile(pwd,'proj.m' )) ;
% close Antx-GUI
antcb('close')
% close Antx-GUI & exit from snips-GUI
snips('close');
antcb('close'); exit
% ___________... |
88f733fa90b09317e03cf83c79625331537037f144b11e8b4324c47d6cd3bd42 | NEURON | 841 | 70 | TITLE SEClamp
NEURON {
POINT_PROCESS MySEClamp
ELECTRODE_CURRENT i
RANGE dur1, amp1, dur2, amp2, dur3, amp3, rs, vc, i
}
UNITS {
(nA) = (nanoamp)
(mV) = (millivolt)
(uS) = (microsiemens)
}
PARAMETER {
rs = 1 (megohm) <1e-9, 1e9>
dur1 (ms)
amp1 (mV)
dur2 (ms) <0, 1e9>
amp2 ... |
92c8c533c10b8861cec0326c01a6522bd5d4b494774d9d7ed9004bebef4fd441 | NEURON | 882 | 64 | begintemplate BallStick
public init
public soma, dend
public all
objref all
create soma, dend
proc init() {
topol()
all = new SectionList()
soma all.wholetree()
geom_nseg()
biophys()
shape3D()
}
proc topol() {
connect dend(0), soma(1)
}
proc geom_nseg() {
soma {
L = 2
... |
b4f0c1bd95943f74548d33ec56637d465cb0d5249666e7059d85efd0fc13c10d | NEURON | 2,558 | 159 | : Vector stream of events
COMMENT
A VecStim is an artificial spiking cell that generates
events at times that are specified in a Vector.
HOC Example:
// assumes spt is a Vector whose elements are all > 0
// and are sorted in monotonically increasing order
objref vs
vs = new VecStim()
vs.play(spt)
// now launch a si... |
6089b5a4eacf1ec5c7b0c8950eb8c5e3f2f8cbf373eb7d709ca97596a995420b | NEURON | 2,692 | 109 | TITLE AMPA and NMDA receptor with presynaptic short-term plasticity
COMMENT
AMPA and NMDA receptor conductance using a dual-exponential profile
presynaptic short-term plasticity based on Fuhrmann et al. 2002
Implemented by Srikanth Ramaswamy, Blue Brain Project, July 2009
GUY: Removed plasticity and depression
END... |
b6ebc3a5e4867267dd47fc370886158c613ac449f68416ba05037180310bee37 | NEURON | 3,168 | 162 | TITLE Senn 2014 Neuron plasticity
NEURON {
POINT_PROCESS BP_Syn
RANGE i, g
ELECTRODE_CURRENT i
RANGE lr_start, lr_end, layer_flag
RANGE u_0, u_1, u_2, u_3, u_4, u_5, u_6, u_7, u_8, u_9
RANGE s_0, s_1, s_2, s_3, s_4, s_5, s_6, s_7, s_8, s_9, s_sum, s_u_soma
RANGE tgt_0, tgt_1, tgt_2, tgt_3, tgt_4, tgt_... |
e5fa1377b71f9c37d964578075eb4f81ee2534167de3e49256832540c8f125e7 | NEURON | 10,638 | 411 | : $Id: netstim.mod 2212 2008-09-08 14:32:26Z hines $
: comments at end
: the Random idiom has been extended to support CoreNEURON.
: For backward compatibility, noiseFromRandom(hocRandom) can still be used
: as well as the default low-quality scop_exprand generator.
: However, CoreNEURON will not accept usage of the ... |
d7d40352df570341caa6f01acaea339d0262cdec0d5716792b72c3769932b953 | NEURON | 11,858 | 423 | begintemplate cell0603_11_model_937
// Based on models of the BBP: https://bbp.epfl.ch/nmc-portal/microcircuit
// Active properties were fitted using the MOO algorithm.
// See Eyal et al 2017 for details.
public init, init_rc, delete_axon , init_biophys, insertChannel,biophys,distribute,geom_nseg,geom_nsec,delete_spin... |
f69a2d5dd998d24e7f6c3d263eb3fe1c8d46e5ca5407a70569093f10699212a2 | NEURON | 12,037 | 424 | begintemplate PassiveHPC
// Based on models of the BBP: https://bbp.epfl.ch/nmc-portal/microcircuit
// Active properties were fitted using the MOO algorithm.
// See Eyal et al 2017 for details.
public init, init_rc, delete_axon , init_biophys, insertChannel,biophys,distribute,geom_nseg,geom_nsec,delete_spine,add_few_s... |
baa2cbbb493da598ffecd5aad07af2f032272d08fd3eb80c1dae21939e1397d5 | Perl | 245 | 8 | use ExtUtils::MakeMaker;
WriteMakefile(
NAME => 'Tabix',
VERSION_FROM => 'Tabix.pm',
LIBS => ['-lz -L.. -ltabix'],
DEFINE => '-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE',
INC => '-I..',
);
|
feecd75830df54e22d81122e9b57613671b55952c026a1e84a1204a464fd80fc | Perl | 249 | 21 | #!/usr/bin/perl
use warnings;
use strict ;
my $sum = 0;
my $n = 0;
while(<STDIN>){
chomp;
my @l = split /\t/, $_;
$sum += $l[4];
$n++;
}
my $mean = $sum / $n;
print STDERR "sum\t$sum\n";
print STDERR "n\t$n\n";
print $mean;
|
f240896f52c93f586807da078ba6acee72d565234ce168aa43faae39d0d7a985 | Perl | 615 | 30 | #!/usr/bin/perl
use warnings;
use strict ;
my $low = 0;
my $normal = 0;
my $high = 0;
my $total = 0;
while(<STDIN>){
chomp;
my @l = split /\t/, $_;
my $len = $l[2] - $l[1];
$low += $len if($_ =~ /_ld/) ;
$normal += $len if($_ =~ /_nd/) ;
$high += $len if($_ =~ /_hd/) ;
... |
e4ba8322a9099e4946a08b3ff8bcf0811d469437031e7c09a73552e2ca9f59a9 | Perl | 837 | 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... |
778d8151041104d3ea80f1e33c1dd442b3c23a5400e9dea4fe8221e4893adf2f | Perl | 1,109 | 40 | #! /usr/bin/perl
use strict;
my $vcf = shift;
my $vcf_out = $vcf;
$vcf_out =~ s/.vcf$/_CONVERT.vcf/;
open OUT, ">$vcf_out" or die "Cannot create file\n$!\n";
open VCF, $vcf;
while(my $line = <VCF>) {
chomp($line);
print OUT $line . "\n" if $line =~ /^#/;
next if $line =~ /^#/;
my ($chrom, $pos, $id, $ref, $alt, ... |
c6f0a625a1592a760286180028ca51f24f850221dbfad0394cbefa6c88e1fa00 | Perl | 1,135 | 47 | #!/usr/bin/perl
#
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================
#Construct the modl_reg() function from a pro... |
80fee0fad32b99631de7fb68232cf9a90e21d70e5c9610d1c680b7afb536ae02 | Perl | 1,203 | 38 | #!/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... |
72094643a8f3dd7870a60fd9c8f02b804a0c09040a30e5307d9bfbcb877bca66 | Perl | 1,421 | 51 | #!/usr/bin/perl -w
use strict;
#run kinship alalysis on vcf input file.
#requires plink, king and vcftools;
#to be incorporated: read in proposed ped file with fam structure and parse results file. warn if kinship values disagree with the ped file!
#Relationship Kinship coefficient Coeffcient of related... |
7e87ed252b68c1fdc290afb06ffedd1793816f6efccd814f69f6be6a0f746888 | Perl | 1,521 | 95 | #!/usr/bin/perl -w
# split_unmapped_to_fasta.pl
# (c) 2012 - Ryan M. Layer
# Hall Laboratory
# Quinlan Laboratory
# Department of Computer Science
# Department of Biochemistry and Molecular Genetics
# Department of Public Health Sciences and Center for Public Health Genomics,
# University of Virginia
# rl6sf@... |
f6bca8e029847974b0dec31e6cad4227a16d6d9cc34dd09ed1f85a5769cc487a | Perl | 1,528 | 57 | #!/usr/bin/perl -w
use strict;
use POSIX qw(tmpnam);
my $email = "i.nijman\@umcutrecht.nl";
my $snpEff_path = "/hpc/cog_bioinf/data/ies/src/snpEff";
my $SAP42_path = "/hpc/cog_bioinf/common_scripts/SAP42-HPC";
my $vcf = $ARGV[0];
die "vcf file invalid or non-existent...\n" unless -e $vcf;
my @jids;
mkdir "SAP42_an... |
d8ffca47d2bfc0a05e6c89591c97b82bb246cb4943c1782440b64cd421492534 | Perl | 1,535 | 47 | #!/usr/bin/perl -w
use strict;
use Number::Format;
#collect flagstats and tally up the totals.
my $fn=new Number::Format( -thousands_sep => '.',
-decimal_point => ',');
my @files = `find \$PWD -iname \"*MERGED*.flagstat\"`;
print scalar @files, " flagstats found\n";
my %totals;
foreach my $file (@files) {
... |
d24e13dcb8d1e021c06cecc38911dd6918476755c77b9999f0e71957e4f43bbb | Perl | 1,590 | 58 | #!/usr/bin/perl
##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published... |
810701e01f3e5b483c30ea87e0b85ca9bd8a0c8319f4cb841c02c12004d355b5 | Perl | 1,711 | 91 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Getopt::Long;
use Carp;
my $prog = basename ($0);
my $verbose = 0;
#my $strandaware = 0;
GetOptions (
"v|verbose"=>\$verbose
# "s"=>\$strandaware
);
if (@ARGV != 2)
{
print STDERR "bed format to junctions\n";
print STDERR "Usage:... |
3040471972b4627237d8f86aba1d75003410c024f29eb7912b9bcd14243ff666 | Perl | 2,018 | 53 | #!/usr/bin/perl
########## LICENCE ##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as publish... |
e30b1c9bab7e3fe66e096ed02f25ce65d1eb0a4114abb8f1c6b50b63cdb0985d | Perl | 2,635 | 101 | #!/usr/bin/perl
##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published... |
2b203942a71a7be03b7ef2aa07f20bb048114d0b8716abbd76c6c2bcd0e4c57e | Perl | 2,870 | 134 | #!/usr/bin/perl -I /booleanfs/sahoo/scripts
if (scalar(@ARGV) <= 0) {
print "perl analyze.pl <cmd> <args>\n";
exit(1);
}
use U;
use Hegemon;
use JSON;
use Data::Dumper;
my $cmd = shift(@ARGV);
if ($cmd eq "tindex") {
&analyzeTherapeuticIndex(@ARGV);
}
if ($cmd eq "uc-map") {
&analyzeUCmap(@ARGV);
}
if ($... |
9deeca00998a004ed70401905ea288f239b66195497a1f7f43d19a00cce5116f | Perl | 2,950 | 87 | #!/usr/bin/env perl
# Copyright 2010-2012 Microsoft Corporation
# Johns Hopkins University (author: Daniel Povey)
# 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:... |
4251575484dcef595eed41f14820059a8a548b058229571bd4f86da3451405a7 | Perl | 2,962 | 97 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 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 being map... |
0ab5feabbb4eaa4a11663053a13ebb5aac6545902e89b517422d9cff90d5b98e | Perl | 3,275 | 112 | #!/usr/bin/perl -w
use strict;
use Getopt::Long;
#parse (or run) output from PhaseByTransmission MedelianViolation file
#CHROM POS AC FAMILY TP MOTHER_GT MOTHER_DP MOTHER_AD MOTHER_PL FATHER_GT FATHER_DP FATHER_AD FATHER_PL CHILD_GT CHILD_DP CHILD_AD CHILD_PL
my $pwd = `pwd`;
chomp($pwd);
my (%vars);
my ($help, $deb... |
f9e4bf04a7a3b314d4c32a6529be8a2672788b96096d3bd2d358d8e1ebe96c06 | Perl | 3,468 | 148 | #!/usr/bin/perl
##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of ascatNgs.
#
# cgpVcf is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published b... |
98f7f4c8741d9bef608d59e94d6cb79ad982a651a15e444a7b4990c423ec8fe2 | Perl | 3,552 | 119 | #!/usr/bin/perl
##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published... |
e36b066d5735b987d00002ebb921bef1b8cde4edeb223402ffbd348d88b99763 | Perl | 3,917 | 128 | #!/usr/bin/perl
########## LICENCE ##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as publish... |
aa3c3987fcc417826249e11131489cfd350831c0af61f34abbf91bbbecc4e104 | Perl | 4,500 | 136 | #!/usr/bin/env perl
#
#===============================================================================
# Copyright 2017 Johns Hopkins University (author: Yenda Trmal <jtrmal@gmail.com>)
# Johns Hopkins University (author: Daniel Povey)
#
# Licensed under the Apache License, Version 2.0 (the "License");... |
7580676a37e7f94bf42ebccf631a621549d9804d2af43fe400895bbf0dbb3063 | Perl | 5,382 | 170 | #!/usr/bin/env perl
# Copyright 2010-2012 Microsoft Corporation
# 2012-2016 Johns Hopkins University (author: Daniel Povey)
# 2015 Xiaohui 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 ... |
8cc865cf86b626af1ce0d701a2a22572bb69a56d42511bd91a9f490d8ad7fe17 | Perl | 5,582 | 184 | #!/usr/bin/perl -w
###################################################
### illumina_createConfig.pl
### - Creates a config file based on user input
### Author: R.F.Ernst
###################################################
use strict;
use Cwd qw( abs_path );
use File::Basename qw( dirname );
use Getopt::Long... |
38eadb22b3b2cc0f4934aa85c54bfeae05f8850a791114d468bc15d9d194c2c6 | Perl | 6,589 | 206 | #!/usr/bin/perl
##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published... |
74b301316f575121542176ef95d2aa8c57a4de7f0548f9baeafff7d4238bc256 | Perl | 7,256 | 340 | #!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
use Carp;
use File::Basename;
use Getopt::Long;
my $prog = basename ($0);
my $separateBed = 0;
my $printUniqOnly = 0;
my $verbose = 0;
my $useRNAStrand = 0; # use the strand of the RNA instead of the read
GetOptions (
"u|uniq"=>\$printUniqOnly,
"r|u... |
2907fb3acb11d3c88214752a6a59300aaad078186d5edf5670ae6f33e9ce5f0c | Perl | 7,618 | 255 | #!/usr/bin/perl
########## LICENCE ##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as publish... |
dee8306ee0e0003b843727bd18a1edbc24f880494f518a8e2a5724d8927f120a | Perl | 7,730 | 212 | #!/usr/bin/perl
##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published... |
6ca39f64ee2f219bce80faa59ea59a516303f4267e3c18f6bd3e4285c3fd3a5a | Perl | 7,992 | 219 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
use Cwd;
use File::Basename;
# This program is like run.pl except rather than just running on a local
# machine, it can be configured to run on remote machines via ssh.
# It requires that you have set up passwordless access to those machines,
# ... |
4a44683c33f74cd1af4f03bb10977db4299da9711a33ba8fc6f1e23b1f65ae81 | Perl | 8,229 | 211 | #!/usr/bin/env perl
# MODULES
use strict;
use warnings;
use Getopt::Long;
# GET PARAMETERS
my $sHelp = 0;
my $sOutputPrefix = "leafviz-annotations";
GetOptions("help!" => \$sHelp, "output:s" => \$sOutputPrefix);
# GLOBALS
my %hMultiCopyTags = ('tag'=>'','Dbxref'=>'','gbkey'=>'','Name'=>'','product'=>'','No... |
a903e82052705a9c46a16d4965e383c2ebe242145a1ea50c189586904791346c | Perl | 9,463 | 246 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# See ../../COPYING for clarification regarding multiple authors
#
# 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://... |
261454a8c2dd910ec7ac2e25aa16fe6236efe778d5c235eaeaa4060f8dcfde49 | Perl | 10,211 | 282 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# In general, doing
# run.pl some.log a b c is like running the command a b c in
# the bash shell, and putting the standard error and output into some.log.
# To run parallel jobs (backgrounded on the host machine), you can do (e.g.)
# run.pl JO... |
3e03a91411b73594b79614bc9feb31a25c49ca916253ca44f30030cc8854de24 | Perl | 10,495 | 284 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# In general, doing
# stdout.pl some.log a b c is like running the command a b c in
# the bash shell, and putting the standard error and output into some.log.
# To run parallel jobs (backgrounded on the host machine), you can do (e.g.)
# stdout... |
a9fdac3b291bb1ac3782cf04a89961c2636c1a549af949b75b1a1ed9bc547d4f | Perl | 13,219 | 390 | #!/usr/bin/perl
##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of ascatNgs.
#
# cgpVcf is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published b... |
ea943b30c397b07e36a9c72e8ae17b34a87cdaf45ad5f8ef746c950f54391f4b | Perl | 13,840 | 328 | #!/usr/bin/perl
##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published... |
8f5daf82a315c641d4a71cee8ec8e6252db1b5c8c7b60723258c13e3659c2dd3 | Perl | 21,447 | 757 | #!/usr/bin/perl -I ..
if (scalar(@ARGV) < 1) {
print "Usage: analyze.pl cmd <args> \n";
print "cmd args:\n";
print " text <?.annot.csv>\n";
exit(1);
}
use U;
use Hegemon;
use JSON;
my $cmd = shift @ARGV;
if ($cmd eq "network") {
&analyzeNetwork(@ARGV);
}
if ($cmd eq "n-cls") {
&analyzeNameCLS(@... |
fef851a1ee2e1ca43e819ebb809eaa85f982e4afcfd64f9c1b7d196421387240 | Perl | 21,702 | 775 | #!/usr/bin/perl -I ..
# Author: Debashis Sahoo <dsahoo@ucsd.edu>
if (scalar(@ARGV) <= 0) {
print "perl analyze.pl <cmd> <args>\n";
exit(1);
}
use U;
use Network;
use Graph;
use Hegemon;
use LWP::UserAgent;
use Data::Dumper;
use JSON;
my $cmd = shift(@ARGV);
if ($cmd eq "toidx") {
&U::convertidx(@ARGV);
}
i... |
f27e00c1323306bab61fb402a2219fc8b4c07a2aa9b1baf3a229550b98211e08 | Perl | 23,753 | 624 | #!/usr/bin/env perl
use strict;
use warnings;
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey).
# 2014 Vimal Manohar (Johns Hopkins University)
# Apache 2.0.
use File::Basename;
use Cwd;
use Getopt::Long;
# queue.pl has the same functionality as run.pl, except that
# it runs the job in qu... |
7d443abca314fd00d2f2d3928017a497e0805709edfe2f0aaf93376311d29b7a | Perl | 24,037 | 627 | #!/usr/bin/env perl
use strict;
use warnings;
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey).
# 2014 Vimal Manohar (Johns Hopkins University)
# 2015 Johns Hopkins University (Yenda Trmal <jtrmal@gmail.com>>)
# Apache 2.0.
use File::Basename;
use Cwd;
use Getopt::Long;
# slurm... |
06d36d292270ec69d0655713dbf6aca4e706fcf0d2c4e15cfd8da6fbd883fd9d | Perl | 33,140 | 1,223 | #!/usr/bin/perl -I .
# Author: Debashis Sahoo <dsahoo@ucsd.edu>
if (scalar(@ARGV) <= 0) {
print "perl analyze.pl <cmd> <args>\n";
exit(1);
}
use U;
use Network;
use Graph;
use Hegemon;
use LWP::UserAgent;
use Data::Dumper;
use JSON;
my $cmd = shift(@ARGV);
if ($cmd eq "toidx") {
&U::convertidx(@ARGV);
}
if... |
6c0e698d1df5ed28aaffbf396bd3fe3f9cd80ba9323d1f8a34486d64dcc0b5ee | Perl | 34,073 | 1,253 | #!/usr/bin/perl -I .
# Author: Debashis Sahoo <dsahoo@ucsd.edu>
if (scalar(@ARGV) <= 0) {
print "perl analyze.pl <cmd> <args>\n";
exit(1);
}
use lib '..';
use U;
use Network;
use Graph;
use Hegemon;
use LWP::UserAgent;
use Data::Dumper;
use JSON;
my $cmd = shift(@ARGV);
if ($cmd eq "toidx") {
&U::convertid... |
2d90971f354a8c28796fcdb94a35ac35147bcfb83330280214709029f70a5476 | Perl | 54,942 | 874 | #!/usr/bin/perl -w
##########################################
### illumina_pipeline.pl
### - Main pipeline script
### - Read and check config and ini file
### - Start selected modules
###
### Author: S.W.Boymans & R.F.Ernst
##########################################
### Load common perl modules ####
use strict;
use PO... |
9eba8ebb4aa8e2c748a5ba5006416c76342332f83423c6e1bda907f22ed800b3 | Perl | 57,624 | 1,689 | #!/usr/bin/perl -I /booleanfs/sahoo/scripts
if (scalar(@ARGV) <= 0) {
print "perl analyze.pl <cmd> <args>\n";
exit(1);
}
use IPC::Open2;
use U;
use Hegemon;
use Data::Dumper;
use JSON;
my $cmd = shift(@ARGV);
if ($cmd eq "dynrange") {
&analyzeDynRange(@ARGV);
}
if ($cmd eq "select-noad") {
&analyzeNOAD(@... |
677d9d57f7d9283ea6f8b12e8d64c0b21ad2d85bbc0a8924af5fb10fefc3b65b | Python | 16 | 1 | ## Blank Load ## |
f1ed2c77776dafb4cfee15c45800f6c947a409e4414dc08b8c4763799569306a | Python | 19 | 1 | from .psf import *
|
3abbf3b30c284d1258b30cbfb00ff823ac9b6943dc4cce4c601e80fa24f9f16b | Python | 20 | 1 | __version__="5.7.1"
|
d30aa65bad30ad7ce524b92348b506504cfb13ec8944157033d30393c3c4e936 | Python | 20 | 1 | from ._impl import * |
273209fdb6fac2997c62f5550925a1da787e293d124f09018fd4f84ea7ecbe70 | Python | 21 | 1 | __version__="1.5.15"
|
cd88851ea47b2706ef74af5dbcaae1f914cd7d4aa31d4c02e024dc1403d560b7 | Python | 22 | 1 | __version__ = "0.6.3"
|
2769344e4b9ef357422817e707dd3b525b0169f616a5209cdaad8cbe310d0178 | Python | 23 | 1 | __version__ = "2.14.0"
|
4f086be217fcf857ab7c39dfd990ce41445a970db80d4ff7486e5e72875d9fe6 | Python | 23 | 1 | __version__ = '0.5.0'
|
e47f0362e3f754e34e8cbd0057377303a4753d47bfc8ccbf4531035c549bdb9b | Python | 23 | 1 | from .clip import load
|
a6374900493d8e3093685d121b5cf7b66a39ffcfb315ea1db66ab83650c68172 | Python | 25 | 1 | from .api import clipkit
|
d34cc4a044c9af6db60f792cb843c28aa1d1fdb1843eddf331dc4f0965a04b08 | Python | 27 | 1 | from .main import DSModel
|
acdf2f9a668a873753ccd5b67667415f695c36c79d63e12cece72c012f1b7c2b | Python | 29 | 1 | from .utils import * # NOQA
|
f602920f6970cb1b3cf73760c6d48d76fe341950ffc0b81377367e9160e8a152 | Python | 32 | 1 | from latentvelo.tools import *
|
7ebb0db8d3bed07f3b1b400f40b489235a9af3f6f2f0df1b9de8391a18d344da | Python | 33 | 1 | from optimizer.Adams import Adams |
2768d9302919a27e050694f9abb53598fdd0ee14262b812079e6c5151a23ce32 | Python | 35 | 1 | from latentvelo.plotting import *
|
8a2c984ec0252035079d76a27010cb25677001e2da5451059221eb9b6b677e0e | Python | 35 | 1 | from .eva_base import get_evaluator |
c330a25fbf4ee0d0a3bc22405a2ee72eecd3473ad589009ce07c766f58b88960 | Python | 36 | 1 | from latentvelo.evaluation import *
|
3928de94cbf5a16e140df9d2371f015ee0f0595f379a52bd5e55bf29f43c189b | Python | 38 | 2 | import pandas as pd
import numpy as np |
22dae9258125128b8e010e47d0823f62eaf40f0de6b171b75f704d59db5ffbe8 | Python | 43 | 1 | from nengo.conftest import * # noqa: F403
|
5151e27c1da94795970b5d2acfbe8ecc3e5c3badceb5e22c71d2d9bf7c5d00f3 | Python | 43 | 2 | from .config import *
from .figure import * |
105540e2520ca84c793c591186403daca9fb9a596a9e3c093356b9c1490699a5 | Python | 44 | 2 | def test_hello():
print('Hello World!')
|
48ce9882b6ba42f643f8305481a48902ddee97aa4f07bca13e44fea1b7d104ea | Python | 46 | 3 | from .stoi import stoi
__version__ = '0.4.1'
|
5e371515d7e8856b8873a6b0c7b69621777ff72f9143b4dfe93c129df30de23c | Python | 48 | 3 | # -*- coding: utf-8 -*-
__version__ = "0.6.2a"
|
74d5b0db71042c45352f64e225663a4185556d0e7bbb58f750a102fc25fd9edf | Python | 50 | 1 | from attention.attention import Attention # noqa
|
af6874b10e333081c2a02a7afa2cf8445065f58f6aaa18f56f73b90c0f94cf9d | Python | 50 | 1 | import rits_i, brits_i, rits, brits, gru_d, m_rnn
|
37945bf8b42c4c20534062ffab3cf7ccf6dba2305821c130d9491b6862b5bcba | Python | 51 | 1 | from daart.models.base import Segmenter, Ensembler
|
d1ee4ed732fd6e356dd08d7aec395060ff0b4c0d57f86135aef82ee33fd3fcd7 | Python | 52 | 2 | n = Numbers("mcmc_likes_0", col=1, skip=0)
n.plot()
|
f00222ee9706513b03ea75b2da11c07ef8a7e67a161df0e45ae1e0f84a12bf1b | Python | 53 | 1 | from . import clipping_aware_rescaling # noqa: F401
|
92b4b57635170051e2981981f0743a3bdc3cbe20cdafadec26dbd6ea099d8c9d | Python | 60 | 2 | from .data import getDataset
from .data import getDataloader |
11418525bade59f605c1d8b02b39f0df5c96c9308c18e5bc84d7bf0f8bc99e8a | Python | 61 | 3 | from .msa.msa_module import MSAModel
__all__ = ['MSAModel']
|
516fb20039c4173d5d2b5fe94b4475f7f7fed7182e135a3505f42b2f9d2b7e7b | Python | 61 | 2 | """Neuroimaging statistics toolbox."""
__version__ = "0.7.0"
|
5e394093f088cad454cb47160b6db88ac8af6df9a2182c16ccec9965a86b744d | Python | 61 | 3 | import os
ROOT = os.path.abspath(os.path.dirname(__file__))
|
856bbc005f02282eb6f49cd4b630a8025043b6314b2d89e8af3ddfabbd2cb88b | Python | 64 | 3 | from torch.optim import * # NOQA
from .radam import * # NOQA
|
5a9d642ba94e222665223f87438147f69e3db6f63c4a53ac708bd4be03eea5ac | Python | 65 | 3 | from . import load_data
from . import models
from . import utils
|
4d3d27bfd112074da7eff41f2de2dfc2f0c0a58e88c64e6f13d445da0099cd62 | Python | 67 | 1 | from .DeepTransferClassification import DeepTransferClassification
|
c9331c7c2de2deb1013c5921d680a79d857f256ddf76d86892f48e5db73e8812 | Python | 68 | 3 | from .model import create_classifier
__all__ = [create_classifier]
|
3510c3ee3392c90585c54ac6637fcd3f4ba40d001cea802a1b358dd12f6acebe | Python | 70 | 2 | from pydapsys.toc.entry import Folder, StreamType, Stream, EntryType
|
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