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Merge pull request #68 from Jumitti/beta
Genome assembly
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,168 @@ | ||
| import requests | ||
| import time | ||
|
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| def get_gene_info(gene_id): | ||
| """ | ||
| Récupère les informations d'un gène via l'API NCBI Entrez en utilisant l'ID du gène. | ||
| """ | ||
| url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" | ||
| params = { | ||
| "db": "gene", # On cherche dans la base "gene" | ||
| "id": gene_id, # ID du gène obtenu via esearch | ||
| "retmode": "json" # Retourne le résultat en format JSON | ||
| } | ||
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| response = requests.get(url, params=params) | ||
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| # Vérifier si la requête est réussie | ||
| if response.status_code == 200: | ||
| print(response.text) | ||
| return response.json() | ||
| else: | ||
| print(f"Erreur : Impossible de récupérer les informations (status code: {response.status_code})") | ||
| return None | ||
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| def extract_genomic_info(gene_info): | ||
| print(gene_info) | ||
| time.sleep(1) | ||
| """ | ||
| Extrait les NC_, chrstart et chrstop de la réponse JSON. | ||
| Ne garde que les accession versions qui partagent la même base avant le point. | ||
| """ | ||
| accession_dict = {} | ||
|
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| # Extraction depuis la section locationhist | ||
| location_hist = gene_info.get('locationhist', []) | ||
| if len(location_hist) == 0: | ||
| location_hist = gene_info.get('genomicinfo', []) | ||
| for loc in location_hist: | ||
| nc_accver = loc.get('chraccver') # Extrait le NC_XXXXX.YY | ||
| chrstart = loc.get('chrstart') | ||
| chrstop = loc.get('chrstop') | ||
| print(nc_accver, chrstart, chrstop) | ||
|
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||
| if nc_accver: | ||
| base_accession = nc_accver | ||
| if base_accession not in accession_dict: | ||
| accession_dict[base_accession] = (chrstart, chrstop) | ||
| else: | ||
| # Conserver la première occurrence des coordonnées | ||
| existing_start, existing_stop = accession_dict[base_accession] | ||
| accession_dict[base_accession] = (min(existing_start, chrstart), max(existing_stop, chrstop)) | ||
|
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| print(accession_dict) # Afficher le dictionnaire des NC_ sans les suffixes | ||
| return accession_dict | ||
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| def fetch_nc_info(nc_accver): | ||
| time.sleep(1) | ||
| """ | ||
| Récupère les informations détaillées pour un NC_ via l'API NCBI. | ||
| """ | ||
| url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" | ||
| params = { | ||
| "db": "nuccore", | ||
| "id": nc_accver, | ||
| "retmode": "json" | ||
| } | ||
|
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| response = requests.get(url, params=params) | ||
|
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| if response.status_code == 200: | ||
| print(response.text) | ||
| return response.json() | ||
| else: | ||
| print(f"Erreur : Impossible de récupérer les informations pour {nc_accver} (status code: {response.status_code})") | ||
| return None | ||
|
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| def main(): | ||
| gene_id = input("Entrez l'ID du gène (par ex. 4843 pour NOS2) : ").strip() | ||
|
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| # Étape 1 : Récupérer les informations du gène via son ID | ||
| gene_info = get_gene_info(gene_id) | ||
|
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| if gene_info and 'result' in gene_info and gene_id in gene_info['result']: | ||
| gene_details = gene_info['result'][gene_id] | ||
| print(gene_details) | ||
| print(f"Informations pour le gène (ID: {gene_id}):") | ||
|
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||
| # Étape 2 : Extraire les NC_, chrstart et chrstop | ||
| nc_dict = extract_genomic_info(gene_details) | ||
| print("\nNC_ Accession, chrstart, chrstop:") | ||
|
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| # Affichage des NC_ et leurs informations de position | ||
| for base_accver, (chrstart, chrstop) in nc_dict.items(): | ||
| print(f"{base_accver}: chrstart={chrstart}, chrstop={chrstop}") | ||
|
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| # Filtrer pour garder uniquement les entrées qui commencent par "NC_" | ||
| nc_dict = {base_accver: (chrstart, chrstop) for base_accver, (chrstart, chrstop) in nc_dict.items() if | ||
| base_accver.startswith("NC_")} | ||
|
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| # Si le dictionnaire n'est pas vide, récupérez la base avant le point du premier élément | ||
| if nc_dict: | ||
| first_base = next(iter(nc_dict)).split('.')[0] # Récupérer la base avant le point de la première clé | ||
|
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| # Filtrer le dictionnaire pour ne garder que les éléments avec la même base | ||
| nc_dict = {base_accver: (chrstart, chrstop) for base_accver, (chrstart, chrstop) in nc_dict.items() if | ||
| base_accver.split('.')[0] == first_base} | ||
|
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| # Votre code existant pour afficher le dictionnaire filtré | ||
| print("\nDictionnaire filtré :") | ||
| for base_accver, (chrstart, chrstop) in nc_dict.items(): | ||
| print(f"{base_accver}: chrstart={chrstart}, chrstop={chrstop}") | ||
|
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| # Trouver l'entrée avec le chiffre le plus grand et le plus petit après le point | ||
| max_version = -1 | ||
| max_accver = None | ||
| max_coords = None # Pour stocker les coordonnées associées à la version maximale | ||
| min_version = float('inf') # Initialiser à l'infini pour trouver la plus petite version | ||
| min_accver = None | ||
| min_coords = None # Pour stocker les coordonnées associées à la version minimale | ||
|
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| for base_accver in nc_dict.keys(): | ||
| version = int(base_accver.split('.')[1]) # Extraire la version après le point | ||
|
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| # Mise à jour pour la version maximale | ||
| if version > max_version: | ||
| max_version = version | ||
| max_accver = base_accver | ||
| max_coords = nc_dict[base_accver] # Stocker les coordonnées | ||
|
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| # Mise à jour pour la version minimale | ||
| if version < min_version: | ||
| min_version = version | ||
| min_accver = base_accver | ||
| min_coords = nc_dict[base_accver] # Stocker les coordonnées | ||
|
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| # Afficher les résultats | ||
| if max_accver: | ||
| print(f"\nL'accès avec la version la plus élevée est : {max_accver} avec la version {max_version}.") | ||
| print(f"Coordonnées : chrstart={max_coords[0]}, chrstop={max_coords[1]}") | ||
| else: | ||
| print("\nAucun accès trouvé.") | ||
|
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| if min_accver: | ||
| print(f"L'accès avec la version la plus basse est : {min_accver} avec la version {min_version}.") | ||
| print(f"Coordonnées : chrstart={min_coords[0]}, chrstop={min_coords[1]}") | ||
| else: | ||
| print("Aucun accès trouvé.") | ||
|
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| # Étape 3 : Faire une requête sur chaque accession version pour récupérer les infos détaillées | ||
| for base_accver in nc_dict.keys(): | ||
| nc_info = fetch_nc_info(base_accver) | ||
| if nc_info and 'result' in nc_info and base_accver in nc_info['result']: | ||
| nc_details = nc_info['result'][base_accver] | ||
| print(f"\nDétails pour {base_accver} :") | ||
| print(f"Organisme : {nc_details.get('organism', {}).get('scientificname', 'Inconnu')}") | ||
| print(f"Description : {nc_details.get('title', 'Inconnu')}") | ||
| else: | ||
| print(f"Aucune information détaillée trouvée pour {base_accver}.") | ||
|
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| else: | ||
| print(f"Aucune information détaillée trouvée pour l'ID {gene_id}.") | ||
|
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| if __name__ == "__main__": | ||
| main() |
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