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EnsEMBL search generates a CSV file (comma delimited) of EnsEMBL identifier entries.
Usage: ensembl_search [OPTIONS] --certificate --index --file --output
Options:
-c, --certificate A DER-encoded X.509 file
-i, --index A column index to take the set of values
-d, --delimiter The delimiter character that separates each field value (e.g. ',', ';', '\t')
-f, --file The flat file (e.g. CSV, TSV) file path to parse for identifiers
-n, --no-headers A flag that indicates no header row is present
-O, --output The output file name and path to write a CSV file
-h, --help Print help information
-V, --version Print version information
Given the following file /home/user/data/csv/gene_expressions.csv with the following entries:
| Gene name | Gene | Tissue region | Transcripts per million |
|---|---|---|---|
| CLHC1 | ENSG00000162994 | cerebral cortex | 0.9 |
| CLHC1 | ENSG00000162994 | basal ganglia | 1.4 |
| CLHC1 | ENSG00000162994 | hippocampal formation | 1.5 |
| SLC19A2 | ENSG00000117479 | hippocampal formation | 2.0 |
| SLC19A2 | ENSG00000117479 | cerebral cortex | 3.5 |
| SETD9 | ENSG00000155542 | midbrain | 0.7 |
| ... | ... | ... |
The following command will return a list of EnsEMBL identifiers:
ensembl_search \
--file "/home/user/data/csv/gene_expressions.csv" \
--index 1 \
--certificate "/home/user/data/certificates/authorities.pem" \
--certificate "/home/user/data/certificates/additional_authorities.pem" \
--output "/home/user/data/csv/EnsEMBL_entries.csv"
| assembly_name | biotype | canonical_transcript | db_type | description | display_name | dna | end | id | logic_name | object_type | seq_region_name | source | species | start | strand | version |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GRCh38 | protein_coding | ENST00000285947.5 | core | SET domain containing 9 [Source:HGNC Symbol;Acc:HGNC:28508] | SETD9 | GACAGCCGT... | 56925532 | ENSG00000155542 | ensembl_havana_gene_homo_sapiens | Gene | 5 | ensembl_havana | homo_sapiens | 56909260 | 1 | 12 |
| GRCh38 | protein_coding | ENST00000401408.6 | core | clathrin heavy chain linker domain containing 1 [Source:HGNC Symbol;Acc:HGNC:26453] | CLHC1 | TTTTTATGT... | 55232563 | ENSG00000162994 | ensembl_havana_gene_homo_sapiens | Gene | 2 | ensembl_havana | homo_sapiens | 55172547 | -1 | 16 |
| GRCh38 | protein_coding | ENST00000236137.10 | core | solute carrier family 19 member 2 [Source:HGNC Symbol;Acc:HGNC:10938] | SLC19A2 | TTTGATTAA... | 169485944 | ENSG00000117479 | ensembl_havana_gene_homo_sapiens | Gene | 1 | ensembl_havana | homo_sapiens | 169463909 | -1 | 15 |
Identifiers outputs to standard output a set of identifiers from a column present in a flat file (e.g. CSV, TSV).
Usage: identifiers [OPTIONS] --index --file
Options:
-i, --index A column index to take the set of values
-d, --delimiter The delimiter character that separates each field value (e.g. ',', ';', '\t')
-f, --file The flat file (e.g. CSV, TSV) file path to parse for identifiers
-n, --no-headers A flag that indicates no header row is present
-h, --help Print help information
-V, --version Print version information
Given the following file /home/user/data/csv/gene_expressions.csv with the following entries,
| Gene name | Gene | Tissue region | Transcripts per million |
|---|---|---|---|
| CLHC1 | ENSG00000162994 | cerebral cortex | 0.9 |
| CLHC1 | ENSG00000162994 | basal ganglia | 1.4 |
| CLHC1 | ENSG00000162994 | hippocampal formation | 1.5 |
| SLC19A2 | ENSG00000117479 | hippocampal formation | 2.0 |
| SLC19A2 | ENSG00000117479 | cerebral cortex | 3.5 |
| SETD9 | ENSG00000155542 | midbrain | 0.7 |
The following command,
identifiers \
--file "/home/user/data/csv/gene_expressions.csv" \
--index 1
will output EnsEMBL identifiers to standard output:
ENSG00000162994
ENSG00000117479
ENSG0000015554
Constructs an SVG image of a suffix tree from a string provided as input. Usage: suffix_tree [OPTIONS] --string --file
Options:
-s, --string A string to construct a suffix tree
-f, --file A file path and name
-h, --help Print help information
-V, --version Print version information
The command,
suffix_tree \
--string cacao
--file ./output.svg
will generate the image:
