Discussion :

[tomaprice]

Bonjour,

j'essaye désespérément de parser le texte suivant. Mon but est de faire en sorte que chaque élément entre {{ }} soit un élément d'une liste.

J'utilise pour cela la fonction findall mais sans succès.

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

re.findall("{{ ?.*|\s* ?}}",snp_page)

Merci d'avance pour votre aide.

Le texte à parser.

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
{{Rsnum
|rsid=1799966
|Gene=BRCA1
|Chromosome=17
|position=43071077
|Orientation=minus
|ReferenceAllele=A
|MissenseAllele=G
|GMAF=0.3274
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(A;A)
|geno2=(A;G)
|geno3=(G;G)
|Gene_s=BRCA1
}}{{ population diversity
| geno1=(A;A)
| geno2=(A;G)
| geno3=(G;G)
| CEU | 45.5 | 46.4 | 8.2
| HCB | 46.3 | 41.9 | 11.8
| JPT | 53.1 | 38.9 | 8.0
| YRI | 63.3 | 35.4 | 1.4
| ASW | 50.9 | 45.6 | 3.5
| CHB | 46.3 | 41.9 | 11.8
| CHD | 29.4 | 55.0 | 15.6
| GIH | 31.6 | 50.0 | 18.4
| LWK | 62.7 | 32.7 | 4.5
| MEX | 41.4 | 43.1 | 15.5
| MKK | 60.9 | 35.9 | 3.2
| TSI | 41.2 | 51.5 | 7.2
| HapMapRevision=28
}}

This SNP, a variant in the [[BRCA1]] gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for [[breast cancer]]. {{PMID|17341484}}

For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for [[breast cancer]], refer to the SNPedia [[breast cancer]] entry.

For this particular SNP, the risk (minor) allele is (G).

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
{{ClinVar
|rsid=1799966
|Reversed=1
|FwdREF=A
|FwdALT=G,T
|REF=T
|ALT=A,C
|RSPOS=41223094
|CHROM=17
|GMAF=0.3274
|dbSNPBuildID=89
|SSR=0
|SAO=0
|VP=0x05016800000017051f100101
|GENEINFO=BRCA1:672
|GENE_NAME=BRCA1
|GENE_ID=672
|WGT=0
|VC=SNV
|CLNALLE=1; 2
|CLNHGVS=NC_000017.10:g.41223094T>A; NC_000017.10:g.41223094T>C
|CLNSIG=2
|CLNCUI=
|CLNACC=
RCV000031194.2; RCV000048673.2; RCV000034753.1; RCV000048672.2
|Tags=RV;PM;PMC;SLO;VLD;G5A;G5;HD;GNO;KGPhase1;KGPilot123;KGPROD;OTHERKG;PH3;LSD
|CAF=0.6726; 0.3274
|CLNDBN=Breast-ovarian cancer, familial 1; Familial cancer of breast; not provided
|CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet; GeneReviews:MedGen:OMIM:SNOMED_CT
|CLNDSDBID=NBK1247:C2676676:604370:145; NBK1247:C0346153:114480:254843006
|COMMON=1
|Disease=Breast-ovarian cancer; Familial cancer of breast; not provided
}}
 
{{PMID Auto
|PMID=18559551
|Title=Pathway analysis of single-nucleotide polymorphisms potentially associated with glioblastoma multiforme susceptibility using random forests.
}}
 
{{GET Evidence
|gene=BRCA1
|aa_change=Ser1634Gly
|aa_change_short=S1634G
|impact=not reviewed
|qualified_impact=Insufficiently evaluated not reviewed
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs1799966
|overall_frequency_n=3203
|overall_frequency_d=10758
|overall_frequency=0.297732
|n_genomes=3
|n_genomes_annotated=0
|n_haplomes=3
|n_articles=0
|n_articles_annotated=0
|qualityscore_in_silico=1
|qualitycomment_in_silico=Y
|gene_in_genetests=Y
|genetests_testable=Y
|genetests_reviewed=Y
|nblosum100=2
|autoscore=2
|webscore=N
}}
 
{{on chip | 23andMe v1}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | FTDNA2}}
{{on chip | FTDNA}}
{{on chip | Illumina Human 1M}}

[VinsS]

Salut,

Si je fais ça:

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
 
# -*- coding: utf-8 -*-
 
import re
 
txt = """
{{Rsnum
|rsid=1799966
|Gene=BRCA1
|Chromosome=17
|position=43071077
|Orientation=minus
|ReferenceAllele=A
|MissenseAllele=G
|GMAF=0.3274
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(A;A)
|geno2=(A;G)
|geno3=(G;G)
|Gene_s=BRCA1
}}{{ population diversity
| geno1=(A;A)
| geno2=(A;G)
| geno3=(G;G)
| CEU | 45.5 | 46.4 | 8.2
| HCB | 46.3 | 41.9 | 11.8
| JPT | 53.1 | 38.9 | 8.0
| YRI | 63.3 | 35.4 | 1.4
| ASW | 50.9 | 45.6 | 3.5
| CHB | 46.3 | 41.9 | 11.8
| CHD | 29.4 | 55.0 | 15.6
| GIH | 31.6 | 50.0 | 18.4
| LWK | 62.7 | 32.7 | 4.5
| MEX | 41.4 | 43.1 | 15.5
| MKK | 60.9 | 35.9 | 3.2
| TSI | 41.2 | 51.5 | 7.2
| HapMapRevision=28
}}
"""
 
rgx = re.compile('(?<={{)(.*?)(?=}})', re.DOTALL)
 
content = rgx.findall(txt)
data = []
for c in content:
    data.append([i.strip() for i in c.split('|')])
 
for d in data:
    print d

j'obtiens ça:

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

1
2
3
4
 
['Rsnum', 'rsid=1799966', 'Gene=BRCA1', 'Chromosome=17', 'position=43071077', 'Orientation=minus', 'ReferenceAllele=A', 'MissenseAllele=G', 'GMAF=0.3274', 'Assembly=GRCh38', 'GenomeBuild=38.1', 'dbSNPBuild=141', 'geno1=(A;A)', 'geno2=(A;G)', 'geno3=(G;G)', 'Gene_s=BRCA1']
 
['population diversity', 'geno1=(A;A)', 'geno2=(A;G)', 'geno3=(G;G)', 'CEU', '45.5', '46.4', '8.2', 'HCB', '46.3', '41.9', '11.8', 'JPT', '53.1', '38.9', '8.0', 'YRI', '63.3', '35.4', '1.4', 'ASW', '50.9', '45.6', '3.5', 'CHB', '46.3', '41.9', '11.8', 'CHD', '29.4', '55.0', '15.6', 'GIH', '31.6', '50.0', '18.4', 'LWK', '62.7', '32.7', '4.5', 'MEX', '41.4', '43.1', '15.5', 'MKK', '60.9', '35.9', '3.2', 'TSI', '41.2', '51.5', '7.2', 'HapMapRevision=28']

bon ou pas bon ?

[tomaprice]

pas tout a fait mais c'est ma faute, je me suis mal exprimé.
J'ai tout de même réussi à obtenir ce que je souhaitais.

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

re.findall("{{\s*[(\w=.*(-;:>,\s*\|)*]*\s*}}",snp_page)

résultat :

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

['{{Rsnum\n|rsid=4986852\n|Gene=BRCA1\n|Chromosome=17\n|position=43092412\n|Orientation=plus\n|ReferenceAllele=G\n|MissenseAllele=A\n|GMAF=0.01194\n|Assembly=GRCh38\n|GenomeBuild=38.1\n|dbSNPBuild=141\n|geno1=(A;A)\n|geno2=(A;G)\n|geno3=(G;G)\n|Gene_s=BRCA1\n}}', '{{ population diversity\n| geno1=(A;A)\n| geno2=(A;G)\n| geno3=(G;G)\n| CEU | 0.0 | 8.8 | 91.2\n| HCB | 0.0 | 0.0 | 100.0\n| JPT | 0.0 | 0.0 | 100.0\n| YRI | 0.0 | 0.0 | 100.0\n| ASW | 0.0 | 5.6 | 94.4\n| CHB | 0.0 | 0.0 | 100.0\n| CHD | 0.0 | 1.0 | 99.0\n| GIH | 0.0 | 3.1 | 96.9\n| LWK | 0.0 | 0.0 | 0.0\n| MEX | 0.0 | 0.0 | 0.0\n| MKK | 0.0 | 2.6 | 97.4\n| TSI | 0.0 | 0.0 | 0.0\n| HapMapRevision=28\n}}', '{{PMID|7894493}}', '{{ neighbor\n| rsid = 1800709\n| distance = 598\n}}', '{{ neighbor\n| rsid = 2227945\n| distance = 299\n}}', '{{omim\n|id=113705\n|rsnum=4986852\n|variant=0011\n}}', '{{ClinVar\n|rsid=4986852\n|Reversed=1\n|FwdREF=G\n|FwdALT=A\n|REF=C\n|ALT=T\n|RSPOS=41244429\n|CHROM=17\n|GMAF=0.0119\n|dbSNPBuildID=113\n|SSR=0\n|SAO=1\n|VP=0x050168000000150517110101\n|GENEINFO=BRCA1:672\n|GENE_NAME=BRCA1\n|GENE_ID=672\n|WGT=0\n|VC=SNV\n|CLNALLE=1\n|CLNHGVS=NC_000017.10:g.41244429C>T\n|CLNSRC=OMIM Allelic Variant\n|CLNORIGIN=1\n|CLNSRCID=113705.0011\n|CLNSIG=255\n|CLNCUI=C2676676\n|CLNDBN=Breast-ovarian cancer, familial 1; not provided; Familial cancer of breast\n|Disease=Breast-ovarian cancer; not provided; Familial cancer of breast\n|CLNACC=RCV000019239.1; RCV000034739.1; RCV000048074.2\n|Tags=RV;PM;PMC;SLO;VLD;G5;HD;GNO;KGPhase1;KGPROD;OTHERKG;PH3;LSD;OM\n|CAF=0.9881; 0.01194\n|CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet; GeneReviews:MedGen:OMIM:SNOMED_CT\n|CLNDSDBID=NBK1247:C2676676:604370:145; NBK1247:C0346153:114480:254843006\n|COMMON=1\n}}', '{{PMID Auto\n|PMID=16111488\n|Title=Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.\n|OA=1\n}}', '{{PMID Auto\n|PMID=19644020\n|Title=Genotyping of frequent BRCA1/2 SNPs with unlabeled probes: a supplement to HRMCA mutation scanning, allowing the strong reduction of sequencing burden.\n|OA=1\n}}', '{{GET Evidence\n|gene=BRCA1\n|aa_change=Ser1040Asn\n|aa_change_short=S1040N\n|impact=pathogenic\n|qualified_impact=Insufficiently evaluated pathogenic\n|inheritance=unknown\n|quality_scores=Array\n|dbsnp_id=rs4986852\n|overall_frequency_n=185\n|overall_frequency_d=10758\n|overall_frequency=0.0171965\n|n_genomes=1\n|n_genomes_annotated=0\n|n_haplomes=1\n|n_articles=0\n|n_articles_annotated=0\n|gene_in_genetests=Y\n|in_omim=Y\n|pph2_score=0.024\n|genetests_testable=Y\n|genetests_reviewed=Y\n|nblosum100=0\n|autoscore=4\n|webscore=N\n|n_web_uneval=10\n}}', '{{on chip | 23andMe v1}}', '{{on chip | 23andMe v2}}', '{{on chip | 23andMe v3}}', '{{on chip | 23andMe v4}}', '{{on chip | FTDNA2}}', '{{on chip | FTDNA}}', '{{on chip | HumanOmni1Quad}}', '{{on chip | Illumina Human 1M}}']