whitef19 / GI

Project GI

Élaboration d'une base de donnée détaillée des îlots génomiques à partir de bases de données existantes.

• IslandViewer
• PAI-DB
• ICEberg
• Islander

# Colonnes de la base de données
ID	ACC_NB	ORGANISME	START	STOP	SEQUENCE	INSERTION*	REFERENCES  DETECTION*

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Sources de données

ICEberg

site web

Inputs :

• page_x.html 467 pages html de la base de données

# ICEberg
python3 parsing.py -i input/iceberg/ -pos input/SupTable1.xlsx -neg input/SupTable2.xlsx  -db iceberg -bp 50

output : table.iceberg.tsv

Islands : 468
Uniques : 354
NA : 258 (39 ont des souches inconnus ('Unknown strain'))

Islander

site web

Inputs:

• island_sequence.06.03.2015.fasta
• islander.08.03.2015.sql

# Islander
python3 parsing.py -i input/islander.08.03.2015.sql -pos input/SupTable1.xlsx -neg input/SupTable2.xlsx  -db islander -bp 50

output :table.islander.08.03.2015.sql.tsv

Islands : 4 208
Uniques : 4 208
NA : 1

IslandViewer

site web
publication

Inputs :

• all_gis_islander_iv4.txt
• all_gis_islandpick_iv4.txt
• all_gis_islandpath_dimob_iv4.txt
• all_gis_sigi_hmm_iv4.txt
• all_gis_islandviewer_iv4.txt
• Supp1: positive dataset
• Supp2: negative dataset
• Supp3: 80 GIs ranging in size from 3 to 133 kb
• Additional_file_1.xls
• Additional_file_2.xls
• Additional_file_3.xls
• Additional_file_8.xls

# IslandViewer 4 islander
python3 parsing.py -i input/all_gis_islander_iv4.txt -pos input/SupTable1.xlsx -neg input/SupTable2.xlsx  -db iv -bp 50

output : table.all_gis_islander_iv4.txt.tsv

Islands : 3 170
Uniques : 3 170
NA : 0

# IslandViewer 4 islandpath dimob
python3 parsing.py -i input/all_gis_islandpath_dimob_iv4.txt -pos input/SupTable1.xlsx -neg input/SupTable2.xlsx  -db iv -bp 50

output : table.all_gis_islandpath_dimob_iv4.txt.tsv

Islands : 51 425
Uniques : 51 425
NA : 0

# IslandViewer 4 islandpick
python3 parsing.py -i input/all_gis_islandpick_iv4.txt -pos input/SupTable1.xlsx -neg input/SupTable2.xlsx  -db iv -bp 50

output :table.all_gis_islandpick_iv4.txt.tsv

Islands : 43 469 Uniques : 43 469 NA : 0

# IslandViewer 4 islandviewer
python3 parsing.py -i input/all_gis_islandviewer_iv4.txt -pos input/SupTable1.xlsx -neg input/SupTable2.xlsx  -db iv -bp 50

output :table.all_gis_islandviewer_iv4.txt.tsv

Islands :110 914
Uniques :110 914
NA : 0

# IslandViewer 4 sigi hmm
python3 parsing.py -i input/all_gis_sigi_hmm_iv4.txt -pos input/SupTable1.xlsx -neg input/SupTable2.xlsx  -db iv -bp 50

output :table.all_gis_sigi_hmm_iv4.txt.tsv

Islands : 63 917
Uniques : 63 917
NA : 0

PAIDB

site web

Inputs :

• PAIDB_REI.html : REsistance Islands
• PAIDB_PAI.html : PAthogenicity Islands

# PAIDB PAI
python3 parsing.py -i input/PAIDB_PAI.html -pos input/SupTable1.xlsx -neg input/SupTable2.xlsx  -db paidb -bp 50

output :table.PAIDB_PAI.html.tsv

Islands : 986
Uniques : 986
NA : 904

# PAIDB REI
python3 parsing.py -i input/PAIDB_REI.html -pos input/SupTable1.xlsx -neg input/SupTable2.xlsx  -db paidb -bp 50

output :table.PAIDB_REI.html.tsv

Islands : 108
Uniques : 108
NA : 95

Analyse

Temps de calcul : voir log_parsing_1.0

 
# Nombre d'island 
wc -l table.all_gis_islander_iv4.txt.tsv
# Nombre d'island uniques
sort -k3 table.all_gis_islander_iv4.txt.tsv | sort -k1 |uniq | wc -l
# Island avec numéro d'accession et positions
awk '$1=="NA" || $3=="NA" || $4=="NA"' table.all_gis_islander_iv4.txt.tsv | wc -l
mv table.all_gis_islander_iv4.txt.tsv Tables/.

Concatenation des sources

# L'option "cat" permet donner 9 arguments et lance la fonction concatenate  
python3 parsing.py -cat Tables/*

output: database_1.0.tsv

Islands : 181 699
NA : 9 221