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Metagenomics
metagenedb
Commits
60bb9b65
Commit
60bb9b65
authored
Jun 12, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
remove deprecated fields used for POC
parent
0c66ad71
Changes
4
Hide whitespace changes
Inline
Side-by-side
web/metagenedb/apps/catalog/migrations/0001_initial.py
deleted
100644 → 0
View file @
0c66ad71
# Generated by Django 2.2.1 on 2019-06-07 08:47
from
django.db
import
migrations
,
models
class
Migration
(
migrations
.
Migration
):
initial
=
True
dependencies
=
[
]
operations
=
[
migrations
.
CreateModel
(
name
=
'Gene'
,
fields
=
[
(
'id'
,
models
.
AutoField
(
auto_created
=
True
,
primary_key
=
True
,
serialize
=
False
,
verbose_name
=
'ID'
)),
(
'gene_id'
,
models
.
CharField
(
db_index
=
True
,
max_length
=
100
,
unique
=
True
)),
(
'gene_length'
,
models
.
IntegerField
()),
(
'taxonomic_genus'
,
models
.
CharField
(
max_length
=
100
)),
(
'taxonomic_phylum'
,
models
.
CharField
(
max_length
=
100
)),
],
),
]
web/metagenedb/apps/catalog/models.py
View file @
60bb9b65
...
...
@@ -4,8 +4,6 @@ from django.db import models
class
Gene
(
models
.
Model
):
gene_id
=
models
.
CharField
(
max_length
=
100
,
unique
=
True
,
db_index
=
True
)
gene_length
=
models
.
IntegerField
()
taxonomic_genus
=
models
.
CharField
(
max_length
=
100
)
taxonomic_phylum
=
models
.
CharField
(
max_length
=
100
)
def
__str__
(
self
):
return
self
.
gene_id
web/metagenedb/apps/catalog/serializers.py
View file @
60bb9b65
...
...
@@ -6,4 +6,4 @@ class GeneSerializer(serializers.ModelSerializer):
class
Meta
:
model
=
Gene
fields
=
(
'gene_id'
,
'gene_length'
,
'taxonomic_genus'
,
'taxonomic_phylum'
)
fields
=
(
'gene_id'
,
'gene_length'
)
web/scripts/import_igc_data.py
View file @
60bb9b65
...
...
@@ -18,11 +18,27 @@ _LOGGER = logging.getLogger(__name__)
def
create_gene
(
raw_line
):
"""
IGC annotation columns:
0: Gene ID Unique ID
1: Gene Name Unique name
2: Gene Length Length of nucleotide sequence
3: Gene Completeness Status Stating a gene is complete or partial according to the gene predictor
4: Cohort Origin Stating the cohort contributing the representative gene
5: Taxonomic Annotation(Phylum Level) Annotated phylum for a gene
6: Taxonomic Annotation(Genus Level) Annotated genus for a gene
7: KEGG Annotation Annotated KO(s) for a gene
8: eggNOG Annotation Annotated eggNOG(s) for a gene
9: Sample Occurence Frequency Occurrence frequency in samples based on gene profile
10:Individual Occurence Frequency Occurrence frequency in individuals based on gene profile
11: KEGG Functional Categories KEGG functional category(ies) of the annotated KO(s)
12: eggNOG Functional Categories eggNOG functional category(ies) of the annotated eggNOG(s)
13: Cohort Assembled Stating the metagenomic sequencing cohort(s) contributing the
representative gene or a redundant gene belonging to it
"""
gene_info
=
raw_line
.
rstrip
().
split
(
'
\t
'
)
gene
=
Gene
(
gene_id
=
gene_info
[
1
],
gene_length
=
gene_info
[
2
],
taxonomic_genus
=
gene_info
[
6
],
taxonomic_phylum
=
gene_info
[
5
])
gene_length
=
gene_info
[
2
])
return
gene
...
...
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