I hereby claim:
- I am holgerbrandl on github.
- I am holgerbrandl (https://keybase.io/holgerbrandl) on keybase.
- I have a public key ASA1uMjcmPjfn1Ii4hjNU3NRu7UTizjmBlgr89dWRgWPFAo
To claim this, I am signing this object:
Holger Brandl holgerbrandl
holgerbrandl
/ gist:6ba45dfb3e09ddcea7b6
Last active
August 29, 2015 14:01
Example for ddply numerics problem
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| library(plyr) | |
| exampleData <- structure(list(movie = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, | |
| 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "my_movie", class = "factor"), | |
| normS1 = c(-0.00000514991529017386, 0.00000434044351014654, | |
| 0.000011374474150384, 0.00000791328447026715, 0.00000180037689006078, | |
| -0.00000259589226008764, -0.000014779838190499, -0.0000025679794400867, | |
| -0.0000208090073107025, -0.00000607103835020496, 0.00000872275625029448, | |
| -0.00000428461787014465, -0.000000851341010028744, -0.00000168872561005701, | |
| 0.00000796911011026904, 0.00000787141524026574, 0.00000436835633014748, |
holgerbrandl
/ fasta_length_filter.kts
Last active
December 1, 2016 16:26
A kscript/kotlin tool to filter fasta files by length
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| //DEPS de.mpicbg.scicomp:kutils:0.4 | |
| //KOTLIN_OPTS -J-Xmx5g | |
| import de.mpicbg.scicomp.bioinfo.openFasta | |
| import java.io.File | |
| import kotlin.system.exitProcess | |
| if (args.size != 2) { | |
| System.err.println("Usage: fasta_filter <fasta> <length_cutoff>") | |
| exitProcess(-1) |
holgerbrandl
/ keybase.md
Created
June 14, 2017 09:49
holgerbrandl
/ gist:de4d88628f98ff046a0000b80a23c4ac
Created
December 1, 2017 19:36
Create build basic gralde in current directory
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| curl https://raw.githubusercontent.com/JetBrains/kotlin-examples/master/gradle/hello-world/build.gradle |
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| ## Inspired by | |
| #http://runkeeper.com/download/activity?activityId=181462294&downloadType=googleEarth | |
| #http://cnr.lwlss.net/GarminR/ | |
| #install.packages("lubridate") | |
| library(XML) | |
| library(plyr) | |
| library(lubridate) | |
| library(stringr) |
holgerbrandl
/ fastq_read_lengths.kts
Created
March 9, 2018 09:57
Output read ids and corresponding read lengths for a fastq argument file
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| #!/usr/bin/env kscript | |
| @file:DependsOn("de.mpicbg.scicomp:kutils:0.9.0") | |
| import de.mpicbg.scicomp.bioinfo.openFastq | |
| openFastq(args[0]).forEach { println(it.id+""+it.sequence.length) } |
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| //DEPS de.mpicbg.scicomp:kutils:0.7 | |
| //KOTLIN_OPTS -J-Xmx10g -J-server | |
| import de.mpicbg.scicomp.bioinfo.openFastq | |
| import java.io.File | |
| //val args = listOf("ID.txt", "../lanereps_pooled/s1_WT_A_R1_paired.fastq") | |
| val filterIds = File(args[0]).readLines().map{ "@" + it} | |
holgerbrandl
/ shuffle_fasta.kts
Last active
April 9, 2018 14:41
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| @file:DependsOn("de.mpicbg.scicomp:kutils:0.10") | |
| @file:KotlinOpts("-J-Xmx5g") | |
| import de.mpicbg.scicomp.bioinfo.openFasta | |
| import java.io.File | |
| //val inputFasta = File("test.fasta") | |
| val inputFasta = File(args[0]) | |
| openFasta(inputFasta).shuffled().forEach{ println(it.toEntryString())} |
holgerbrandl
/ gist:821313db8ecaf17134b2b3ce089eb111
Created
April 24, 2018 16:05
thread dump of deadlock in org.deeplearning4j.bagofwords.vectorizer.TfidfVectorizerTest#testTfIdfVectorizer
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| "main@1" prio=5 tid=0x1 nid=NA waiting | |
| java.lang.Thread.State: WAITING | |
| at java.lang.Object.wait(Object.java:-1) | |
| at java.lang.Object.wait(Object.java:502) | |
| at org.deeplearning4j.models.word2vec.wordstore.VocabConstructor$VocabRunnable.awaitDone(VocabConstructor.java:536) | |
| at org.deeplearning4j.models.word2vec.wordstore.VocabConstructor.buildJointVocabulary(VocabConstructor.java:221) | |
| at org.deeplearning4j.bagofwords.vectorizer.BaseTextVectorizer.buildVocab(BaseTextVectorizer.java:53) | |
| at org.deeplearning4j.bagofwords.vectorizer.BaseTextVectorizer.fit(BaseTextVectorizer.java:58) | |
| at org.deeplearning4j.bagofwords.vectorizer.TfidfVectorizerTest.testTfIdfVectorizer(TfidfVectorizerTest.java:71) | |
| at sun.reflect.NativeMethodAccessorImpl.invoke0(NativeMethodAccessorImpl.java:-1) |
holgerbrandl
/ gist:095c8eb7a486626676882c94269bc741
Created
April 25, 2018 04:56
Thread dump of deadlock in org.deeplearning4j.streaming.kafka.NDArrayPublisherTests#testPublish
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| Full thread dump | |
| "main@1" prio=5 tid=0x1 nid=NA waiting | |
| java.lang.Thread.State: WAITING | |
| at sun.misc.Unsafe.park(Unsafe.java:-1) | |
| at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175) | |
| at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039) | |
| at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442) | |
| at org.apache.camel.component.seda.SedaPollingConsumer.receive(SedaPollingConsumer.java:41) | |
| at org.apache.camel.impl.ConsumerCache.receive(ConsumerCache.java:202) |
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