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Perl
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164
#!/usr/bin/perl -w use strict; use Getopt::Long; use FindBin qw($Bin); use lib "$Bin/../lib"; use Miner; my $snippetBefore = 20; my $snippetAfter = 35; my $maxChar = 160; my $usage = <<END crossrefSnippets.pl -tokenfile token -papers epmc_pop.papers -dir cache -out snippets The token file should contain a single lin...
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Perl
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#!/usr/bin/perl -w # submitter.pl -- submit jobs and wait for them to finish use strict; use POSIX qw(sys_wait_h); my $debug = 0; my $wait = 2; my $verbose = 0; my $nCPUs = $ENV{MC_CORES} || (`egrep -c '^processor' /proc/cpuinfo`); my $maxload = $ENV{SUBMITTER_MAXLOAD} || $ENV{MC_CORES} || $nCPUs+1; my $n = $ENV{SUBM...
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Perl
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#!/usr/bin/perl -w use strict; use Getopt::Long; use FindBin qw{$RealBin}; use lib "$RealBin/../lib"; use Steps qw{ReadOrgTable}; use pbutils qw{ReadTable NewerThan}; use DBI; my $stepBase = "$RealBin/../gaps"; my $resultsDir = "$RealBin/../tmp"; my $set = "aa"; my ($stepDir, $queryDir); my $usage = <<END checkCurate...
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Perl
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#!/usr/bin/perl -w use strict; use Getopt::Long; use LWP::UserAgent; use LWP::Simple qw(get); use JSON; use FindBin qw{$RealBin}; use lib "$RealBin/../lib"; use pbutils qw{ReadTable}; my $usage = <<END loadProdoric.pl -out directory > curated_parsed Fetches all protein information, references, and weight matrices fro...
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Perl
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#!/usr/bin/perl -w # The last phase of the pipeline: building the database use strict; use Getopt::Long; use FindBin qw($Bin); use lib "$Bin/../lib"; use pbutils; use DBI; my @allsteps = qw{sprot ecocyc biolip db stats compare pdbclust}; my $allsteps = join(",",@allsteps); my $comparedir = "$Bin/../data"; my $usage =...
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Perl
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#!/usr/bin/perl -w # The fourth phase of the pipeline: identifying snippets use strict; use Getopt::Long; use FindBin qw($Bin); use lib "$Bin/../lib"; use pbutils; my @allsteps = qw{parse pmclinks oa am elsevier crossref pubmed comb generif stats}; my $allsteps = join(",", @allsteps); my $usage = <<END run_snippets.pl...
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Perl
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#!/usr/bin/perl -w # Given the hits from querying EuropePMC, look for any expected hits from the # EuropePMC-provided links to UniProt and to PubMed. For these, create a new # hits file. Calls pubmedFields.pl to get the metadata about the papers use strict; use FindBin qw{$Bin}; use Getopt::Long; my $usage = <<END ad...
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Perl
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#!/usr/bin/perl -w # The first phase of the pipeline: downloading use strict; use Getopt::Long; use FindBin qw($Bin); use lib "$Bin/../lib"; use pbutils; my @allsteps = qw{ecocyc oa am pmclinks refseq generif pubmed uniprot pdb biolip}; my $dosteps = join(",", @allsteps); my $usage = <<END download.pl -dir downloads ...
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Perl
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#!/usr/bin/perl -w use strict; use DBI; use Getopt::Long; use FindBin qw{$RealBin}; my $minCoverage = 0.7; my $minIdentity = 0.35; my $usage = <<END compareStepDbs.pl -in oldDir newDir Compares two directories that contain curated.db, curated.faa.udb, and steps.db. This is most useful to see the impact of changing to...
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Perl
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#!/usr/bin/perl -w # Join unsorted files, using lots of memory # # Example: # # ./join.pl -match Gene1ID=Gene1ID,Gene2ID=Gene2ID -keep 1.Group,1.Gene1ID,1.Gene1Name,1.Gene2ID,1.Gene2Name -rename 12.FisherLarge=flGitton&flOurs,12.LinearR=rGitton&rOurs /data/Gitton2002/clusters.Mm.comparisons /data/mouse-unigene-nov02/Gi...
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Perl
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#!/usr/bin/perl -w # Build the sqlite3 database of curated proteins for GapMind and Curated Clusters use strict; use DBI; use Getopt::Long; use FindBin qw{$RealBin}; use lib "$RealBin/../lib"; use pbutils qw{ReadFastaEntry ReadTable SqliteImport}; sub DescToEc($); my $staticDir = "$RealBin/../static"; my $usage = <<EN...
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Perl
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#!/usr/bin/perl -w # The second phase of the pipeline: identifying query terms use strict; use Getopt::Long; use FindBin qw($Bin); use lib "$Bin/../lib"; use pbutils; my @allsteps = qw{explodeam explodeeco parsepm pm pmc am mo generif refseq sprot byorg comb stats}; my $allsteps = join(",",@allsteps); my $usage = <<E...
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Perl
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#!/usr/bin/perl -w use strict; use Getopt::Long; use FindBin qw($Bin); use lib "$Bin/../lib"; use pbutils; # for ReadFastaEntry sub PrintCuratedParsed($$$$); my $usage = <<END Usage: parse_BRENDA.pl -in brenda_download.txt -faa uniprot_fasta trembl_fasta -out BRENDA The input should be the brenda_download.txt file ...
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Perl
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#!/usr/bin/perl -w # Given the relevant queries (from gapquery.pl), # execute the searches and make a table of hits (potential candidates) # Operates on orgs files from buildorgs.pl use strict; use Getopt::Long; use DBI; use FindBin qw($RealBin); use lib "$RealBin/../lib"; use pbutils qw{ReadTable}; use Steps qw{ReadO...
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Perl
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#!/usr/bin/perl -w use strict; use Getopt::Long; use FindBin qw{$Bin}; use File::Which; use IO::Handle; # for autoflush my $usage = <<END buildLitDb.pl -dir dir -snippets snippetsFile -prefix prefix1 ... prefixN [ -rif generif_tab.rif ] [ -curated curated_files ] [ -blastdir blast ] E...
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Perl
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#!/usr/bin/perl -w # Build the sqlite3 database of steps for GapMind use strict; use strict; use DBI; use Getopt::Long; use FindBin qw{$RealBin}; use lib "$RealBin/../lib"; use Steps; use pbutils qw{ReadTable ReadFastaEntry SqliteImport}; my $usage = <<END Usage: buildStepsDb.pl -set set [ -dir tmp/path.set ] Assumes...
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Perl
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#!/usr/bin/perl -w use strict; use Getopt::Long; use FindBin qw{$Bin}; use lib "$Bin/../lib"; use pbutils qw{ReadFastaEntry SQLiteLine}; my $outdir = "."; my @outtypes = qw{binding modified functional mutagenesis}; my %outtypes = map { $_ => 1 } @outtypes; my $usage = <<END Usage: buildSiteTables.pl -sprot sprotFt.tab...
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Perl
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#!/usr/bin/perl -w use strict; use Getopt::Long; use FindBin qw($Bin); use lib "$Bin/../lib"; use pbutils; # for ParsePTools, ReadFastaEntry my $usage = <<END Usage: parse_metacyc.pl -data directory -faa uniprot_fasta trembl_fasta -out out The data directory must contain proteins.dat, enzrxns.dat, and reactions.dat (...
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#!/usr/bin/perl -w # Find the relevant queries for a set of gaps # Operates on the PaperBLAST database use strict; use Getopt::Long; use DBI; use FindBin qw($Bin $RealBin); use lib "$RealBin/../lib"; use Steps qw{ReadSteps FetchUniProtSequence}; use pbutils qw{ReadTable ReadFastaEntry CuratedWordMatch}; # The argumen...
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Perl
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#!/usr/bin/perl -w # Identify the best candidates for each step, score them, and score the rules use strict; use Getopt::Long; use List::Util qw{min max}; use FindBin qw{$RealBin}; use DBI; use lib "$RealBin/../lib"; use pbutils qw{ReadTable}; use Steps qw{ReadOrgTable ReadOrgProtein ParseOrgLocus}; my $maxCand = 5; m...
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Perl
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236
use strict; #use warnings; print STDERR "gene symbol column number: "; my $geneSymbolCol=<STDIN>; chomp($geneSymbolCol); $geneSymbolCol--; my $expFile="probe.txt"; my $gplFile="ann.txt"; my $expFileWF="geneMatrix.txt"; my %hash=(); my @sampleName=(); open(EXP,"$expFile") or die $!; while(my $exp=<EXP>...
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# __init__
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# __init__
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# noqa: D104
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"""Main module"""
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name = "lang2vec"
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from .dec import DEC
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__version__ = '0.0.2'
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__version__ = "3.10"
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__version__ = '0.1.2'
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__version__ = "0.0.1"
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__version__ = '0.2.2'
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__version__ = '1.2.2'
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__version__ = "2.0.16"
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from ._cli import cli
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__version__ = "0.1.1"
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__version__ = '1.5.0'
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__version__ = '1.3.0'
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__version__ = "0.0.4"
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from .coder import Coder
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"""Tests for sbmlcore."""
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from .cli import aretomo_cli
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"""Index interaction code"""
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from .cli import main main()
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"""Synthetic toy datasets."""
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from .neural_network import *
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from .incmodel import IncModel
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from escargot.multiagent import *
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"""For testing utils.py file."""
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from .main import CrystalTracerApp
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from ToM2.envs.grid_env1 import *
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from .formisano_protocol import *
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from numpy.version import version
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from .controller import Controller
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class BaseExtensionTests: pass
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from . import blocks, config, logs
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from .Experiment import Experiment
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__version__ = "stereoscope : 0.3.1"
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from .tilt_series import RlnTiltSeries
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"""Unit test package for arcos4py."""
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from .create_prerandom_orders import *
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from src.argus_models import MouseModel
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"""Miscellaneous plotting functions."""
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"""Tools for plotting temporal data."""
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from .TQA import * from .utils import *
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"""Tools for geometric calculations."""
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from .bnt import BrainNetworkTransformer
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"""Tools for creating synthetic data."""
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"""Tools for modelling fNIRS signals."""
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""" Spike sorting results evaluation """
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"""Tests for the dereplicate workflow"""
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from escargot.memory.memory import Memory
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from . import train __version__ = '1.0.0'
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from .gwdt import gwdt __all__ = ['gwdt']
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"""Functionality for time-domain NIRS."""
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Python
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from .models import * from .losses import *
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from .memgraph import * from .neo4j import *
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"""Contains tests for distance calculation"""
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"""Contains tests for file input functions"""
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__all__ = ["ViSNetBlock", "EquivariantScalar"]
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1
"""Functionality for frequency-domain NIRS."""
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Python
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"""Contains tests for diagnostics functions"""
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"""Multimodal signal decomposition methods."""
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"""Contains tests for benchmarking workflow"""
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from .chronognosis import * __all__ = ['main']
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"""Contains tests for database functionality"""
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from yass.phy.run import run __all__ = ['run']
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from ._user_array_impl import __doc__, container
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"""Contains purely network-related utilities."""
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Python
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from dp5.dft.base_dft_method import BaseDFTMethod
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"""For modules related to installing packages."""
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Python
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from escargot.parser.parser import ESCARGOTParser
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1
from .image import load_mrtrix, save_mrtrix, Image
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Python
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"""Contains integration tests for all workflows"""
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Python
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from yass.augment.run import run __all__ = ['run']
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from .builder import get_encoder, has_CONCH, has_UNI
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from . import descriptor from . import fingerprint
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from .spherical_harmonics import spherical_harmonics
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2
__version__ = '0.0.3' from escargot.escargot import *
b42a31e92683b8c800cf2b4cec2840fe8afb5d70aa9a44fa7c66ef60b854fdb5
Python
54
4
from yass.residual.run import run __all__ = ['run']