2.7. Loading Feature Additional Info

Please notice the features must be loaded in advance. If the annotation or sequence was loaded previously, it will be replaced.

2.7.1. Load Annotation

python manage.py load_feature_annotation --file feature_annotation.tab --soterm polypeptide --cvterm display --organism 'Arabidopsis thaliana'

• Loading this file can be faster if you increase the number of threads (–cpu).

python manage.py load_feature_annotation --help

–file	Two-column tab separated file (feature.accession<TAB>annotation text). *
–organism	Species name (eg. Homo sapiens, Mus musculus) *
–soterm	SO Sequence Ontology Term (eg. mRNA, polypeptide) *
–cvterm	cvterm.name from cv feature_property. (eg. display, note, product, alias, ontology_term, annotation) *
–doi	DOI of a reference stored using load_publication (eg. 10.1111/s12122-012-1313-4)
–cpu	Number of threads

* required fields

2.7.2. Remove Annotation

If, by any reason, you need to remove a feature annotation you should use the command remove_feature_annotation.

python manage.py remove_feature_annotation --help

2.7.3. Load Sequence

python manage.py load_feature_sequence --organism 'Arabidopsis thaliana' --file Athaliana_transcripts.fasta --soterm mRNA

• Loading this file can be faster if you increase the number of threads (–cpu).

python manage.py load_feature_sequence --help

–file	FASTA file. *
–organism	Species name (eg. Homo sapiens, Mus musculus) *
–soterm	SO Sequence Ontology Term (eg. chromosome, assembly, mRNA, polypeptide) *
–cpu	Number of threads

* required fields

2.7.4. Remove Sequence

If, by any reason, you need to remove a feature sequence you should use the command load_feature_sequence itself and provide a FASTA file with no sequence. For example:

>chr1

>chr2

2.7.5. Load Publication

python manage.py load_feature_publication --organism 'Arabidopsis thaliana' --file feature_publication.tab

• Loading this file can be faster if you increase the number of threads (–cpu).

python manage.py load_feature_publication --help

–file	Two-column tab separated file (feature.accession<TAB>DOI). *
–organism	Species name (eg. Homo sapiens, Mus musculus) *
–cpu	Number of threads

* required fields

2.7.6. Remove Publication

If, by any reason, you need to remove a feature publication attribution, you should use the command remove_publication.

python manage.py remove_publication --help

2.7.7. Load DBxRef

python manage.py load_feature_dbxrefs --organism 'Arabidopsis thaliana' --file feature_dbxrefs.tab --soterm mRNA

• Loading this file can be faster if you increase the number of threads (–cpu).

python manage.py load_feature_dbxrefs --help

–file	Two-column tab separated file (feature.accession<TAB>db:dbxref). *
–organism	Species name (eg. Homo sapiens, Mus musculus) *
–soterm	SOTERM SO Sequence Ontology Term (eg. chromosome, assembly, mRNA, polypeptide) *
–cpu	Number of threads

* required fields