Skip to content

Commit

Permalink
update api table
Browse files Browse the repository at this point in the history
  • Loading branch information
@rpetit3
rpetit3 committed Aug 9, 2024
1 parent bfc7402 commit 51a1a4a
Showing 1 changed file with 23 additions and 8 deletions.
31 changes: 23 additions & 8 deletions docs/api/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,26 @@ custom workflows.

Currently the following modules are available in the `camlhmp` API:

| Type | Module | Function | Description |
|--------|-------------------------------------------|---------------------------------------------------------------------------------------|------------------------------------------------|
| Engine | [camlhmp.engines.blast](engines/blast.md) | [run_blast](engines/blast.md#camlhmp.engines.blast.run_blast) | Run BLAST program |
| Engine | [camlhmp.engines.blast](engines/blast.md) | [run_blast](engines/blast.md#camlhmp.engines.blast.run_blastn) | Alias for `run_blast` with `blastn` specified |
| Engine | [camlhmp.engines.blast](engines/blast.md) | [run_blast](engines/blast.md#camlhmp.engines.blast.run_tblastn) | Alias for `run_blast` with `tblastn` specified |
| Parser | [camlhmp.parsers.blast](parsers/blast.md) | [get_blast_allele_hits](parsers/blast.md#camlhmp.parsers.blast.get_blast_allele_hits) | Parse BLAST output for allele hits |
| Parser | [camlhmp.parsers.blast](parsers/blast.md) | [get_blast_region_hits](parsers/blast.md#camlhmp.parsers.blast.get_blast_region_hits) | Parse BLAST output for region hits |
| parser | [camlhmp.parsers.blast](parsers/blast.md) | [get_blast_target_hits](parsers/blast.md#camlhmp.parsers.blast.get_blast_target_hits) | Parse BLAST output for target hits |
| Type | Module | Function | Description |
|-----------|-------------------------------------------|---------------------------------------------------------------------------------------|-----------------------------------------------------|
| Engine | [camlhmp.engines.blast](engines/blast.md) | [run_blast](engines/blast.md#camlhmp.engines.blast.run_blast) | Run BLAST program |
| Engine | [camlhmp.engines.blast](engines/blast.md) | [run_blast](engines/blast.md#camlhmp.engines.blast.run_blastn) | Alias for `run_blast` with `blastn` specified |
| Engine | [camlhmp.engines.blast](engines/blast.md) | [run_blast](engines/blast.md#camlhmp.engines.blast.run_tblastn) | Alias for `run_blast` with `tblastn` specified |
| Framework | [camlhmp.framework](framework.md) | [read_framework](framework.md#camlhmp.framework.read_framework) | Read the framework YAML file |
| Framework | [camlhmp.framework](framework.md) | [print_version](framework.md#camlhmp.framework.print_version) | Print the version of the framework |
| Framework | [camlhmp.framework](framework.md) | [get_types](framework.md#camlhmp.framework.get_types) | Get the types from the framework |
| Framework | [camlhmp.framework](framework.md) | [check_types](framework.md#camlhmp.framework.check_types) | Check the types against the results |
| Framework | [camlhmp.framework](framework.md) | [check_regions](framework.md#camlhmp.framework.check_regions) | Check the region types against the results |
| Parser | [camlhmp.parsers.blast](parsers/blast.md) | [get_blast_allele_hits](parsers/blast.md#camlhmp.parsers.blast.get_blast_allele_hits) | Parse BLAST output for allele hits |
| Parser | [camlhmp.parsers.blast](parsers/blast.md) | [get_blast_region_hits](parsers/blast.md#camlhmp.parsers.blast.get_blast_region_hits) | Parse BLAST output for region hits |
| Parser | [camlhmp.parsers.blast](parsers/blast.md) | [get_blast_target_hits](parsers/blast.md#camlhmp.parsers.blast.get_blast_target_hits) | Parse BLAST output for target hits |
| Utils | [camlhmp.utils](utils.md) | [execute](utils.md#camlhmp.utils.execute) | Execute a command |
| Utils | [camlhmp.utils](utils.md) | [check_dependencies](utils.md#camlhmp.utils.check_dependencies) | Check if all dependencies are installed |
| Utils | [camlhmp.utils](utils.md) | [get_platform](utils.md#camlhmp.utils.get_platform) | Get the platform of the executing machine |
| Utils | [camlhmp.utils](utils.md) | [validate_file](utils.md#camlhmp.utils.validate_file) | Validate a file exists and not empty |
| Utils | [camlhmp.utils](utils.md) | [file_exists_error](utils.md#camlhmp.utils.file_exists_error) | Determine if a file exists and raise an error |
| Utils | [camlhmp.utils](utils.md) | [parse_seq](utils.md#camlhmp.utils.parse_seq) | Parse a sequence file containing a single record |
| Utils | [camlhmp.utils](utils.md) | [parse_seqs](utils.md#camlhmp.utils.parse_seqs) | Parse a sequence file containing a multiple records |
| Utils | [camlhmp.utils](utils.md) | [parse_table](utils.md#camlhmp.utils.parse_table) | Parse a delimited file |
| Utils | [camlhmp.utils](utils.md) | [parse_yaml](utils.md#camlhmp.utils.parse_yaml) | Parse a YAML file |
| Utils | [camlhmp.utils](utils.md) | [write_tsv](utils.md#camlhmp.utils.write_tsv) | Write the dictionary to a TSV file |

0 comments on commit 51a1a4a

Please sign in to comment.