Mercurial > repos > proteore > proteore_id_converter

annotate README.rst @ 10:ec2adfa349bc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author proteore
date Mon, 27 Aug 2018 06:05:23 -0400
parents 59da262c572c
children 659f1248f535
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
1 Wrapper for ID Converter tool
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
2 =============================
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
3
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
4 **Authors**
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
5
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
7
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
9
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
11
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
13
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
14 =============================
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
15
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
16 This tool converts a list of IDs to another identifier type, select the source and target type from the dropdown menus above (see below supported source and target types).
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
17
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
18 After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to.
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
19
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
20 If your input is a list of IDs or a single-column file, the tool will return a file containing the mapped IDs.
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
21
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
22 If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file.
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
23
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
24 **Available databases**
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
25
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
26 * neXtProt ID (e.g. NX_P31946)
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
27
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
28 * Uniprot accession number (e.g. P31946)
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
29
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
30 * Uniprot ID (e.g 1433B_HUMAN)
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
31
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
32 * Entrez gene ID (e.g. 7529)
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
33
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
34 * RefSeq (NCBI) protein (e.g. NP_003395.1; NP_647539.1; XP_016883528.1)
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
35
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
36 * GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448; 377656701; 67464627; 78101741)
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
37
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
38 * Protein DataBank ID (e.g. 2BR9:A; 3UAL:A; 3UBW:A)
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
39
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
40 * GOterms (Gene Ontology) ID (e.g. GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634)
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
41
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
42 * Protein Information Resource ID (e.g. S34755)
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
43
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
44 * OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
45
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
46 * Unigene ID (e.g. Hs.643544)
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
47
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
48 * Ensembl gene ID (e.g. ENSG00000166913)
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
49
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
50 * Ensembl transcript ID (e.g. ENST00000353703; ENST00000372839)
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
51
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
52 * Ensembl protein ID (e.g. ENSP00000300161; ENSP00000361930)
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
53
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
54 This tool converts human IDs using file built from:
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
55
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
56 * HUMAN_9606_idmapping_selected.tab
1
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
57 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
3b654cb3f6ad planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
proteore
parents:
diff changeset
58
7
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
59 * nextprot_ac_list_all.txt
59da262c572c planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
proteore
parents: 3
diff changeset
60 Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/