sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b41083c019bc7aa27d1e4b4f82ef570bfb0f44aab306f48ac9d80ce8b3b34ed0 | NEURON | 766 | 21 | module github.com/runmark/fledge
go 1.16
require (
github.com/cosmos72/gomacro v0.0.0-20220601173042-2c1a92efdc9b // indirect
github.com/dapr/go-sdk v1.1.0
github.com/gin-gonic/gin v1.7.2
github.com/json-iterator/go v1.1.11 // indirect
github.com/marmotedu/gopractise-demo v0.0.1
github.com/peterh/liner v1.2.2 /... |
d6fa64e15c8d1ae5eee7ed0a702533aae6ffecbccd92c74472f01647f5a0ad68 | NEURON | 844 | 32 | // LOAD CONTROL MENU
/*
objref contrl
contrl = new VBox()
{
contrl.intercept(1)
nrncontrolmenu()
contrl.intercept(0)
contrl.map("Control",0,75,-1,-1) // left, top, width, height
}
*/
/*
proc ncWeightUpdate(){
for m=1,numSyn{
ncAMPA[m-1].weight = ampaWeightB
ncNMDA[m-1].weight = nmdaWeightB
}
}
*/
// DISPLAY ... |
90e946c20488a378eccb1d1f9a2d2f244ed03e413ee17dc62d5e5e81bd75895e | NEURON | 903 | 30 | // RETURN A CUMULATIVE HISTOGRAM
// INPUT1: the vector values with which to create cumulative histogram
// INPUT2: low value for histogram
// INPUT3: high value for histogram
// INPUT4: numer of bins
// OUTPUT1: histogram of results, named "curHist"
// OUTPUT2: cum histogram of results, named "curCumHist"
// OUTPUT2: x... |
b6befd126a2fc284cb71e3c962528065e8c291ead00090ced9d54825b402dd86 | NEURON | 919 | 35 | ///////////////////////////////////////////////////////////////////////////////////////////
//
// DO A COMPREHENSIVE ANALYSIS OF SEVERAL VARIABLES WITHIN THE SIMULATION
// ACROSS THE MORPHOLOGY
//
// Note: voltage is not initialized to a perfect steady state at time zero, which is
// related to the calcium handling mec... |
5c139e8474fb9ad7bf926acce08922206da893729ee77189bc50a84607f02230 | NEURON | 943 | 48 | /* ----------------------------------------------------
example_morphology.hoc
This hoc file creates a neuron of the following shape:
\
\
\ /
\ /
V
|
|
|
O
... |
9e662cf715108c1b9698d3174f1850614fa50e6ed41f0e78925ad66ae5aa6ca3 | NEURON | 988 | 48 | COMMENT
This code comes from LFPy tests. It has been written by Espen Hagen.
Since this is an electrode current, positive values of i depolarize the cell
and in the presence of the extracellular mechanism there will be a change
in vext since i is not a transmembrane current but a current injected
directly to the ... |
ad971cc982e40b4fa8085d8aa05de67a64991d9bd640a5a7f5cb2fc22e699e85 | NEURON | 1,104 | 34 | ///////////////////////////////////////////////////////////////////////////////
// FOR HISTOGRAMS, SOMETIMES IT IS INFORMATIVE TO PLOT AS BARGRAPHS. THIS
// ROUTINE TAKES AN x- AND y-AXIS AND COMPUTES THE AXES NEEDED TO
// VISUALIZE AS A BAR GRAPH, RATHER TAHN A LINE GRAPH
///////////////////////////////////////////... |
dc47637da28e308dbed3683ac89357b2e4f7233449cfd3065a21ab4732cb4136 | NEURON | 1,131 | 37 | // The below function is designed to return a integral, with the baseline
// removed.
// NOTE: requires a fixed time step.
// INPUT 1: vector to integrate
// INPUT 2: step size, in msec, used in experiments
// INPUT 3: time that indicates when to take the beginning of the integral
// INPUT 4: time that indicates when t... |
fe6865811d5e00e47c1fabcc638c1d6d9573dd121852c9d0000491580ea1ae22 | NEURON | 1,236 | 58 | // Adapted from Poirazi et al 2003
// This template creates the Oblique Path lists, starting from the
// section attached to the trunk and ending with the basal tip section
// written by Terrence Brannon, modified by Yiota Poirazi, July 2001, poirazi@LNC.usc.edu
begintemplate ObliquePath
public dtrunk_to_tip, trunk_... |
6c5f38206bd9fc7bbeb761db63d13c5b7965acd6e4e0c9f3129ae78823e1f634 | NEURON | 1,344 | 44 | // The below function is designed to return a voltage integral, with the offset
// removed, in accordance with Yujin's analysis.
// NOTE: requires a fixed time step.
// INPUT 1: vector of voltages
// INPUT 2: step size, in msec, used in experiments
// INPUT 3: time that indicates the beginning of the integral
// INPU... |
4cab84c9dbafb4ecb02f51a57f374b991f9b3364cf97fe9698074f99e421701c | NEURON | 1,564 | 60 | ////////////////////////////////////////////////////////////////////////////////
//
// A MODEL FOR eLife 2015;10.7554/eLife.06414
// Yujin Kim*, Ching-Lung Hsu*, Mark Cembrowski, Brett Mensh, Nelson Spruston
//
// MODEL AUTHORS: Mark Cembrowski and Ching-Lung Hsu
//
// TO SUPPLEMENT EXPERIMENTS BY Yujin Kim and Ching-... |
8b7a115b58139f4bbb9c46570a1cd2382dd408373b2d9a104d294eb2b2f59ae5 | NEURON | 1,837 | 100 | TITLE K-DR channel
: from Klee Ficker and Heinemann
: modified to account for Dax et al.
: M.Migliore 1997
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
(mol) = (1)
}
NEURON {
SUFFIX kdr
USEION k READ ek WRITE ik
RANGE gkdr,gkdrbar,ik
RANGE ninf,taun
GLO... |
903ca646a25ae05b58fc345fc2de1659d114ace911d41a26dd5b4010191fa840 | NEURON | 2,032 | 52 | ttxSoma = 0 // simulate 20nM TTX in bath? 0 = no; 1 = yes
celsius = 35
v_init = -70
global_ra=200.00 // internal resistivity in ohm-cm
Cm=1.5 // 1.5specific membrane capacitance in uF/cm^2
Cmy=0.075 // capacitance in myelin
Rm=40000 // specific membrane resistivity in ohm-cm^2
Rn=50 // nodal resistiv... |
f5705f1dcd2da85645fe972ce1b71f4f45f6727d0894ff426b57697946c4a4d5 | NEURON | 2,037 | 52 | ttxSoma = 0 // simulate 20nM TTX in bath? 0 = no; 1 = yes
celsius = 35
v_init = -70
global_ra=100.00 // internal resistivity in ohm-cm
Cm=1.0 // 1.5specific membrane capacitance in uF/cm^2
Cmy=0.075 // capacitance in myelin
Rm=20000 // specific membrane resistivity in ohm-cm^2
Rn=50 // nodal resistiv... |
13ce0ce2e53b7726118f021c0174f0f1cd52812234056a831a9ba6e745d90ae6 | NEURON | 2,055 | 100 | TITLE CaGk
: Calcium activated mAHP K channel.
: From Moczydlowski and Latorre (1983) J. Gen. Physiol. 82
: Code updated to run with CVODE (BPG 20-8-09)
UNITS {
(molar) = (1/liter)
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
(mM) = (millimolar)
}
INDEPENDENT {t FROM 0 TO 1 WITH 100 (ms)}
NEURON {
SUFFIX kmA... |
a48c093d033bd1d8e4e4b2ee970cebbc666565185e796220f26cbcec4583c0f7 | NEURON | 2,113 | 90 | TITLE Ca L-type channel with high treshold of activation
: inserted in distal dendrites to account for distally
: restricted initiation of Ca++ spikes
: uses channel conductance (not permeability)
: written by Yiota Poirazi, 1/8/00 poirazi@LNC.usc.edu
NEURON {
SUFFIX calH
USEION ca READ eca WRITE ica
RANGE g... |
110fa8e5ec2d669dcf608017179f17efd3917583ccbc4665cfd7f02e83d0c4ab | NEURON | 2,133 | 110 | TITLE Ca L-type channel with high treshold of activation
: inserted in distal dendrites to account for distally
: restricted initiation of Ca++ spikes
: uses channel conductance (not permeability)
: written by Yiota Poirazi, 1/8/00 poirazi@LNC.usc.edu
NEURON {
SUFFIX calH
USEION ca READ eca WRITE ica
RANGE g... |
57fa4b4a71d47e9d4527b234b242395a7882c506b2e3bf426a02f660c4e88892 | NEURON | 2,184 | 123 |
COMMENT
T-type Ca channel
ca.mod to lead to thalamic ca current inspired by destexhe and huguenrd
Uses fixed eca instead of GHK eqn
changed from (AS Oct0899)
changed for use with Ri18 (B.Kampa 2005)
ENDCOMMENT
INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}
NEURON {
SUFFIX it
USEION ca READ eca WRITE ica
RANGE m, h, gc... |
587c9e2997214bec4fcc1ee48afb37909de2f249891102d519815ecbacba5aad | NEURON | 2,450 | 117 |
COMMENT
26 Ago 2002 Modification of original channel to allow variable time step and to correct an initialization error.
Done by Michael Hines(michael.hines@yale.e) and Ruggero Scorcioni(rscorcio@gmu.edu) at EU Advance Course in Computational Neuroscience. Obidos, Portugal
kv.mod
Potassium channel, Hodgkin-Huxle... |
5763a8e55a1a6f22a7b3e4b472184100a689b649a2ef264f1bade26bd1eb1937 | NEURON | 2,457 | 116 | TITLE Modified SpikeGenerator of M. Hines
NEURON{
POINT_PROCESS SpGen2
RANGE y, t01,t02
RANGE fast_freq, slow_freq, APinburst, startbursting, endbursting
RANGE noise
}
PARAMETER {
t01=20 (ms)
t02=420000 (ms)
fast_freq = 100 (/s) : time between spikes in a burst (msec)
slow_freq = 0.00000001 (/s)... |
a4081d0a94d32a63f1a54eeb3ade924a84daa615d25565b71c5336870d86f922 | NEURON | 2,463 | 116 | TITLE Modified SpikeGenerator of M. Hines
NEURON{
POINT_PROCESS SpGen2
RANGE y, t01,t02, burst
RANGE fast_freq, slow_freq, APinburst, startbursting, endbursting
RANGE noise
}
PARAMETER {
t01=20 (ms)
t02=420000 (ms)
fast_freq = 100 (/s) : time between spikes in a burst (msec)
slow_freq = 0.000000... |
c100fdb947afdd89b7a86e98e8f521b4b7bb793f1a87772d7739b4e61e0bec16 | NEURON | 2,539 | 132 | TITLE na3
: Na current
: from Jeff M.
: ---------- modified -------M.Migliore may97
NEURON {
SUFFIX nax
USEION na READ ena WRITE ina
RANGE gbar, ar2, ina
GLOBAL minf, hinf, mtau, htau, sinf, taus, qinf, thinf
}
PARAMETER {
gbar = 0.010 (mho/cm2)
tha = -30 (mV) : v 1/2 for act
qa = 7.2 (mV... |
20ea948ed12a3b39a84f7da48ba78028c9b96c22336e7f73791ffeabce7481c7 | NEURON | 2,620 | 103 | TITLE Ca R-type channel with high threshold for activation
: HVA calcium channels are inserted in the spine head
: Activation and inactivation parameters taken from
: Foehring RC, Mermelstein PG, Song W, Ulrich S and Surmeier DJ
: Unique properities of R-type calcium currents in neucortical and neostriatal neurons
: J... |
3ead96bf395f5ffbbc1cf5c8c2382a4c163a70c2d9aacbac4030fce4179d9e28 | NEURON | 2,801 | 117 | COMMENT
Author: Mark Cembrowski, 2012
This is an extension of the Exp2Syn class to incorporate NMDA-like properties,
and incorporates some NMDA features from Elena Saftenku, 2001.
First, Exp2Syn is described:
Two state kinetic scheme synapse described by rise time tau1,
and decay time constant tau2. The normalized ... |
89d2959c6c4dbc2c39c1d367b75413c52529724fb11a7d931ccf7abc1d57c378 | NEURON | 2,801 | 117 | COMMENT
Author: Mark Cembrowski, 2012
This is an extension of the Exp2Syn class to incorporate NMDA-like properties,
and incorporates some NMDA features from Elena Saftenku, 2001.
First, Exp2Syn is described:
Two state kinetic scheme synapse described by rise time tau1,
and decay time constant tau2. The normalized ... |
4bd75742ec9212d2d8aafb23d9df17f02d0d996bcb59beb9313429fced6c6ccf | NEURON | 2,802 | 117 | TITLE L-type calcium channel with low threshold for activation
: used in somatic and proximal dendritic regions
: it calculates I_Ca using channel permeability instead of conductance
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
FARADAY = 96520 (coul)
R = 8.3134 (joule/degK)
KTOMV = .0853 (mV/degC)
}
INDEPENDENT... |
434bfa87f1ddcdecf918316cab8ca6083e6e3f3a1c1867a5936a47d70976f163 | NEURON | 2,977 | 138 | COMMENT
Two state kinetic scheme synapse described by rise time tau1,
and decay time constant tau2. The normalized peak condunductance is 1.
Decay time MUST be greater than rise time.
The solution of A->G->bath with rate constants 1/tau1 and 1/tau2 is
A = a*exp(-t/tau1) and
G = a*tau2/(tau2-tau1)*(-exp(-t/tau1) + ex... |
62cc7aae67447e703d0cb80aad4d09708b4385a6dc49475cb4d273642228354e | NEURON | 2,983 | 138 | COMMENT
Two state kinetic scheme synapse described by rise time tau1,
and decay time constant tau2. The normalized peak condunductance is 1.
Decay time MUST be greater than rise time.
The solution of A->G->bath with rate constants 1/tau1 and 1/tau2 is
A = a*exp(-t/tau1) and
G = a*tau2/(tau2-tau1)*(-exp(-t/tau1) + ex... |
141d3607537ffe54a8ceb29a5dae885333bb1606f0fe2fb6c7b38233a69b9e0a | NEURON | 3,153 | 108 | TITLE decay of internal calcium concentration
:
: Internal calcium concentration due to calcium currents and pump.
: Differential equations.
:
: Simple model of ATPase pump with 3 kinetic constants (Destexhe 92)
: Cai + P <-> CaP -> Cao + P (k1,k2,k3)
: A Michaelis-Menten approximation is assumed, which reduces th... |
dac87aeca36b0c3be55125ee10673a208725e296f0b5e951fccf2d14dc780e6d | NEURON | 3,415 | 157 |
COMMENT
26 Ago 2002 Modification of original channel to allow variable time
step and to correct an initialization error.
Done by Michael Hines(michael.hines@yale.e) and Ruggero
Scorcioni(rscorcio@gmu.edu) at EU Advance Course in Computational
Neuroscience. Obidos, Portugal
11 Jan 2007
Glitch in trap where (v/... |
fe681bedcef923fc938297fb9e81be4cc3d46c63561e38973a062a904da46b82 | NEURON | 3,635 | 134 | /*************************************************
* section lists *
*************************************************/
objref soma
somaA soma = new SectionRef()
objref distTuft
distTuft = new SectionList()
numDistNeurites = 0
forsec "dendA5_01111111111111111" {
if (strcmp(secname(),... |
5907bad19dfd0de182b54ad41a92ad21ec6d309f99118089f502bd007916ed7c | NEURON | 5,216 | 147 | COMMENT
This is a mechanism for computing sliding BCM threshold based on recent spike count (Benuskova et al. PNAS 2001, Benuskova and Abraham JCNS 2007):
alpha_scount_d = alpha_d * scount for depression
alpha_scount_p = alpha_p * scount for potentiation
The averaged postsynaptic activity scount expresses the weight... |
1dd14e42015a56768908a61cb4f67e63863be1564adc8cc6fde35c0cda824996 | NEURON | 7,004 | 206 | COMMENT
Author: Ching-Lung Hsu (adapted from Hines and Carnevale, 2000)
Calcium ion handling mechanisms with endogenous buffer, radial & longitudinal diffusion and pump
A mobile calcium indicator OGB-1 is included
ENDCOMMENT
NEURON {
SUFFIX cdp
USEION ca READ cao, cai, ica WRITE cai, ica
RANGE ica_pmp
GLOBA... |
35fff24cf469894f154c1e8c0bcfa52feba3912e04efe10054309364f1a3972f | NEURON | 7,226 | 200 | COMMENT
This is a synaptic mechanism implementing a form of stream-specific voltage based event-timing-dependent plasticity (ETDP).
The mechanism uses simple STDP rule that depends entirely on the interval between the pre- and postsynaptic spikes. This is the nearest-neighbor multiplicative implementation of STDP, that... |
ecba0400b159da25299c7e9723dfd1cde8a6c0b90bec4c8d47766f57b07950a6 | NEURON | 7,318 | 311 | // DECLARE OBJECTS TO BE ASSIGNED DURING initchannels() CALL
objref osec[10]
objref neurAreas,neurNames,curSecname[1] // parameters inherent to determining surface area of branches
objref seclistDist // list of distal neurites
objref normNeurAreas,nnaInt, randGen, randGenAnat // used for distributing input across bran... |
95b5c6669048d7e94d65a5df9b54cbdfddb3fa79d3c174acad010ba04825e378 | NEURON | 8,019 | 254 | ///////////////////////////////////////////////////////////////////////////////
// PEAK ANALYSIS FOR SYNAPTIC LOCATIONS
///////////////////////////////////////////////////////////////////////////////
// for unsorted responses
objref voltACSFPeak,voltDrugPeak
objref nmdaACSFPeak,nmdaDrugPeak,ogbACSFPeak,ogbDrugPeak
v... |
b66224c7ea740f3336dbe0da485ad7d57069d1d3e1e2bcf2175cd81c59ab6112 | NEURON | 8,378 | 283 | create hill,iseg,\
node[2],\
inode[3]
proc geometry() { local i, j
/* connect primary neurites */
somaA connect hill (0), 0.5
hill connect iseg (0), 1
iseg connect inode[0] (0), 1
inode[0] connect node[0] (0), 1
node[0] connect inode[1] (0), 1
inode[1] connect no... |
a07b5d8af0e03e9071b4da49e09bd25cf6911cf213baad3c2715c4d11c3e2db0 | NEURON | 9,461 | 321 | ////////////////////////////////////////////////////////////////////////////////
//
// PLOT RESULTS
//
////////////////////////////////////////////////////////////////////////////////
{
load_file("../commonFcns/getCumHist.hoc")
load_file("../commonFcns/getBargraphVec.hoc")
load_file("../commonFcns/decimal.hoc")
... |
94c541322ce90e4166fe4c94f5481afbc853346a9f411517918e5a963f12c02c | NEURON | 9,668 | 1 | // Adapted from Poirazi et al 2003
// Make a set of lists, each containing the oblique sections
// that form a continuous path: starting from the section attached
// to the trunk and ending at the apical tip section.
load_file("ObliquePath.hoc")
objref pl[150],opl[150]
plcount=0
pl[plcount] = new SectionList()
dend5... |
abf6d642fc79ce9ce570b57d3ee0a2f8feebbcd16bd6445599bee164ed631781 | NEURON | 11,360 | 432 | ////////////////////////////////////////////////////////////////////////////////
//
// GENERATE VECTORS OF THE SECTIONS/SEGMENTS WHERE SYNAPSES ARE LOCATED,
// AS WELL AS THE DISTANCE FOR EACH SECTION
//
// IN ADDITION, CREATE numScan LOCATIONS ACROSS THE TUFT, DISTRIBUTED
// AT RANDOM, TO TRACK MEMBRANE PROPERTIES
//... |
f13347d6a31ab56ea19f0413e6f27ac9a31cc373f8de32b4b4a105796d41e545 | NEURON | 200,000 | 5,089 | /*---------------------------------------------------------------------------*/
/* Neuron morphology registered to standard barrel field with NeuroMap */
/* Registered home barrel: E2 */
/*---------------------------------------------------------------------------*/
... |
0236ded218959648d2d475e13e9c6c0719f6c81d4030b7d955f9ddd7f37d20e4 | Perl | 180 | 6 | # substitutes 'ENAMEX TYPE' with 'ENAMEXTYPE' for tokenization
s/ENAMEX TYPE/ENAMEXTYPE/g;
# removes S_OFF="." and E_OFF="."
s/ S_OFF="[1-9]+">/>/g;
s/ E_OFF="[1-9]+">/>/g;
|
b2a55236d076113adb11fcb0cd6805aa2398fb4969375ff048c3050c44944dc9 | Perl | 234 | 9 |
while ( <> ) {
if ($_=~/!ARTICLE/) { $sentnum = -1; }
if ($_=~/^\(/ || $_=~/^!ARTICLE/ || $_=~/^ *$/) { $sentnum++; $toknum = 1; }
#print "$sentnum$toknum:$_";
printf ( "%02d%02d:%s", $sentnum, $toknum, $_ );
$toknum++;
}
|
b9081e8628c4e79597c5066e994291b2a9cf0abe0f715dde5a3626ad360bf44b | Perl | 266 | 11 | #!/usr/bin/perl
use strict;
use lib '../../';
use GAL::Parser::trait_o_matic;
my $parser = GAL::Parser::trait_o_matic->new(file => 'data/trait_o_matic.gff');
while (my $feature_hash = $parser->next_feature_hash) {
print $parser->to_gff3($feature_hash) . "\n";
}
|
f42d3e5af9b38fdddb4a11c9ad3d4d024b1590a3283cb63c38c462a64dbac790 | Perl | 272 | 11 | #!/usr/bin/perl
use strict;
use lib '../../';
use GAL::Parser::samtools_pileup;
my $parser = GAL::Parser::samtools_pileup->new(file => 'data/samtools_pileup.txt');
while (my $feature_hash = $parser->next_feature_hash) {
print $parser->to_gff3($feature_hash) . "\n";
}
|
0ef50073f9cb8e0e160ec21297d290423799ca4fa97dc025509295964dcc4e15 | Perl | 309 | 15 | #!/usr/bin/perl
use strict;
use warnings;
use lib '../../';
use GAL::Parser::dbsnp_flat;
my $parser = GAL::Parser::dbsnp_flat->new(file => 'data/dbsnp_flat.txt',
assembly => 'reference',
);
while (my $feature = $parser->next_feature_hash) {
print $parser->to_gff3($feature);
print '';
}
|
001639632704d5b1a3e21be69ac64cafde4c5759f8b5675eeb6553cb19f0eb98 | Perl | 314 | 12 | #!/usr/bin/perl
use strict;
use lib '../../';
use GAL::Parser::smith_ant_snps;
my $parser = GAL::Parser::smith_ant_snps->new(file => '../data/smith_ant_snps.gff',
fasta => '../data/fasta_ant/');
while (my $feature_hash = $parser->next_feature_hash) {
print $parser->to_gff3($feature_hash) . "\n";
}
|
51af8aec554f8c986b673d13d6c6c2a2dd4951dc1052d04808de4195d11f7f2d | Perl | 314 | 11 | #!/usr/bin/perl
use strict;
use lib '../../';
use GAL::Parser::1000_genomes_genotypes;
my $parser = GAL::Parser::1000_genomes_genotypes->new(file => '../data/CEU.low_coverage.2010_07.genotypes.short.vcf');
while (my $feature_hash = $parser->next_feature_hash) {
print $parser->to_gff3($feature_hash) . "\n";
}
|
07a7522cf2fa2989e69c9b16e4b200e7f41bae6a58cd5c1992bb190305bbe8c9 | Perl | 322 | 21 | #!/usr/bin/perl
$fshmprev = "shm_last";
$fshmthis = "shm_this";
$notes = "usage: $0
diffs current ipcs -s -m & /tmp/qi*
against '$fshmprev'
";
`(ipcs -m && ipcs -s && ls /tmp/qi* 2> /dev/null) > $fshmthis`;
`touch $fshmprev` if !-e !-e $fshmprev;
print `diff $fshmprev $fshmthis`;
`mv $fshmthis $fshmprev`;
... |
5f90f7c8cb6ff770843ce894da38482f732b65148f5a27e2b6cedb645b7e535d | Perl | 392 | 17 | #!/usr/bin/perl
use strict;
use warnings;
use GAL::Annotation;
my $annotation = GAL::Annotation->new(dsn => 'DBI:SQLite:database=gal_annotation_test',
parser => 'gff3',
storage => 'SQLite',
);
$annotation->load_file('./data/soap_snp.gff');
while (my $feature = $annotation->next_fea... |
05f680aed5f4009adf54cae541be2742e78540ff39246ea96859e3d362e5b57b | Perl | 402 | 17 |
# remove empty heads
s/\*[^ \n<>]*\*?(-[0-9]+)?//g;
s/ 0 / /g;
# tokenize hyphens
#s/(\w)-(\w)/\1 - \2/g;
# un-tokenize hyphens that are part of '-AMP-'
#s/ - AMP - /-AMP-/g;
# move coref id to end and turn recursive corefs anglebrackets into braces
while ( s/<COREF ID="([0-9]+)"[^>]+> *([^<]*?) *<\/COREF>/\{COREF\}... |
1c9f79113b2c8f54a71e8d58a0a73ddaac7b31a28977a1418758438317b240ca | Perl | 418 | 16 | #!/usr/bin/perl
use strict;
use warnings;
use GAL::Annotation;
my $annotation = GAL::Annotation->new(dsn => 'DBI:mysql:pg_chinese_snp');
my $feature_rs = $annotation->schema->resultset('Feature');
while (my $feature = $feature_rs->next) {
my $id = $feature->id;
my $ref_allele = $feature->att... |
7846f8c458929415454e92d6cd150e6846ef8303338f76906b73e69669d95e9e | Perl | 446 | 15 | #! /usr/bin/perl
use demotic_blast;
$swiss_wu = "/misc/data0/databases/Uniprot/uniprot_sprot_wu.fasta";
open(BLAST, "blastp $swiss_wu example.fa 2>/dev/null |");
while (demotic_blast::parse(\*BLAST))
{
for ($i = 0; $i < $demotic_blast::nhits; $i++) {
printf "%.2g\t%.1f\t%s\t%s\n", $demotic_blast::hit_Eva... |
5c002a57b14eaf3f190e896ceb5c1cd1ab490e89d2cd18e2ab9cc1d905a8a227 | Perl | 503 | 20 | #!/usr/bin/perl
use strict;
use warnings;
use lib '../';
# This script uses full DBIx::Class object inflation. It takes about
# 2.6 hours to process 4 million features.
use GAL::Schema;
my $schema = GAL::Schema->connect('DBI:mysql:database=pg_chinese_snp');
my $feature_rs = $schema->resultset('Feature');
whil... |
d682c0f0ebe316d6b66d665883547b2b43eb65ddc0350a9dd426f59b106553eb | Perl | 519 | 20 | #!/usr/bin/perl
use strict;
use warnings;
use lib '../';
# This script uses DBI directly to access the data. It can process 4
# million features in 2 minutes.
use DBI;
my $dbh = DBI->connect('DBI:mysql:database=pg_chinese_snp');
my $statement = 'select f.feature_id, a.value from feature f, attribute a where f.fea... |
fdafd3488da5763a1aa00459856ac1a5bcafbdc22bc0030d6bcd81acdafb86db | Perl | 707 | 41 | #! /usr/bin/perl
$nsearches = 2809;
require "getopts.pl";
&Getopts('n:X:x:');
if ($opt_n) { $nsearches = $opt_n; }
if ($opt_X) {
open(EXCLUDEFILE,$opt_X) || die;
while (<EXCLUDEFILE>) {
if (/^\s*(\S+)/) { $nsearches--; $excluded{$1} = 1; }
}
close EXCLUDEFILE;
}
if ($opt_x) { $nsearches--; $exclude... |
db11f942a3418f0de6bf80cddf9b8f26009563b743b30edde7145afa98ee8c2f | Perl | 712 | 37 | #!/usr/bin/perl -w
use strict;
unless (@ARGV == 2){
print "perl $0 blastoutFile TagName\n";
exit;
}
my $file = shift;
my $name = shift;
my %hash;
my ($id1,$id2,$ident,$TSD,$trash);
open(IN,$file) or die $!;
while(<IN>){
chomp;
next if(/^#/);
($id1,$id2,$ident,$TSD,$trash) = split(/\t/,$_,5);
next if ($id1 eq $... |
12ed67b343a67df9f22f9543075cbd1538a25e48d5d5ec0d4b5f4cceb238b856 | Perl | 772 | 26 | #!/usr/bin/perl
use strict;
use warnings;
use lib '../';
# This script uses a resultset cursor to access the data. It can
# process 4 million features in 1.3 hours.
use GAL::Schema;
my $schema = GAL::Schema->connect('DBI:mysql:database=pg_chinese_snp');
my $feature_rs = $schema->resultset('Feature');
my $attri... |
e36b8bc41bf361a6c5e83071c3cca7ce71a8c7ee5557167cce31ae2c592f6dd6 | Perl | 910 | 31 | #!/usr/bin/perl
use strict;
use warnings;
use lib '../';
use DBIx::Class::ResultClass::HashRefInflator;
# This script uses DBIx::Class::ResultClass::HashRefInflator to skip
# object creation. It can process 4 million features in about 1.6
# hours
use GAL::Schema;
my $schema = GAL::Schema->connect('DBI:mysql:databa... |
374a53e8e9b68cb155982c3938488bce3309ed2d280614c32c568b3f989b15a7 | Perl | 958 | 35 | # break line at terminal punctuation mark (but not if next word is lower case)...
##s/([\.\!\?][\.\"\'\)]*) +(?![ a-z])/\1\n/g;
s/([\.\!\?][\.\"\'\)]*) +(?=[\`\'\"\(\[]*[A-Z0-9])/\1\n/g;
# translate initial and final quotes...
s/(?:\"|\'\')(?![ \t\n\.,!?])(?!\))/\`\`/g;
s/([^ ])\"/\1''/g;
s/(?<![\w\,\.\!\?\'])\'(?! |\... |
b2053adc529391f7e5fc55f41786db932f3367ce17eede78da98c44900a183f2 | Perl | 1,072 | 15 |
# propagate subject to object control complement (+ in subj-aux inverted clause + via conjunction left + via conjunction right + via passive + via tough construction)
while ( s/((\w*)\/0\/[^ ]*-b{.-a(?![^}]*-g).* \2r\/1\/([^- ]+) \2r\/2\/(\d+)(?!.*\4r\/.\/\3).*? \4r\/.\/)-/\1\3/ ||
s/(\w*)r\/1\/-(.* (\w*)\/0\/... |
12b0e6b111b35935473b013f56b65add78d36ba3f01751e4a363beffe88a2268 | Perl | 1,147 | 46 | #! /usr/bin/perl
# Bug #h82: hmmbuild corrupts resave alignment on all-insert seq
#
# Usage: ./i16-build-allins.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i16-build-allins.pl .. .. tmpfoo
#
# SRE, Sun Jun 13 12:09:54 2010 [UA231 IAD->SAN]
BEGIN {
$builddir = shift;
$srcdir = shi... |
6474c3d3d3b510683fb256a2159ef5bedf299467c7a2514dcbe52dddc597cb93 | Perl | 1,194 | 68 | #!/usr/bin/perl
use strict;
#use warnings;
die "Usage:$0 <muscle.out> \n" if @ARGV < 1;
my $out = shift;
my $Pep1;
my $Pep2;
open IN,$out or die "$!\t$out";
$/=">";<IN>;$/="\n";
my $id1 = <IN>;
$id1 =~ s/^(\S+)\s*.*\n/$1/ or die "$!\t$out";
$/=">";
$Pep1 = <IN>;
chomp $Pep1;
$Pep1 =~ s/\s//g;
$/="\n";
my $id2 = ... |
3adcebbc07b8d82b0142da9695af167c545ff1327601b561068f37cc8192ae14 | Perl | 1,241 | 59 | #!/usr/bin/perl
use strict;
use Test::More 'no_plan'; # tests => 10;
BEGIN {
use lib '../../';
#TEST 1
use_ok('GAL::Parser::quake');
}
my $path = $0;
$path =~ s/[^\/]+$//;
$path ||= '.';
chdir($path);
my $parser = GAL::Parser::quake->new(file => 'data/quake.txt');
# TEST 2
isa_ok($parser, 'GAL::Parser::quake');... |
3990f2ff4d70788e7811dbab133d17f6ab2a4d149b78e6d44672a3329da9f39d | Perl | 1,243 | 46 | #! /usr/bin/perl
# Test the ability of hmmbuild to deal with crappy alignments
# of lots of sequence fragments.
#
# Usage: ./i7-hmmbuild-fragments.pl <hmmbuild binary> <tmpfile prefix>
# Example: ./i7-hmmbuild-fragments.pl ../src/hmmbuild tmpfoo
#
# SRE, Tue Jun 16 13:37:05 2009
$hmmbuild = shift;
$tmppfx =... |
a03b43e62010ce178a552a5ea54a5c90603536b8ea38634deb7fc5329339f749 | Perl | 1,253 | 59 | #!/usr/bin/perl
use strict;
use Test::More 'no_plan'; # tests => 10;
BEGIN {
use lib '../../';
#TEST 1
use_ok('GAL::Parser::soap_snp');
}
my $path = $0;
$path =~ s/[^\/]+$//;
$path ||= '.';
chdir($path);
my $parser = GAL::Parser::soap_snp->new(file => 'data/soap_snp.gff');
# TEST 2
isa_ok($parser, 'GAL::Parser:... |
9ee1b98fa3894baa08ed51284db0d2ab20dddf270c0eb44b7ca9db6c8625e3a7 | Perl | 1,261 | 59 | #!/usr/bin/perl
use strict;
use Test::More 'no_plan'; # tests => 10;
BEGIN {
use lib '../../';
#TEST 1
use_ok('GAL::Parser::soap_indel');
}
my $path = $0;
$path =~ s/[^\/]+$//;
$path ||= '.';
chdir($path);
my $parser = GAL::Parser::soap_indel->new(file => 'data/soap_indel.gff');
# TEST 2
isa_ok($parser, 'GAL::P... |
041668fcb6a09c4727b6d31aaa0dd2be90133d50ca6c6daa0db69a35c4adc6b9 | Perl | 1,269 | 59 | #!/usr/bin/perl
use strict;
use Test::More 'no_plan'; # tests => 10;
BEGIN {
use lib '../../';
#TEST 1
use_ok('GAL::Parser::celera_indel');
}
my $path = $0;
$path =~ s/[^\/]+$//;
$path ||= '.';
chdir($path);
my $parser = GAL::Parser::celera_indel->new(file => 'data/celera_indel.gff');
# TEST 2
isa_ok($parser, '... |
39898a109105f02ce6e6535826ecc8b7918af8db3b360dfe5531182ad4b4878f | Perl | 1,277 | 59 | #!/usr/bin/perl
use strict;
use Test::More 'no_plan'; # tests => 10;
BEGIN {
use lib '../../';
#TEST 1
use_ok('GAL::Parser::illumina_indel');
}
my $path = $0;
$path =~ s/[^\/]+$//;
$path ||= '.';
chdir($path);
my $parser = GAL::Parser::illumina_indel->new(file => 'data/illumina_indel.gff');
# TEST 2
isa_ok($par... |
a07281f187286b904aad7abe3cdabde9d1705c5500610405272f60f21fb0372c | Perl | 1,289 | 59 | #!/usr/bin/perl
use strict;
use Test::More 'no_plan'; # tests => 10;
BEGIN {
use lib '../../';
#TEST 1
use_ok('GAL::Parser::complete_genomics');
}
my $path = $0;
$path =~ s/[^\/]+$//;
$path ||= '.';
chdir($path);
my $parser = GAL::Parser::complete_genomics->new(file => 'data/complete_genomics.csv');
# TEST 2
is... |
1da7214806400bf9d1c74c43e8e553dd5856f3d5df3ae060f4599768b88d0dba | Perl | 1,305 | 59 | #!/usr/bin/perl
use strict;
use Test::More 'no_plan'; # tests => 10;
BEGIN {
use lib '../../';
#TEST 1
use_ok('GAL::Parser::illumina_sanger_indel');
}
my $path = $0;
$path =~ s/[^\/]+$//;
$path ||= '.';
chdir($path);
my $parser = GAL::Parser::illumina_sanger_indel->new(file => 'data/illumina_sanger_indel.gff');
... |
8277cca6239ea15dcc1b4605eb20c589ad534b6c31aa1626e5adc730caa51d4d | Perl | 1,324 | 59 | #!/usr/bin/perl
use strict;
use Test::More 'no_plan'; # tests => 10;
BEGIN {
use lib '../../../';
#TEST 1
use_ok('GAL::Parser::annovar_exonic');
}
my $path = $0;
$path =~ s/[^\/]+$//;
$path ||= '.';
chdir($path);
my $parser = GAL::Parser::annovar_exonic->new(file => '../data/NA12878.annovar_input_short.exonic_va... |
7e568a4702343672a10ec00b3abb56d8bae33f36d805e5c6259e2aa9e2c92fd0 | Perl | 1,371 | 43 | #!/usr/bin/perl -w
use strict;
die "Usage: <bed>\n" unless @ARGV == 1;
open (IN,$ARGV[0]) or die;
my %hash;
while(<IN>){
chomp;
my($sca,$begin,$end,$info,$score,$stand,$cluster)=split(/\s+/,$_,7);
if (exists $hash{$cluster}) {
if($hash{$cluster}{"score"} < $score){
#my $tempp=$hash{$cluster}{"score"};
... |
a54922f1521d7f4eda36500903b9086f3b8e2cb0a63bcc69b6c63a2349ad203b | Perl | 1,475 | 71 | #!/usr/bin/perl
# $debug++;
$dir = shift || die "usage: $0 develop -or- develop_stage\n";
die "usage: $0 develop -or- $0 develop_stage\n" if $dir !~ /^develop(_stage|)$/;
$us3 = $ENV{'us3'} || die "can't find env variable us3\n";
$fconfig = "$us3/somo/us3add.txt";
$f = $fconfig;
open IN, $f || die "$0: $f $!\n";
... |
4fbc84d5e0a64283881e694284140db406e3952af2429862b8fe6cfe1c41f384 | Perl | 1,567 | 70 | #!/usr/bin/perl -w
#######################################################
# Author : Aurelie K
# date : v1.0, Feb 2013
# email : 4urelie.k@gmail.com
# Purpose : Read a repeat masker output file => write TEs in a bed file
######################################################
use strict;
use warni... |
876d60b86e3552dc16b9d4a5ccf7c4bbd9b5fa4b8d9d7b969e877c586e9d3f72 | Perl | 1,705 | 76 | #! /usr/bin/perl
# rmanprocess.pl <rman LaTeX2e output>
#
# Example:
# rman -f LaTeX2e foo.man | rmanprocess.pl > foo.tex
#
# Converts a man page to a HMMER User's Guide section.
# Written to operate with PolyglotMan v3.0.5, by Thomas Phelps
# Obtain from ftp.cs.berkeley.edu:/ucb/people/phelps/tcltk/rman.tar.Z
#
#... |
cae22ae7af078b819294c0074bde63d7ae847c06dc7fb71a6435c84f18885a67 | Perl | 1,713 | 43 | #! /usr/bin/perl
# Nightly builds for HMMER3
#
# Usage: hmmer_autobuilds.pl <srcdir>
# Example: hmmer_autobuilds.pl ~/nightlies/hmmer/trunk > /tmp/hmmer_autobuilds.log
@buildconfigs = (
{ name => "intel-linux-icc-intel64-mpi", host => "login-eddy" },
{ name => "intel-linux-icc-ia32-mpi", host => ... |
74c5d4e4af32735136ea29f4cc0b98cdf71847f134bb9b7cc887f79fd9c29eb2 | Perl | 1,726 | 68 | #!/usr/bin/perl
$debug++;
$exec++;
$part1++;
$| = 1;
sub cmd {
print "$_[0]\n" if $debug;
$result = `$_[0]` if $exec;
print $result;
}
while ( @ARGV )
{
$_ = shift;
if ( /^(c|co|com|comp|compile)$/ )
{
$compile++;
print "compiling on\n";
next;
}
die "$0: unre... |
376cf3d5cc96aec73349babb697b2fa19670a60c2a7667d37de00c46cd224d36 | Perl | 1,733 | 68 | #!/usr/bin/perl
$notes = "usage: $0
make propri.tgz which includes specific us3 versions of pro & pri files
new programs and edits will be overwritten on next regen of us3 from us2 unless they are in this file
";
$us3 = $ENV{'us3'} || die "can't find env variable us3\n";
#$us3somo = $ENV{'us3somo'} || die "can't fin... |
e1607de5f1db76ef9820bf64b44b4202e8895c34b0e93faf430079144cbbd8fa | Perl | 1,739 | 30 |
$COPS = '(?:be|is|\'s|was|are|\'re|were|been|being)';
# delete all punctuation
s/ (\w*)\/0\/[-,\.\!\?\;\:\`\'].*? \1r\/1\/\w*//g;
# propagate subject to object control complement (+ via conjunction left + via conjunction right + via passive + via tough construction)
while ( s/((\w*)\/0\/[^ ]*-b{.-a(?![^}]*-g).* \2r\... |
93033ed632e9ed5763734cb666a9cf7bbbc15c7001b2fae998b0c204e643a61f | Perl | 1,885 | 45 | #! /usr/bin/perl
# Test the hmmalign --mapali option.
#
# Usage: ./i6-hmmalign-mapali.pl <hmmalign binary> <esl-reformat binary> <testsuitedir> <tmpfile prefix>
# Example: ./i6-hmmalign-mapali.pl ../src/hmmalign ../easel/miniapps/esl-reformat . foo
#
# SRE, Mon May 25 09:52:48 20... |
45de0501f148bc4e55dc21f8296b45c698c425a55b9783622236bc72d336ecd9 | Perl | 1,901 | 71 | #!/usr/bin/perl
$debug++;
$exec++;
$part1++;
$| = 1;
sub cmd {
print "$_[0]\n" if $debug;
$result = `$_[0]` if $exec;
print $result;
}
while ( @ARGV )
{
$_ = shift;
if ( /^(c|co|com|comp|compile)$/ )
{
$compile++;
print "compiling on\n";
next;
}
die "$0: unre... |
de13a29fa6f0a9cf0affab0b7a90d55298593996d2d72082d4bae527df5724d6 | Perl | 1,903 | 51 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
1242b4f6a4b42b9413cedb16d93c5aa15468c6f92539d1705d74571d53117060 | Perl | 1,989 | 95 | #!/usr/bin/perl
while ( $ARGV[ 0 ] =~ /^-/ )
{
$arg = shift;
if ( $arg =~ /-d/ )
{
$debug++;
next;
}
if ( $arg =~ /-c/ )
{
$commit++;
next;
}
if ( $arg =~ /-s/ )
{
$show_diffs++;
next;
}
die "usage: $0 { options }
vali... |
a63bfdad914853ee0baa9125f1f4c21feb99c1f1c571042afa5ebcd4b9180ef5 | Perl | 2,015 | 79 | #!/usr/bin/perl
$dir = shift || die "usage: $0 develop-directory\n";
$addcout = '
static std::basic_ostream<char>& operator<<(std::basic_ostream<char>& os, const QString& str) {
return os << qPrintable(str);
}
';
@cpps = `find $dir -name "*.cpp"`;
grep chomp, @cpps;
for ( $i = 0; $i < @cpps; $i++ )
{
$f = $c... |
f5d097e7bf0e0590db9d42772f8bfaad0b9b7196366533b15666f8575de40b64 | Perl | 2,040 | 67 | #! /usr/bin/perl
# Component speed benchmarks
#
# Usage: ./component-benchmark.pl <top_builddir> <top_srcdir>
# Example: ./component-benchmark.pl ../build-icc-mpi .. > component-benchmark.out
#
# For a range of models of different sizes, run a speed benchmark for
# each component of H3's pipeline. Output an ... |
98fc613fd5a08e6a14985af821649917570132756421c69d883c1403b5373f09 | Perl | 2,063 | 69 | #! /usr/bin/perl
# Bug #h77: hmmalign corrupts column preceding an all-delete column
#
# Usage: ./i12-delete-corruption.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i12-delete-corruption.pl .. .. tmpfoo
##
#
# This test is now obsolete. hmmalign by default now saves all
# consensus columns, whi... |
7653b3cc64ca9cbf6b612a9914888a8d499d75d322a1b3e9ee695dc423186859 | Perl | 2,144 | 85 | #!/usr/bin/perl
# just collect everything up in the outermost qstrings until closing
# $debug++;
sub is_ok {
my $l = $_[0];
my @n;
my @l = split //, $l;
for ( my $i = 0; $i < @l; $i++ ) {
if ( $l[$i] =~ /%/ ) {
push @n, sprintf("%d", substr($l,$i+1));
}
}
my $ok = ... |
e4f31858c91ebc86faa25b008b11003ed5b38c1d50e6c6f542f2712f23157fbb | Perl | 2,164 | 58 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
699459e54e5ff4616a11a7d270b6d5ebec0623179375d113db788b00a4f1b662 | Perl | 2,262 | 84 | #!/usr/bin/perl
## n.b. when adding a new image, it's best to pull the base image, esp. if multiples might be selected
### otherwise, buildpkg might appear to hang waiting for a selection which never is displayed
### e.g.
#### STEP 1/70: FROM rockylinux:8.7
#### ? Please select an image:
#### ▸ container-registry.o... |
62dbe45db9b542c965f4f3e2efdf64f280f7ceb33f327e8627fccb0eccc0eee4 | Perl | 2,286 | 58 | #! /usr/bin/perl
# Integrated test of hmmpress
#
# Usage: ./hmmpress.itest.pl <hmmpress binary> <hmmfile> <tmpfile prefix>
# Example: ./hmmpress.itest.pl ./hmmpress ../testsuite/minifam.hmm foo
#
# The testsuite creates and presses minifam.hmm.
# If you need to do it yourself:
# cd testsuite
# ../src/hmmbuild ... |
e77365ba9b485794708194783e25b0e7ff0e8fa6b779e58b9d956c2325bd6551 | Perl | 2,335 | 63 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
da180e6bcc7a83a419cad5b8d01c6c4c77a542b86f1fd254cd71b8eccf18ed07 | Perl | 2,437 | 62 | #!/usr/bin/perl -w
use strict;
use List::Util qw(min max);
use FindBin qw($Bin $Script);
unless (@ARGV == 5){
print "perl $0 distance[10,15,20] InList[20k-85.list] workDir fasta OutList\n";
exit;
}
my $dist= shift;
my $in_lst = shift;
my $WorkDir = shift;
`mkdir -p $WorkDir/tmpTSD_$dist/`;
my $fasta = shift;
my $Out... |
1b61939415170d1b67101b8993485c9fa13364156f12671ad5cff9d221a6708e | Perl | 2,496 | 72 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
ddb57941b9c03022d07568fbc9dae52c76541172f455fc7c786c42919d2fbc03 | Perl | 2,512 | 90 | #! /usr/bin/perl
# Usage: ./speedA-list.pl <Pfam.hmm.stats>
# Example: hmmstat Pfam-A.hmm | ./speedA-list.pl
#
# Read all the models and their lengths from hmmstat output
while (<>)
{
if (/^\d+\s+(\S+)\s+\S+\s+\d+\s+\S+\s+(\d+)/) { $lengths{$1} = $2; }
}
# sort
sub bylength { $lengths{$a} <=> $lengths{$b}; ... |
39bc989051fe2e437c49459d8e6009058f1ab2c5c43108ea74eb52ca5e8e03ce | Perl | 2,513 | 81 | #! /usr/bin/perl
# Another test of the hmmalign --mapali option, after Elena reports
# bug #h73 in bad interaction of checksum calculation and marking
# fragments.
#
# Usage: ./i11-hmmalign-mapali.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i11-hmmalign-mapali.pl .. .. tmpfoo
#
# SRE, Mon Dec ... |
c7a5d8dc37a2ee309a9d20c29795f9eea020ebc1b12631d72a35b9e932e1f42a | Perl | 2,574 | 94 | #! /usr/bin/perl
# Bug #e5: blank text line following #=GF <tag> handled improperly.
#
# Easel was allowing blank text, because we want to allow blank #=GF CC
# lines for line spacing in human-readable comments.
#
# Problem is that then blank DE or AC lines are also accepted. HMMER
# then propagates blank DESC or ACC ... |
e759637fb05ddbc4340dd2f2a6d56de4a5f11d0ec37d134618e1877e31b98f75 | Perl | 2,724 | 81 | #! /usr/bin/perl
# Tests hmmemit -c and hmmemit -C consensus-generating options.
#
# Usage: ./i14-hmmemit-consensus.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i14-hmmemit-consensus.pl .. .. tmpfoo
#
# SRE, Fri May 14 11:34:28 2010 [Janelia]
BEGIN {
$builddir = shift;
$srcdir = s... |
95e46d6a130dcf3ab6fa27b464c335d532957002539be8ea8dcb5e237a9f0459 | Perl | 2,742 | 77 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
ad57c9a703277d9f1c7053e994231bc7788c5b68d41d872baa3134e3137a9c98 | Perl | 2,746 | 81 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
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