sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4f7f1c80ee19ec1ff7c5df8e42df7692dc796f4b13bb88374600052900c80baf | Perl | 3,783 | 124 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Carp;
use Nuc_translator;
use Fasta_reader;
use Getopt::Long qw(:config pass_through);
my $usage = "\n\nusage: $0 fasta_file [DEBUG] [--genetic_code name]\n\n";
# translate with the genetic code in use, so redundancy... |
88dd08e6517aea25c0832489d020249e377788e8efab434bc707ff6ad6933daa | Perl | 3,807 | 123 | #!/usr/bin/env perl
use strict;
my $mainBranchLabel = "main";
if ($#ARGV < 0) {
print qq{
$0 <tag>
Run this from the ANTs/ directory to tag a release.
Given a tag "vX.Y.Z", the script will
1. Check user is on the ${mainBranchLabel} branch, with no uncommitted changes
2. Update Version.cmake to set the ver... |
a4af6e3692fb0547f4148fc8f8d6604780f70243f70c3f01c4baf96228dda7d7 | Perl | 3,824 | 102 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
use Nuc_translator;
use Kozak_model;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
# Train the start-codon (Kozak) context model used by start_codon_refinement.pl: log2... |
92fc585189261aaad283354a73afb893a67345163e830ee0bfdd0c1e730a3491 | Perl | 4,178 | 158 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
use Nuc_translator;
use Getopt::Long qw(:config pass_through);
## hexamer stats
my %framed_kmers;
my %background_base_probs;
my $usage = "usage: $0 targetCDSs base_probs.dat [--genetic_code name]\n\n... |
10649915779b315471cceeb6e4586a2832c09640a2ce168d2bfe58887557f95b | Perl | 4,725 | 167 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use Fasta_reader;
use GFF3_utils2;
use Carp;
use Nuc_translator;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
################################... |
04d1e5aa18ec4dcd94d2a8b70fc828fa2942094a072bf5a222c15ea15088187d | Perl | 5,291 | 169 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use lib ("$FindBin::Bin/../PerlLib");
use Pipeliner;
my $utildir = "$FindBin::Bin/PWM";
my $help_flag;
my $pwm_left = 20;
my $pwm_right = 10;
# Training needs this ... |
ca0ac59776b6897f1c0b6d5188ec30c23a512fa8cee7e839f438ec097a413602 | Perl | 8,140 | 226 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Fasta_reader;
use Nuc_translator;
use Carp;
use List::Util qw (min max);
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use File::Basename;
use Kozak_mod... |
7004b344cb261df64a1ff8e070b0dd747a29aaeadfe43b5bb63b732f0a0c9315 | Perl | 9,248 | 282 | #!/usr/bin/perl
#NB THIS SCRIPT SHOULD NOT BE USED IN ACTUAL MD SIMULATIONS BUT FOR VISUALISATION PURPOSES ONLY, IT WILL NOT REPRODUCE ANGLES AND DIHEDRALS
#NB
#NB
#NB
#NB
# Adapted from Graham Smith's script gmx2mmc
# modified by Marc Baaden (080901)
# COPYRIGHT MARC BAADEN
# modified by Miro A. Astore 2020
# LICENS... |
38920fafa4711ea162db53b7835bcbaa6cff63f8d916b116fb4b1e0b65a8fb51 | Perl | 10,187 | 267 | #!/usr/bin/env perl
# Target-decoy q-values of candidate ORFs (TransDecoder.Predict ORF selection).
#
# Decoy mode: each transcript is dinucleotide-shuffled (--shuffles copies; 0 = enough for ~20 Mb of decoy
# sequence, at most 50), decoy ORFs are found by TransDecoder.LongOrfs with the settings of the
# original run ... |
1ef1bc3f204803bded3e3e083fd33796de07ac38f9856177dacde3844477f9f9 | Perl | 12,997 | 411 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Data::Dumper;
use Fasta_reader;
my $usage = "\nusage: $0 cdna_orfs.genes.gff3 cdna_genome.alignments.gff3 cdna.fasta [DEBUG]\n\n";
my $cdna_orfs_gff3 = $ARGV[0] or die $usage... |
94441b18cec4339add94708f2d2c3b691d2fa91082311bfa6f98560ed92982bd | Perl | 13,111 | 453 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Carp;
use Data::Dumper;
use DelimParser;
use Nuc_translator;
use List::Util qw (max);
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
require "overlapping... |
bfabb39d12cd47864daba70c855f41fbe21ee68387d3b01ac33a9158f6e7bdbb | Perl | 17,394 | 484 | #!/usr/bin/perl
#################################################################################################################
# Copyright (C) 2019 Xiaowei Wang (email: xiaowei.wang@wustl.edu), Washington University in St. Louis
#
# This program is free software; you can redistribute it and/or
# modify it under t... |
c5b7cb5366056688ddd175bac4fadd95657fa40f004bb2c5c8f3c611af73ebf8 | Perl | 17,588 | 500 | #!/usr/bin/env perl
# ***************************************************************************
# * _ _ ____ _
# * Project ___| | | | _ \| |
# * / __| | | | |_) | |
# * | (__| |_| | _ <| |___
# * ... |
ea330f8e396a7a0594a647fb377e69731c48845df56ef28453b6fa74d53e0d26 | Perl | 59,000 | 2,413 | #!/usr/bin/perl
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information (NCBI)
#
# This software/database is a "United States Government Work" under the
# terms of the United States Co... |
0279f92f83e42c1d767b03ba37fed222dd51adc4384f169110e4ae42ec7ede33 | Perl | 103,913 | 4,508 | #!/usr/bin/perl
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information (NCBI)
#
# This software/database is a "United States Government Work" under the
# terms of the United States Co... |
7218deea7e6a3ddeaf7d5bd98052218f93f920cbf61142af529436365576b5cd | Python | 15 | 1 | __version__ = 1 |
a2f82e3f8c334040cd82e733c2266784c9b875145572f9f3987adf42d95108d4 | Python | 15 | 1 | from . import * |
6d2b70ac2ee4100103dddf2d94a7eb6c759695d8403d3f58478149a49ae3f37f | Python | 17 | 1 | VERSION = "0.3"
|
f03c8c486800db83b2749cf86f14edf23f56c74e0c95c0268c990f5202633dd5 | Python | 17 | 1 | # coding = utf-8
|
4bfbae67b3ce108b3212a047e9d4006c56a75364c5ca2f829a7e603e0d51b621 | Python | 18 | 1 | # coding = utf-8
|
0be0ff596ad59010e64260292dc9b4b16361d82808af059f73cfec079bef53e4 | Python | 22 | 1 | __version__ = "1.2.3"
|
3253bdd48f6e7503dce3c29d75d317140f169946994839d58f9b11a38f0cc95b | Python | 22 | 1 | from .corl import CORL |
61063e8bc31e9904ef1e58ddf41a8e1a078912edc5af3bab1374c4283c006b1e | Python | 22 | 1 | __version__ = '0.0.8'
|
773865438d35480246f8e49b52b17faf625ed14df6c19d14dda9c322f3be4a1a | Python | 22 | 1 | __version__ = '0.0.61' |
c30291296954767bd23454bc94e8022f46d188f0e3b82a9ee5ffa466e22ae11e | Python | 22 | 1 | from .losses import *
|
ec4803bfeb62994bb4e8e63a6e40019daa229ff592a517ea10ac12df0e12259e | Python | 22 | 1 | __version__ = '0.0.7'
|
4407c13e405419e89a34bbfb33e290ac1968b7e235955b9953687270d6e0cafa | Python | 23 | 1 | __version__ = '0.1.40'
|
477b8d76a574d566d6c4c248ec2e4a06b2cde3e43683e6aeaab4970cdc8f148d | Python | 23 | 1 | __version__ = '0.1.33'
|
53d094ce3dfccefa6c69826459fa0ed6735e6f447b6676e02a07a93ffac0e611 | Python | 23 | 1 | __version__ = 'v0.2.6'
|
8948f32ca8a59a87d02e9520e317890b93e9d747c04fa02797d79f1ff5d65b82 | Python | 23 | 1 | """Test catalogues."""
|
2ac167fc592aa200bfa5a542843aec39ed0a9f1067cea0ccff66d41863d14e4f | Python | 24 | 1 | """Hybrid test code."""
|
3f1ff9d23922f4a050da032796a4079fd6166471fb1157f9dd266332bb02f141 | Python | 24 | 1 | from .evaluate import *
|
4fdac556022eb54438d46c218b7c4bd44f23e5828d5b6811b2513fb06894adc6 | Python | 24 | 1 | """AQDnet test suite"""
|
a7cfc549e6da0706826448d5bb1e775d0692c7eb9a0c9f71ad84c39b8eb7bc5f | Python | 24 | 1 | """Classifier Tests."""
|
af8334e21c22f1bbfefdfba334d54171653662a0d060e8ee7aaa668cb2a3b386 | Python | 25 | 3 | """
test_behavior.py
"""
|
780842c05ff5fd41060e704a2cd7021b4fafbd505bca5d89422695be4ed503d0 | Python | 26 | 1 | from models.gae import GAE |
ff45db3b171b9a93dd841a34c402bd244ad76ca11441a8ba9e9b46ce490fcc5f | Python | 26 | 1 | __version__ = "0.5.0-dev"
|
1658d7c1dd681c43badde30e9081ee1dedb5f0550f9c8d3837ae9afed5902323 | Python | 27 | 1 | from .DISTS_pt import DISTS |
f13e9dccc331370d484af6d20eca3a7e32fa75396fd7506a5e02741014052e1d | Python | 27 | 1 | from .gen_metrics import *
|
5ba4b0cade340869e74b93f56cf9e72a7a7eedba925ebff5e9359d281bd8af7e | Python | 28 | 1 | """Tests for clustering."""
|
bfd3893a77059e2935cc7843d48a2f3383ac6711ccf79e7f96abf1649104398d | Python | 28 | 1 | """Utils for clustering."""
|
6b4b3d4b0ae4477ccf37d35b2cdcaa1771cfa974e0f9f6d3fc886fd39489d95c | Python | 30 | 1 | """Kernel based test code."""
|
266a0bc36b76da4e77c8ee5426ccec414dcd45df9951585fd25c9f65c30edea6 | Python | 31 | 1 | from .actor_graph import Actor
|
53bd550e1859d7be5926968c0582e1c479a90cbe69f9b1ca22b024d5687daf58 | Python | 31 | 1 | name = "causal_disentangle_pkg" |
f898aff784be70f82043e71d5db22ed2f068bb37cb7b207ae235f91f333b36a8 | Python | 31 | 1 | from .seq2loc import fasta2loc
|
0269273a2c2f7ed3414ea79139c8c613f7dd12451655ae95e7f692c394febeb2 | Python | 32 | 1 | """Interval based test code."""
|
858ddebdaf654b3afa9ca7b666ab51d511ea7442d2784753cafff14b929fe04b | Python | 32 | 1 | """Distance based test code."""
|
a386df95ebe53338db1cdfe498a06acf8e976007b5fab5c4eed2b8904932caa8 | Python | 32 | 1 | EHABI_INDEX_ENTRY_SIZE: int = 8
|
f3619cd7d093fc37287cb8cf381be079bdca204db334c68b95707f5b372dcfcf | Python | 32 | 1 | """Shapelet based test code."""
|
32b4e262e0c053ff4e7561a44e338c6b5c964aae5bd42b35f4e385133d30ea94 | Python | 34 | 1 | """Dummy classifier test code."""
|
46bb4182261d561ad0f2c6ee315f55e1fdd0ec9c96fbe89ff7e35ffb328f67bc | Python | 34 | 1 | """Dictionary based test code."""
|
bc1ba40802aa16edf91dc4ce4c0fa7e2caf801ff15bd4e5989ab96190490f9af | Python | 34 | 1 | """various unspecific utilities""" |
3556b5c04aa14f106f018c342f770e417a066ffbb055749e40b9a33513134491 | Python | 35 | 1 | """Tests for clustering metric."""
|
b62eed9b0737ffa1e5e6563b51d820ae090b2841ff667c8492bd459ce8f628b7 | Python | 35 | 1 | """Tests for data types module."""
|
841a2781c49b9990e2999ee3659dadcde267b853c8a9e01522bb1b09dfeda0b2 | Python | 36 | 1 | from vp_suite.vpsuite import VPSuite |
8f4fbae4e5f7d8cf3733599b3cf438ac37eae800ff7e1d505f40e7816422f21c | Python | 36 | 1 | from .forward import ForwardScanner
|
9f9250ae1fa92d8c29111f1f16c8029271ca5e26ebe706eb92296ca27dd4ce1f | Python | 36 | 1 | """Sklearn classifier test code."""
|
018e780df3d3fd20d25238675d8ec051a08a317d35a11195b02848ca225079a8 | Python | 37 | 1 | """Interface for dataset readers."""
|
17fe07931bf68e36c5bdee48dc6b10dbe48bbf518f9f6e2b17727fc40948514a | Python | 37 | 1 | """Tests for agentic forecasters."""
|
32ba660f6f8f91bca560a5533b5e3d6e6db61a3304a01a8767f49e02407e615f | Python | 37 | 1 | """Tests for time series forests."""
|
3d5815d3c80f38c153f20a5e093868ac6736b4c21d42d50f5f81cd3881e23011 | Python | 37 | 1 | from .solver import GraphMatchSolver
|
4d82acb5932f2fcc03b731e3173b5ad42c920d7507c27ce8ba03d526ab22df98 | Python | 37 | 1 | """Utilities for detection tasks."""
|
70567fc5f503dac47d2ba023f0faa93db848292239a102b280eb948c17c3963b | Python | 38 | 1 | """Conversion auxiliary utilities."""
|
8d94d9687c2385e8e1e7ca360aac205f889c3173c69606f894f579b2a179b6eb | Python | 38 | 1 | """Early classification test code."""
|
8dac94c7918401b8bcae9b2171f0707d4a9c3b96f2ede629a62b348465ef3d48 | Python | 38 | 1 | """Tests for ensemble classifiers."""
|
de5070e3bfffdfa39aae8983ac94ca408053db0eaff4eadb589315848f225b77 | Python | 38 | 1 | """Plotting module for clustering."""
|
0a13f2e9258e2951837290b874db522d99f3fb84e496ae79e7a93146110d12b2 | Python | 39 | 1 | from .dataset import JetMomentaDataset
|
475c07b32c7b5c1e81874042d32616a08e1b01136bb047b0971378bf27788064 | Python | 39 | 1 | """Utilities related to alignments."""
|
5c27d2010adb7779f6c1de8f277ff9061176cf0b8cb9f66f4c8734bedc4b9877 | Python | 39 | 1 | from .merge_data import merge_data_oct
|
83dadb29cba52b8531ef9dafd86f62c3e303fec2b12b8c1e6adfa6a0491a2b4b | Python | 39 | 1 | """Tests for classification tuners."""
|
878679a5b66e321aec9770b19cc851dedcf3298a947c61c6497f83a3f427dda8 | Python | 39 | 1 | """Tests for time series detectors."""
|
333675dc6b2bbe264eeb23d9363daafb2d46db26f23872d928215c3de7608b74 | Python | 40 | 1 | """Tests for clustering compositors."""
|
3fbf7daf3c80a0f47ee1ebc11b3f1af7bc76ee38e1c708875a9ed095cc0441b2 | Python | 41 | 2 | from .box import *
from .vector import *
|
975eaeb10a66a023d96647a2f0c5e99a1f1d64059ed7382d18e9f2beed359bc9 | Python | 41 | 1 | """Generate toy spatio-temporal data."""
|
b43e46eaf77e751c54169cdaa28ac979d503baf4685ca4b001ba51ec7cdb5b9d | Python | 41 | 3 | from .core import *
__version__ = "1.1"
|
fa744617282d41205e0b7986fe30fbddba6940bd0d2d3887d09db36119cc9bb8 | Python | 41 | 1 | from trainers.al_trainer import ALTrainer |
1f9f2ffe33fce5c50ca68c409596df5e5068b58e32dd99610af607cb9d7df650 | Python | 42 | 1 | """Forecasting benchmark entry points."""
|
2ff0c2ec4102dba98a657bf4fa42c9394780945a41a4237fe5d05da18c1b89b9 | Python | 42 | 1 | """Evaluation code shipped with Tabby."""
|
8f405ac9e1299ea49ceec8f087c02ba84e201fb46be23c7607265e306a65dc60 | Python | 42 | 2 | #!/usr/bin/env python3
import context_bug
|
e3aa4200e8a778279788863c6e0d51a5b684a8f0d44d2a9ca467500b7a513a3e | Python | 42 | 2 | class Config:
project_home = '../data' |
18faa7328bc9b3f98995325d7c91feff9d24182478951995d71aa576d190375f | Python | 44 | 2 | from .DiffTreeWidget import DiffTreeWidget
|
1b64b1bd8c0ea9d48e255fc2d6d272f1ec781680862d9233ba370eaac545de13 | Python | 44 | 1 | """Tests for sktime.dist_kernels module."""
|
7163f3b901a4efc30d1bfd6dae8421027342c582699c6bf349f86d456415da52 | Python | 44 | 3 | __all__ = ['vasp']
from pyRDTP.io import *
|
81a67d030e470f5788202088297a4ff983e5bf62fe3c9a1b2787dfbb949af658 | Python | 44 | 1 | """Tests for spatio-temporal clustering."""
|
82d6d686f6ede517266c589fb648e13dd76580b102b9fda1ec7043f63febd02d | Python | 44 | 5 | def stft():
pass
def istft():
pass
|
c3d99772589213bbeb7db5d42c0ad4fbf84932904c41e65857d82fd4ad28c9fb | Python | 44 | 1 | """Tests for sktime.benchmarking module."""
|
420ff3ad26010e761474d8e67519a570696ca28f0a04a689b981844c46dac335 | Python | 46 | 1 | """Tests for compositions for classifiers."""
|
6ba068c5a8d8c9e319fd9d2f8d61c7c5566eb84644b6749c4c7d901cd90e8cf9 | Python | 46 | 3 | from pathlib import Path
import pandas as pd
|
0ebf62878d7c2ed6b975daa5138e69160c067f9e3580f1968480c44bb1bee982 | Python | 47 | 4 | """
This file is intentionally left empty
""" |
0ffa281b463a4ea75384d64564c44033d29469b9751c4c4d43e0ed7bbf0f7404 | Python | 47 | 1 | """Tests for post-hoc benchmark evaluators."""
|
2d9e2028b8caf19b51f9ed498bbd68d617edbbffb9955eea14547aa8775354b4 | Python | 47 | 1 | """TIME forecasting benchmark entry points."""
|
f23bdf43b3da382e9ac997aa462724ba7c197756ffb36efa97a8084d34703811 | Python | 47 | 3 | # coding = utf-8
from .dag_gnn import DAG_GNN
|
5ff147acb2dce37031339ee9dcb74760005fcd38fad0ec190661f9254f1eceae | Python | 49 | 1 | """Tests for pandas/dask conversion adapters."""
|
d7988d180bb527d95e791b9d60427128e88ef066c918b63bedd6d9931da5e19a | Python | 49 | 3 | import numpy as np
print(np.load('result.npy'))
|
f7ec5fa2efae60506bcc6d8286577778bc3c3dfcfd30949d0793fbe7b0164b09 | Python | 49 | 1 | """Implements pairwise and multiple aligners."""
|
051fca9433ec08d0baa490a0b7926a5d5bc011d067ccced64873ba0d3d22089d | Python | 50 | 1 | """Tests for evaluating classification models."""
|
49597862cba59d67d52fc928293b246f54d99781af4f98a91fc604b4b5ad240c | Python | 50 | 5 | from .lamb import Lamb
__all__ = [
'Lamb',
]
|
545c31b00e5d697918650d1ac96ea20ba5952db38fb7e5d9202890e29dd6e7dd | Python | 50 | 1 | #__all__ = ["io", "update", "directorydeterminer"] |
9456c805108ad6875798985fce07cc243ff0bcee00d80ec220c1ae57fb273aba | Python | 50 | 1 | """Code for creating classifier related plots."""
|
c836e656f350f171396852eaa177e11b502f48c959db90e406a25a46357b2696 | Python | 50 | 3 | """Version information."""
__version__ = "1.1.0"
|
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