Code for Avsec et al, Bioinformatics 2017

R 24.21% Jupyter Notebook 59.44% Python 16.30% Shell 0.05%

manuscript_avsec_bioinformatics_2017's Introduction

Manuscript_Avsec_Bioinformatics_2017

Code for Avsec et al, Bioinformatics 2017 (Bioarxiv preprint Avsec et al, Bioarxiv 2017).

Installing requirements

Python

Note, use python>3.5 from anaconda and use virtual environments to not interfere with your default python environment.

pip install -r python3_requirements.txt

R

Start R using: R --vanilla.

Install CRAN R packages:

install.packages(readLines("r_packages.txt"))

Install Bioconductor packages:

source("https://bioconductor.org/biocLite.R")
sapply(readLines("r_bioc_packages.txt"), biocLite)

General repository organization notes

In each experiment folder training predictive models, the main files are:

readme.md - contains further instructions
data.py - contains a data() function returning a tuple of train and test-set arrays
model.py - contains a model() function returning a Keras model
train.py - runs model training and hyper-parameter optimization

R should be started from the repository root.

All data are located either in Data (smaller clip data) or in data/ (everything else).

Download the data

To download the rest of the data not contained in the repository, run:

wget https://i12g-gagneurweb.in.tum.de/public/paper/Avsec_Bioinformatics_2017/data.tar.gz
tar xvfz data.tar.gz

data/ includes intermediary results, trained models, as well as model training/test datasets.

Support

Let me know if you have any problems by creating an issue or sending me an email to avsec-at-in.tum.de.

manuscript_avsec_bioinformatics_2017's People

Contributors

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avsecz

manuscript_avsec_bioinformatics_2017's Issues

Not found file ENCFF886MOW in snakemake execution

While running snakemake I receive the following error:

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	all
	1	append_sequence
	1	create_design_matrix
	1	create_extended_design_matrix
	1	process_raw_data
	20	train_exclude_features
	12	train_predictive_models
	37

[Fri Nov  2 23:10:11 2018]
rule process_raw_data:
    input: data/eclip/raw/metadata.tsv, fasta/gencode.v25.annotation.gtf.rds, fasta/GRCh38.p7.genome.fa, Scripts/RBP/Eclip/0_match_peaks_genes.R
    output: data/eclip/processed/protein_peak_overlaps.rds, data/eclip/processed/peak_center-gene_mapping.rds
    jobid: 36

Loading packages and configuration from src/r/config.R...
Done
During startup - Warning message:
Setting LC_CTYPE failed, using "C" 
[1] "start"
read anno
[fai_load] build FASTA index.
read raw data
Error in open.connection(con, open) : cannot open the connection
Calls: read_encode_eclip_bed ... scanTrackLine -> connectionForResource -> open -> open.connection
In addition: Warning message:
In open.connection(con, open) :
  cannot open file './data/eclip/raw/ENCFF886MOW.bed': No such file or directory
Execution halted
[Fri Nov  2 23:18:14 2018]
Error in rule process_raw_data:
    jobid: 36
    output: data/eclip/processed/protein_peak_overlaps.rds, data/eclip/processed/peak_center-gene_mapping.rds

RuleException:
CalledProcessError in line 58 of /data/Avsec/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile:
Command ' set -euo pipefail;  Rscript /data/Avsec/Manuscript_Avsec_Bioinformatics_2017/.snakemake/scripts/tmpqdw75_6t.0_match_peaks_genes.R ' returned non-zero exit status 1.
  File "/data/Avsec/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile", line 58, in __rule_process_raw_data
  File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /data/Avsec/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/.snakemake/log/2018-11-02T231007.138273.snakemake.log

Running an ls in the data/eclip/raw directory I can find the following:

ENCFF004SPT.bed  ENCFF114TRH.bed  ENCFF235LEG.bed  ENCFF341LOO.bed  ENCFF446GYQ.bed  ENCFF556EAA.bed  ENCFF682ZPF.bed  ENCFF807BTL.bed  ENCFF913PHX.bed
ENCFF004XSV.bed  ENCFF114ZIN.bed  ENCFF239FSU.bed  ENCFF342CVS.bed  ENCFF453WXP.bed  ENCFF557GSC.bed  ENCFF683PRA.bed  ENCFF809MHM.bed  ENCFF916MCG.bed
ENCFF005ASC.bed  ENCFF115ZKB.bed  ENCFF242QPD.bed  ENCFF343XCK.bed  ENCFF454GLW.bed  ENCFF557WJG.bed  ENCFF688PZV.bed  ENCFF810WKM.bed  ENCFF916SVG.bed
ENCFF007KJO.bed  ENCFF117EMD.bed  ENCFF243NGV.bed  ENCFF345FJL.bed  ENCFF454QNQ.bed  ENCFF559TMX.bed  ENCFF688VYF.bed  ENCFF812DRA.bed  ENCFF917CEZ.bed
ENCFF008QVV.bed  ENCFF118GAL.bed  ENCFF244ESX.bed  ENCFF347GOC.bed  ENCFF455ZCD.bed  ENCFF560YRG.bed  ENCFF688YXK.bed  ENCFF813HHP.bed  ENCFF920KVN.bed
ENCFF008SOW.bed  ENCFF118QEP.bed  ENCFF244TWH.bed  ENCFF349ZQI.bed  ENCFF456WXJ.bed  ENCFF562INS.bed  ENCFF689VFH.bed  ENCFF813HZT.bed  ENCFF920OZH.bed
ENCFF009ERS.bed  ENCFF119OMH.bed  ENCFF245ZKN.bed  ENCFF351YUV.bed  ENCFF457MNN.bed  ENCFF563REX.bed  ENCFF689ZAK.bed  ENCFF813JKM.bed  ENCFF921XQP.bed
ENCFF010IIF.bed  ENCFF124DCX.bed  ENCFF248XLD.bed  ENCFF352GMA.bed  ENCFF459AMC.bed  ENCFF564EGL.bed  ENCFF690BKB.bed  ENCFF816KHF.bed  ENCFF922GMC.bed
ENCFF012TOL.bed  ENCFF125BSO.bed  ENCFF249GHN.bed  ENCFF354DYL.bed  ENCFF460RUI.bed  ENCFF570UTN.bed  ENCFF696QAI.bed  ENCFF818WAX.bed  ENCFF923XZP.bed
ENCFF013AAR.bed  ENCFF125NXB.bed  ENCFF249RCK.bed  ENCFF356JGP.bed  ENCFF460UUV.bed  ENCFF571NRK.bed  ENCFF712GUN.bed  ENCFF818ZDH.bed  ENCFF926NDE.bed
ENCFF013GRO.bed  ENCFF128FEU.bed  ENCFF250WLO.bed  ENCFF357NHT.bed  ENCFF462RQB.bed  ENCFF572EKQ.bed  ENCFF713FGP.bed  ENCFF819PCC.bed  ENCFF926YVD.bed
ENCFF013LBJ.bed  ENCFF128SFP.bed  ENCFF251OAT.bed  ENCFF357SOW.bed  ENCFF463IUW.bed  ENCFF573XYN.bed  ENCFF714ZTU.bed  ENCFF822SZT.bed  ENCFF927FBB.bed
ENCFF013XEO.bed  ENCFF129DJK.bed  ENCFF252IAP.bed  ENCFF357WUJ.bed  ENCFF463LTL.bed  ENCFF576FDV.bed  ENCFF716FGZ.bed  ENCFF823PXI.bed  ENCFF929VXO.bed
ENCFF016JYD.bed  ENCFF129EDZ.bed  ENCFF254LKZ.bed  ENCFF359NEI.bed  ENCFF464KEI.bed  ENCFF577HFG.bed  ENCFF724AGV.bed  ENCFF825HPV.bed  ENCFF930OND.bed
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ENCFF030SOE.bed  ENCFF136DYC.bed  ENCFF264TJL.bed  ENCFF365ZOS.bed  ENCFF467VWG.bed  ENCFF587NNZ.bed  ENCFF731EAQ.bed  ENCFF832SRM.bed  ENCFF937SDW.bed
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ENCFF068KHY.bed  ENCFF166LLH.bed  ENCFF296NTJ.bed  ENCFF404RAC.bed  ENCFF494JDZ.bed  ENCFF633SFR.bed  ENCFF765TII.bed  ENCFF867GHS.bed  ENCFF968WVF.bed
ENCFF072EQT.bed  ENCFF173FHO.bed  ENCFF299TLW.bed  ENCFF404VAY.bed  ENCFF499MHW.bed  ENCFF635HSX.bed  ENCFF766CEZ.bed  ENCFF867UTV.bed  ENCFF972AEX.bed
ENCFF073CUN.bed  ENCFF173TLB.bed  ENCFF299UUC.bed  ENCFF405QJO.bed  ENCFF500JSM.bed  ENCFF635OAZ.bed  ENCFF766MHV.bed  ENCFF868AYD.bed  ENCFF974NXR.bed
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ENCFF078MTW.bed  ENCFF179HQN.bed  ENCFF306ZNQ.bed  ENCFF410PTY.bed  ENCFF510QAI.bed  ENCFF641WNV.bed  ENCFF772NRW.bed  ENCFF877CWI.bed  ENCFF978RGR.bed
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ENCFF087BUT.bed  ENCFF182NMK.bed  ENCFF313CFH.bed  ENCFF418GUW.bed  ENCFF518RBJ.bed  ENCFF648IVU.bed  ENCFF779LAQ.bed  ENCFF887DHR.bed  ENCFF981JDY.bed
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ENCFF089XNW.bed  ENCFF185MFP.bed  ENCFF318MQO.bed  ENCFF424HUO.bed  ENCFF525OKR.bed  ENCFF654QLO.bed  ENCFF782STX.bed  ENCFF893YAR.bed  ENCFF987WZB.bed
ENCFF090VQN.bed  ENCFF188WYT.bed  ENCFF321ARP.bed  ENCFF425ASC.bed  ENCFF528XXE.bed  ENCFF655HHB.bed  ENCFF784MYP.bed  ENCFF894MMI.bed  ENCFF988KWU.bed
ENCFF090XDV.bed  ENCFF196VDD.bed  ENCFF321IFP.bed  ENCFF426AYZ.bed  ENCFF529DSE.bed  ENCFF655RBH.bed  ENCFF785IRO.bed  ENCFF895LMB.bed  ENCFF988TLN.bed
ENCFF094XXN.bed  ENCFF201QPI.bed  ENCFF321NHK.bed  ENCFF429QBL.bed  ENCFF529IPP.bed  ENCFF660SOX.bed  ENCFF785PDJ.bed  ENCFF895OXA.bed  ENCFF991KAG.bed
ENCFF096XGF.bed  ENCFF202EVU.bed  ENCFF323APL.bed  ENCFF430BKM.bed  ENCFF529OUY.bed  ENCFF660XYR.bed  ENCFF786NHD.bed  ENCFF897VPQ.bed  ENCFF993GLW.bed
ENCFF097HTJ.bed  ENCFF202TGG.bed  ENCFF325QVX.bed  ENCFF431LLE.bed  ENCFF533NOT.bed  ENCFF668ETU.bed  ENCFF788NXJ.bed  ENCFF898QZA.bed  ENCFF994AMX.bed
ENCFF097YVI.bed  ENCFF205CTB.bed  ENCFF326LAQ.bed  ENCFF433UTA.bed  ENCFF533SOU.bed  ENCFF668YCA.bed  ENCFF795LDZ.bed  ENCFF899FGS.bed  ENCFF994FBZ.bed
ENCFF098AQK.bed  ENCFF206ORA.bed  ENCFF326QNK.bed  ENCFF435RSV.bed  ENCFF537HKR.bed  ENCFF669UKN.bed  ENCFF795NIS.bed  ENCFF904JLR.bed  ENCFF994KXG.bed
ENCFF099GQV.bed  ENCFF207JIK.bed  ENCFF326UZQ.bed  ENCFF438KND.bed  ENCFF538YNL.bed  ENCFF670QMD.bed  ENCFF796NLW.bed  ENCFF907AEP.bed  ENCFF994SDB.bed
ENCFF101WQW.bed  ENCFF212RTC.bed  ENCFF329REE.bed  ENCFF438PZK.bed  ENCFF539NWB.bed  ENCFF671GDQ.bed  ENCFF797WKM.bed  ENCFF907KMM.bed  ENCFF994YUD.bed
ENCFF103MEF.bed  ENCFF213IET.bed  ENCFF330SZX.bed  ENCFF438UEK.bed  ENCFF543CKG.bed  ENCFF673QCY.bed  ENCFF799UKK.bed  ENCFF907ZFN.bed  ENCFF996EIN.bed
ENCFF103OSX.bed  ENCFF214URR.bed  ENCFF331HKI.bed  ENCFF439LWA.bed  ENCFF544QKV.bed  ENCFF675ZIU.bed  ENCFF801TBQ.bed  ENCFF908YJN.bed  ENCFF996VIT.bed
ENCFF104AQW.bed  ENCFF217PNK.bed  ENCFF331RRQ.bed  ENCFF439OHA.bed  ENCFF546CND.bed  ENCFF676PEK.bed  ENCFF804WBU.bed  ENCFF909ZWR.bed  ENCFF997VPG.bed
ENCFF105LFK.bed  ENCFF218RIX.bed  ENCFF332IWJ.bed  ENCFF440FWO.bed  ENCFF548JES.bed  ENCFF677SWL.bed  ENCFF806BND.bed  ENCFF912NCS.bed  files.txt
ENCFF105OLG.bed  ENCFF228KKX.bed  ENCFF334ULI.bed  ENCFF442UPB.bed  ENCFF551QMO.bed  ENCFF679UMY.bed  ENCFF806LMS.bed  ENCFF912RGT.bed  metadata.tsv
ENCFF111ELN.bed  ENCFF230VML.bed  ENCFF335HFQ.bed  ENCFF443POQ.bed  ENCFF554DOS.bed  ENCFF682QWG.bed  ENCFF806OPN.bed  ENCFF912RMI.bed

How can I proceed? Thanks!

Unable to run Eclip, AssertionError in Snakefile

Hello, following the Eclip tutorial, once I get to the snakemake step (I have snakemake version (5.3.0)) I get the following assertion error:

AssertionError in line 17 of /data/Avsec/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile.
  File "/data/Avsec/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile", line 17, in <module>

Now, the assertion called in consideration is:

assert len(RBPS) == 112

Trying to understand the error, I have verified that the RBPS list has length 150.

import pandas as pd
dt = pd.read_table("metadata.tsv")
print(pd.Series([x[0] for x in dt[dt.Assembly == "GRCh38"]["Experiment target"].str.split("-")]).unique().size)
>>> 150

Furthermore, if I comment this assert and proceed anyway, the execution fails after logging an high amount of warnings such as:

File path data/eclip/processed//design_matrix//test/POLR2G_extended.csv contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.

Then another huge amount of red text such as (I do not know if this should be counted as errors):

data/eclip/processed//design_matrix//train/FXR2.csv

Then, the execution stops.

How can I proceed to replicate your results?

Thank you.

RuleException during execution of snakemake

During the execution of snakemake, after having fixed all the errors of the previous issue, I now receive this error:

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	all
	1	append_sequence
	1	create_design_matrix
	1	create_extended_design_matrix
	1	process_raw_data
	20	train_exclude_features
	12	train_predictive_models
	37

[Fri Nov  2 19:18:36 2018]
rule process_raw_data:
    input: data/eclip/raw/metadata.tsv, fasta/gencode.v25.annotation.gtf.rds, fasta/GRCh38.p7.genome.fa, Scripts/RBP/Eclip/0_match_peaks_genes.R
    output: data/eclip/processed/protein_peak_overlaps.rds, data/eclip/processed/peak_center-gene_mapping.rds
    jobid: 36

Loading packages and configuration from src/r/config.R...
Error in library(tictoc) : there is no package called 'tictoc'
Calls: suppressMessages ... withCallingHandlers -> source -> withVisible -> eval -> eval -> library
Execution halted
[Fri Nov  2 19:18:37 2018]
Error in rule process_raw_data:
    jobid: 36
    output: data/eclip/processed/protein_peak_overlaps.rds, data/eclip/processed/peak_center-gene_mapping.rds

RuleException:
CalledProcessError in line 58 of /data/Avsec/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile:
Command ' set -euo pipefail;  Rscript /data/Avsec/Manuscript_Avsec_Bioinformatics_2017/.snakemake/scripts/tmpgvq7njle.0_match_peaks_genes.R ' returned non-zero exit status 1.
  File "/data/Avsec/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile", line 58, in __rule_process_raw_data
  File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

What can I do to proceed? Thank you.

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