Chercher un mot, et extraire la réponse dans un fichier

Version imprimable

Bonjour,

J'ai un fichier tab, je voudrais chercher des mots clés, et extraire la réponse dans un fichier, mon fichier tab est mal organisé et il est plein d 'espace.

Voilà le fichier en question :

Code:

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Entry	Entry name	Status	Protein names	Gene names	Organism	Length	Protein existence	Absorption	Enzyme regulation	pH dependence	DNA binding	Site	Nucleotide binding	Fragment	Gene encoded by	Alternative products (isoforms)	Mass spectrometry	Polymorphism	RNA editing	Sequence caution	Mass	Sequence	Proteomes	Pathway	Active site	Binding site	Catalytic activity	EC number	Cofactor	Function [CC]	Kinetics	Redox potential	Temperature dependence	Calcium binding	Metal binding
P04637	P53_HUMAN	reviewed	Cellular tumor antigen p53 (Antigen NY-CO-13) (Phosphoprotein p53) (Tumor suppressor p53)	TP53 P53	Homo sapiens (Human)	393	Evidence at protein level				DNA_BIND 102 292	SITE 120 120 Interaction with DNA.				ALTERNATIVE PRODUCTS:  Event=Alternative promoter usage, Alternative splicing; Named isoforms=9;  Name=1; Synonyms=p53, p53alpha; IsoId=P04637-1; Sequence=Displayed; Name=2; Synonyms=I9RET, p53beta; IsoId=P04637-2; Sequence=VSP_006535, VSP_006536; Note=Expressed in quiescent lymphocytes. Seems to be non-functional. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.; Name=3; Synonyms=p53gamma; IsoId=P04637-3; Sequence=VSP_040560, VSP_040561; Note=Expressed in quiescent lymphocytes. Seems to be non-functional. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.; Name=4; Synonyms=Del40-p53, Del40-p53alpha, p47; IsoId=P04637-4; Sequence=VSP_040832; Name=5; Synonyms=Del40-p53beta; IsoId=P04637-5; Sequence=VSP_040832, VSP_006535, VSP_006536; Name=6; Synonyms=Del40-p53gamma; IsoId=P04637-6; Sequence=VSP_040832, VSP_040560, VSP_040561; Name=7; Synonyms=Del133-p53, Del133-p53alpha; IsoId=P04637-7; Sequence=VSP_040833; Note=Produced by alternative promoter usage.; Name=8; Synonyms=Del133-p53beta; IsoId=P04637-8; Sequence=VSP_040833, VSP_006535, VSP_006536; Note=Produced by alternative promoter usage and alternative splicing.; Name=9; Synonyms=Del133-p53gamma; IsoId=P04637-9; Sequence=VSP_040833, VSP_040560, VSP_040561; Note=Produced by alternative promoter usage and alternative splicing.; 					43,653	MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD	UP000005640: Chromosome 17						COFACTOR: Name=Zn(2+); Xref=ChEBI:CHEBI:29105; ;  Note=Binds 1 zinc ion per subunit.;	FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA-Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seem to have to effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.					METAL 176 176 Zinc.; METAL 179 179 Zinc.; METAL 238 238 Zinc.; METAL 242 242 Zinc.

Et voilà mon bout de code que je viens de commencer , mais il m'affiche tout le fichier !

Code:

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chaine = "Cellular"
f = open("uniprot-id%3AP04637.tab", "r")
for line in f:
	if chaine in line:
		print line
 
f.close()

08/10/2016, 15h28
CosmoKnacki

Citation:

mon fichier tab est mal organisé et il est plein d 'espace

Les deux lignes d'exemples que tu donnes sont formatées correctement (il y a bien 36 champs séparés par une tabulation pour chaque ligne) et le fait que les champs aient des espaces ne doit pas poser de problème particulier.

Citation:

il m'affiche tout le fichier

Ah bon? Est-ce qu'il affiche la première ligne avec les entêtes (ligne qui ne contient pas le mot "Cellular")? As-tu essayé avec un mot plus rare?
08/10/2016, 15h40
Shyma
En fait mon fichier ne se présente pas sous cette forme là ; Je veux dire en 2 lignes.

Oui j'ai essayé avec d'autres mots, mais il m'affiche toujours tout le fichier !

Là par exemple avec le mot "FUNCTION"
Code:

1 2 3 4 5 6 7 chaine = "FUNCTION" f = open("uniprot-id%3AP04637.tab", "r") for line in f: if chaine in line: print line f.close()
voilà ce qu'il m'affiche :

Code:

P04637 P53_HUMAN reviewed Cellular tumor antigen p53 (Antigen NY-CO-13) (Phosphoprotein p53) (Tumor suppressor p53) TP53 P53Homo sapiens (Human) 393 Evidence at protein level DNA_BIND 102 292 SITE 120 120 Interaction with DNA. ALTERNATIVE PRODUCTS: Event=Alternative promoter usage, Alternative splicing; Named isoforms=9; Name=1; Synonyms=p53, p53alpha; IsoId=P04637-1; Sequence=Displayed; Name=2; Synonyms=I9RET, p53beta; IsoId=P04637-2; Sequence=VSP_006535, VSP_006536; Note=Expressed in quiescent lymphocytes. Seems to be non-functional. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.; Name=3; Synonyms=p53gamma; IsoId=P04637-3; Sequence=VSP_040560, VSP_040561; Note=Expressed in quiescent lymphocytes. Seems to be non-functional. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.; Name=4; Synonyms=Del40-p53, Del40-p53alpha, p47; IsoId=P04637-4; Sequence=VSP_040832; Name=5; Synonyms=Del40-p53beta; IsoId=P04637-5; Sequence=VSP_040832, VSP_006535, VSP_006536; Name=6; Synonyms=Del40-p53gamma; IsoId=P04637-6; Sequence=VSP_040832, VSP_040560, VSP_040561; Name=7; Synonyms=Del133-p53, Del133-p53alpha; IsoId=P04637-7; Sequence=VSP_040833; Note=Produced by alternative promoter usage.; Name=8; Synonyms=Del133-p53beta; IsoId=P04637-8; Sequence=VSP_040833, VSP_006535, VSP_006536; Note=Produced by alternative promoter usage and alternative splicing.; Name=9; Synonyms=Del133-p53gamma; IsoId=P04637-9; Sequence=VSP_040833, VSP_040560, VSP_040561; Note=Produced by alternative promoter usage and alternative splicing.; 43,653 MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD UP000005640: Chromosome 17 COFACTOR: Name=Zn(2+); Xref=ChEBI:CHEBI:29105; ; Note=Binds 1 zinc ion per subunit.; FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA-Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seem to have to effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}. METAL 176 176 Zinc.; METAL 179 179 Zinc.; METAL 238 238 Zinc.; METAL 242 242 Zinc.
08/10/2016, 15h45
CosmoKnacki

J'imagine qu'il y a plus de deux lignes à ton fichier.

Quand tu lui demandes de rechercher "FUNCTION" Il affiche une ligne complète qui contient "FUNCTION", ce n'est pas ce que tu attends? (parce que c'est exactement ce que ton code demande). Quel est la réponse que tu attends?

Est-ce que ton fichier est trouvable quelque part, as-tu un lien vers ce fichier?
08/10/2016, 16h45
Shyma

Il n'affiche pas une ligne, pas la ligne qui contient le mot, mais il m'affiche tout le fichier en entier, je voudrais juste qu'il m'affiche ce que ce mot indique ! Genre :

FUNCTION : FUNCTION: Acts as a tumor suppressor in many tumor types;
08/10/2016, 16h59
wiztricks
Salut,

Citation:

Envoyé par Shyma

Il n'affiche pas une ligne, pas la ligne qui contient le mot, mais il m'affiche tout le fichier en entier, je voudrais juste qu'il m'affiche ce que ce mot indique ! Genre :

FUNCTION : FUNCTION: Acts as a tumor suppressor in many tumor types;

Votre programme affiche ce que vous lui avez demandé d'afficher...

Il faudrait commencer par rendre compte que votre fichier représente un tableau à 2 dimensions: lignes et colonnes.
Par exemple:
Code:

1 2 3 4 5 6 >>> data = '''A\tB\tC\tD ... 1\t2\t3\t4 ... 1\t2\t3\t4 ... ''' >>> data 'A\tB\tC\tD\n1\t2\t3\t4\n1\t2\t3\t4\n'
sont des données ayant la même structure: les lignes sont matérialisées par '\n' et les colonnes par '\t'.
Et si on veut parcourir cette structure là, il suffit de découper cette chaine de caractères aux bons endroits:
Code:

1 2 >>> data.splitlines() ['A\tB\tC\tD', '1\t2\t3\t4', '1\t2\t3\t4']
Et si on découpe chaque ligne en colonnes, çà donne:
Code:

1 2 3 4 5 6 >>> for line in data.splitlines(): ... print(line.split('\t')) ... ['A', 'B', 'C', 'D'] ['1', '2', '3', '4'] ['1', '2', '3', '4']
i.e. des "cases" qui auront un numéro de ligne x colonne.

Cela compris, compliquons les choses:
Code:

1 2 3 4 5 >>> data = 'A\tB\tC\tD\n1\t2\t3\t4:1\n1\t2\t3\t4:2\n' >>> print(data) A B C D 1 2 3 4:1 1 2 3 4:2
Afficher les cases qui contiennent '4' est différent d'afficher les lignes qui contiennent '4':
Code:

1 2 3 4 5 6 7 >>> for line in data.splitlines(): ... if '4' in line: ... print(line) ... 1 2 3 4:1 1 2 3 4:2 >>>
puisque c'est un tableau 2D, accéder aux cases, c'est 2 boucles/2 indices:
Code:

1 2 3 4 5 6 7 8 9 >>> for line in data.splitlines(): ... items = line.split('\t') ... for e in items: ... if '4' in e: ... print(e) ... 4:1 4:2 >>>
Sauf à savoir que ce que vous cherchez est dans la 4ème colonne:
Code:

1 2 3 4 5 6 7 >>> for line in data.splitlines(): ... items = line.split('\t') ... if '4' in items[3]: ... print(items[3]) ... 4:1 4:2
Dans ce cas, plus besoin de la 2ème boucle (on connaît la colonne intéressante) mais il faut quand même découper les lignes en colonnes pour accéder aux "cases". Et pour le reste si vous ne comprenez pas, pour apprendre à utiliser chaînes de caractères et listes de listes il y a de bons tutos...

- W