intermine / intermine/intermine-scripts
Download script - NCBI fasta - delete rubbish files from download
- Lingua principale
- PLpgSQL
- Stelle
- 2
- Fork
- 9
- Metriche di merge delle PR
- Nessuna PR unita negli ultimi 30g
Descrizione
Here are the files we do not want:
```
rm hs_ref_GRCh38.p12_unlocalized.fa hs_ref_GRCh38.p12_unlocalized.mfa hs_ref_GRCh38.p12_unplaced.fa hs_ref_GRCh38.p12_unplaced.mfa
```
Here's the error:
```
Caused by: java.lang.RuntimeException: Couldn't find chromosome identifier ref|NT_187396.1| Homo sapiens unplaced genomic scaffold, GRCh38.p12 Primary Assembly HSCHRUN_RANDOM_100
at org.intermine.bio.dataconversion.NCBIFastaLoaderTask.getIdentifier(NCBIFastaLoaderTask.java:53)
at org.intermine.bio.dataconversion.FastaLoaderTask.processSequence(FastaLoaderTask.java:320)
at org.intermine.bio.dataconversion.FastaLoaderTask.processFile(FastaLoaderTask.java:240)
at org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:50)
at org.intermine.bio.dataconversion.FastaLoaderTask.process(FastaLoaderTask.java:170)
at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
at org.intermine.bio.dataconversion.FastaLoaderTask.execute(FastaLoaderTask.java:215)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
... 38 more
```
We don't want unplaced features so delete these files on download.
Guida per i contributori
Nessuna guida per i contributori indicizzata per questo repository
Direzione di ricerca
Start by locating the NCBI FASTA download script referenced by this issue and inspect where the downloaded files are selected. Exclude the four listed unlocalized and unplaced files, then run the download and loading flow to confirm those files are absent and the reported chromosome-identifier error no longer occurs.
Scritto dal modello di indicizzazione a partire dal testo della issue.
Valutazione
- Stack tecnologico
- java
- Ambito
- tooling
- Tipo di issue
- Bug
- Difficoltà
- 2/5
- Tempo stimato
- 1-3 ore
- Stato di attività
- Ferma
- Chiarezza
- Abbastanza chiara
- Idoneità per principianti
- 38/100