Up: Component summary
Up: Component summary
Component
ExonToPeptideFetches exon-peptide sequences of query exon list.
| Version | 1.0 |
|---|---|
| Bundle | microarray |
| Categories | Exon |
| Authors | Ping Chen (ping.chen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | Ensembl Perl API |
| Source files | component.xml ExonToPeptide.pl |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| ExonList | CSV | Mandatory | A CSV file contains a column of query exon Ensembl IDs. The first row should be headers. |
| connection | Properties | Mandatory | Connection parameters of Ensembl database, including host, database, port, user and driver information. |
Outputs| Name | Type | Description |
|---|---|---|
| ExonSeq | FASTA | A fasta format file for exon sequences. |
| PeptideSeq | FASTA | A fasta format file for peptide sequences of query exons. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| ExonColumn | int | (no default) | The index of column containing exon Ensembl IDs in input ExonList file. |
| SeqType | string | "both" | Output sequence type of interest. It can be "exon-only", "peptide-only" or "both". |
| remove | boolean | true | Remove unmatched records from results. The default value is "true". |
| version | int | (no default) | Ensembl database version number. After version 66, the database schema has changed. Thus, please make sure you enter the correct version number. |
Test cases| Test case | Parameters▼ | IN ExonList |
IN connection |
OUT ExonSeq |
OUT PeptideSeq |
|
|---|---|---|---|---|---|---|
| case1 | properties | ExonList | connection | ExonSeq | PeptideSeq | |
|
ExonColumn=1, |
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| case2 | properties | ExonList | connection | ExonSeq | PeptideSeq | |
|
ExonColumn=1, |
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