API Reference
This page provides API docs for the Python API of blast2galaxy.
Main methods of the Python API
blast2galaxy.blastn
blastn(profile='default', query='', query_str=None, task=ChoicesTaskBlastn.megablast, db=None, evalue='0.001', out='', outfmt='6', html=False, dust=ChoicesYesNo.yes.value, strand=ChoicesStrand.both.value, max_hsps=None, perc_identity=0.0, word_size=None, ungapped=False, parse_deflines=False, qcov_hsp_perc=0.0, window_size=None, gapopen=None, gapextend=None)
blastn
search nucleotide databases using a nucleotide query
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
profile |
Optional[str]
|
the profile ID from .blast2galaxy.toml or runtime configuration |
'default'
|
query |
str
|
file path with your query sequence |
''
|
query_str |
str
|
Python string containing the query sequence, can be used instead of |
None
|
task |
Optional[ChoicesTaskBlastn]
|
the blastn task: megablast or something |
megablast
|
db |
Optional[str | None]
|
the BLAST database to search in |
None
|
evalue |
Optional[str]
|
Expectation value cutoff |
'0.001'
|
out |
str
|
Path / filename of file to store the BLAST result |
''
|
outfmt |
Optional[str]
|
Output format |
'6'
|
html |
Optional[bool]
|
Format output as HTML document |
False
|
dust |
Optional[ChoicesYesNo]
|
Filter out low complexity regions (with DUST) |
yes.value
|
strand |
Optional[ChoicesStrand]
|
Query strand(s) to search against database/subject |
value
|
max_hsps |
Optional[int | None]
|
Maximum number of HSPs (alignments) to keep for any single query-subject pair |
None
|
perc_identity |
Optional[float]
|
Percent identity cutoff |
0.0
|
word_size |
Optional[int | None]
|
Word size for wordfinder algorithm |
None
|
ungapped |
Optional[bool]
|
Perform ungapped alignment only? |
False
|
parse_deflines |
Optional[bool]
|
Should the query and subject defline(s) be parsed? |
False
|
qcov_hsp_perc |
Optional[float]
|
Minimum query coverage per hsp (percentage, 0 to 100) |
0.0
|
window_size |
Optional[int | None]
|
Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default |
None
|
gapopen |
Optional[int | None]
|
Cost to open a gap |
None
|
gapextend |
Optional[int | None]
|
Cost to extend a gap |
None
|
blast2galaxy.blastp
blastp(profile='default', query='', query_str=None, task=ChoicesTaskBlastp.blastp, db=None, evalue='0.001', out='', outfmt='6', html=False, seg=ChoicesYesNo.yes.value, matrix=None, max_target_seqs=500, num_descriptions=500, num_alignments=250, threshold=None, max_hsps=None, word_size=None, ungapped=False, parse_deflines=False, qcov_hsp_perc=0.0, window_size=None, gapopen=None, gapextend=None, comp_based_stats='2', use_sw_tback=False)
blastp
search protein databases using a protein query
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
profile |
str
|
the profile ID from .blast2galaxy.toml or runtime configuration |
'default'
|
query |
str
|
file path with your query sequence |
''
|
query_str |
str
|
Python string containing the query sequence, can be used instead of |
None
|
task |
Optional[ChoicesTaskBlastp]
|
the blastn task: megablast or something |
blastp
|
db |
Optional[str]
|
the BLAST database to search in |
None
|
evalue |
Optional[str]
|
Expectation value cutoff |
'0.001'
|
out |
str
|
Path / filename of file to store the BLAST result |
''
|
outfmt |
Optional[str]
|
Output format |
'6'
|
html |
Optional[bool]
|
Format output as HTML document |
False
|
seg |
Optional[ChoicesYesNo]
|
Filter out low complexity regions (with SEG) |
yes.value
|
matrix |
Optional[str]
|
Scoring matrix name (normally BLOSUM62) |
None
|
max_target_seqs |
Optional[int]
|
Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = 500 |
500
|
num_descriptions |
Optional[int]
|
Number of database sequences to show one-line descriptions for. Not applicable for outfmt > 4. Default = 500 * Incompatible with: max_target_seqs |
500
|
num_alignments |
Optional[int]
|
Number of database sequences to show alignments for. Default = 250 * Incompatible with: max_target_seqs |
250
|
threshold |
Optional[float]
|
Minimum word score such that the word is added to the BLAST lookup table |
None
|
max_hsps |
Optional[int]
|
Maximum number of HSPs (alignments) to keep for any single query-subject pair |
None
|
word_size |
Optional[int]
|
Word size for wordfinder algorithm |
None
|
ungapped |
Optional[bool]
|
Perform ungapped alignment only? |
False
|
parse_deflines |
Optional[bool]
|
Should the query and subject defline(s) be parsed? |
False
|
qcov_hsp_perc |
Optional[float]
|
Minimum query coverage per hsp (percentage, 0 to 100) |
0.0
|
window_size |
Optional[int]
|
Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default |
None
|
gapopen |
Optional[int]
|
Cost to open a gap |
None
|
gapextend |
Optional[int]
|
Cost to extend a gap |
None
|
comp_based_stats |
Optional[str]
|
Use composition-based statistics: D or d: default (equivalent to 2 ); 0 or F or f: No composition-based statistics; 1: Composition-based statistics as in NAR 29:2994-3005, 2001; 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties; 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally |
'2'
|
use_sw_tback |
Optional[bool]
|
Compute locally optimal Smith-Waterman alignments? |
False
|
blast2galaxy.blastx
blastx(profile='default', query='', query_str=None, task=ChoicesTaskBlastx.blastx, db=None, evalue='0.001', out='', outfmt='6', html=False, seg=ChoicesYesNo.yes.value, matrix=None, max_target_seqs=500, num_descriptions=None, num_alignments=None, threshold=None, max_hsps=None, word_size=None, ungapped=False, parse_deflines=False, qcov_hsp_perc=0.0, window_size=None, gapopen=None, gapextend=None, comp_based_stats='2')
blastx
search protein databases using a translated nucleotide query
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
profile |
str
|
the profile ID from .blast2galaxy.toml or runtime configuration |
'default'
|
query |
str
|
file path with your query sequence |
''
|
query_str |
str
|
Python string containing the query sequence, can be used instead of |
None
|
task |
Optional[ChoicesTaskBlastx]
|
the blastn task: megablast or something |
blastx
|
db |
Optional[str]
|
the BLAST database to search in |
None
|
evalue |
Optional[str]
|
Expectation value cutoff |
'0.001'
|
out |
str
|
Path / filename of file to store the BLAST result |
''
|
outfmt |
Optional[str]
|
Output format |
'6'
|
html |
Optional[bool]
|
Format output as HTML document |
False
|
seg |
Optional[ChoicesYesNo]
|
Filter out low complexity regions (with SEG) |
yes.value
|
matrix |
Optional[str]
|
Scoring matrix name (normally BLOSUM62) |
None
|
max_target_seqs |
Optional[int]
|
Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = 500 |
500
|
num_descriptions |
Optional[int]
|
Number of database sequences to show one-line descriptions for. Not applicable for outfmt > 4. Default = 500 * Incompatible with: max_target_seqs |
None
|
num_alignments |
Optional[int]
|
Number of database sequences to show alignments for. Default = 250 * Incompatible with: max_target_seqs |
None
|
threshold |
Optional[float]
|
Minimum word score such that the word is added to the BLAST lookup table |
None
|
max_hsps |
Optional[int]
|
Maximum number of HSPs (alignments) to keep for any single query-subject pair |
None
|
word_size |
Optional[int]
|
Word size for wordfinder algorithm |
None
|
ungapped |
Optional[bool]
|
Perform ungapped alignment only? |
False
|
parse_deflines |
Optional[bool]
|
Should the query and subject defline(s) be parsed? |
False
|
qcov_hsp_perc |
Optional[float]
|
Minimum query coverage per hsp (percentage, 0 to 100) |
0.0
|
window_size |
Optional[int]
|
Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default |
None
|
gapopen |
Optional[int]
|
Cost to open a gap |
None
|
gapextend |
Optional[int]
|
Cost to extend a gap |
None
|
comp_based_stats |
Optional[str]
|
Use composition-based statistics: D or d: default (equivalent to 2 ); 0 or F or f: No composition-based statistics; 1: Composition-based statistics as in NAR 29:2994-3005, 2001; 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties; 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally |
'2'
|
blast2galaxy.diamond_blastp
diamond_blastp(profile='default', query='', query_str=None, task=ChoicesTaskBlastp.blastp, db=None, evalue='0.001', outfmt=ChoicesOutfmtDiamond.blast_pairwise.value, faster=False, fast=False, mid_sensitive=False, sensitive=False, more_sensitive=False, very_sensitive=False, ultra_sensitive=False, strand=ChoicesStrand.both.value, matrix='BLOSUM62', max_target_seqs=500, max_hsps=None, window=None, gapopen=None, gapextend=None, comp_based_stats='1')
diamond_blastp
search protein databases using a protein query with DIAMOND
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
profile |
str
|
the profile ID from .blast2galaxy.toml or runtime configuration |
'default'
|
query |
str
|
file path with your query sequence |
''
|
query_str |
str
|
Python string containing the query sequence, can be used instead of |
None
|
task |
Optional[ChoicesTaskBlastp]
|
the blastn task: megablast or something |
blastp
|
db |
Optional[str]
|
the BLAST database to search in |
None
|
evalue |
Optional[str]
|
Expectation value cutoff |
'0.001'
|
outfmt |
Optional[ChoicesOutfmtDiamond]
|
Output format |
value
|
faster |
Optional[bool]
|
faster mode |
False
|
fast |
Optional[bool]
|
fast mode |
False
|
mid_sensitive |
Optional[bool]
|
mid_sensitive mode |
False
|
sensitive |
Optional[bool]
|
sensitive mode |
False
|
more_sensitive |
Optional[bool]
|
more_sensitive mode |
False
|
very_sensitive |
Optional[bool]
|
very_sensitive mode |
False
|
ultra_sensitive |
Optional[bool]
|
ultra_sensitive mode |
False
|
strand |
Optional[ChoicesStrand]
|
Query strand(s) to search against database/subject |
value
|
matrix |
Optional[str]
|
Scoring matrix name (normally BLOSUM62) |
'BLOSUM62'
|
max_target_seqs |
Optional[int]
|
Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = 500 |
500
|
max_hsps |
Optional[int]
|
Maximum number of HSPs (alignments) to keep for any single query-subject pair |
None
|
window |
Optional[int]
|
Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default |
None
|
gapopen |
Optional[int]
|
Cost to open a gap |
None
|
gapextend |
Optional[int]
|
Cost to extend a gap |
None
|
comp_based_stats |
Optional[str]
|
Use composition-based statistics: D or d: default (equivalent to 2 ); 0 or F or f: No composition-based statistics; 1: Composition-based statistics as in NAR 29:2994-3005, 2001; 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties; 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally |
'1'
|
blast2galaxy.diamond_blastx
diamond_blastx(profile='default', query='', query_str=None, task=ChoicesTaskBlastp.blastp, db=None, evalue='0.001', out='', outfmt=ChoicesOutfmtDiamond.blast_pairwise.value, faster=False, fast=False, mid_sensitive=False, sensitive=False, more_sensitive=False, very_sensitive=False, ultra_sensitive=False, strand=ChoicesStrand.both.value, matrix='BLOSUM62', max_target_seqs=500, max_hsps=None, window=None, gapopen=None, gapextend=None, comp_based_stats='1')
diamond_blastx
search protein databases using a translated nucleotide query with DIAMOND
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
profile |
str
|
the profile ID from .blast2galaxy.toml or runtime configuration |
'default'
|
query |
str
|
file path with your query sequence |
''
|
query_str |
str
|
Python string containing the query sequence, can be used instead of |
None
|
task |
Optional[ChoicesTaskBlastp]
|
the blastn task: megablast or something |
blastp
|
db |
Optional[str]
|
the BLAST database to search in |
None
|
evalue |
Optional[str]
|
Expectation value cutoff |
'0.001'
|
out |
str
|
Path / filename of file to store the BLAST result |
''
|
outfmt |
Optional[ChoicesOutfmtDiamond]
|
Output format |
value
|
faster |
Optional[bool]
|
faster mode |
False
|
fast |
Optional[bool]
|
fast mode |
False
|
mid_sensitive |
Optional[bool]
|
mid_sensitive mode |
False
|
sensitive |
Optional[bool]
|
sensitive mode |
False
|
more_sensitive |
Optional[bool]
|
more_sensitive mode |
False
|
very_sensitive |
Optional[bool]
|
very_sensitive mode |
False
|
ultra_sensitive |
Optional[bool]
|
ultra_sensitive mode |
False
|
strand |
Optional[ChoicesStrand]
|
Query strand(s) to search against database/subject |
value
|
matrix |
Optional[str]
|
Scoring matrix name (normally BLOSUM62) |
'BLOSUM62'
|
max_target_seqs |
Optional[int]
|
Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = 500 |
500
|
max_hsps |
Optional[int]
|
Maximum number of HSPs (alignments) to keep for any single query-subject pair |
None
|
window |
Optional[int]
|
Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default |
None
|
gapopen |
Optional[int]
|
Cost to open a gap |
None
|
gapextend |
Optional[int]
|
Cost to extend a gap |
None
|
comp_based_stats |
Optional[str]
|
Use composition-based statistics: D or d: default (equivalent to 2 ); 0 or F or f: No composition-based statistics; 1: Composition-based statistics as in NAR 29:2994-3005, 2001; 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties; 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally |
'1'
|
blast2galaxy.list_dbs
list_dbs(tool, server='default')
list_dbs
list available databases of a BLAST+ or DIAMOND tool installed on a Galaxy server
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
server |
Optional[str]
|
Server-ID |
'default'
|
tool |
str
|
Tool-ID |
required |
blast2galaxy.list_tools
list_tools(server='default', type=None)
list_tools
list available and compatible BLAST+ and DIAMOND tools installed on a Galaxy server
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
server |
Optional[str]
|
Server-ID |
'default'
|
type |
Optional[ChoicesBlastType | None]
|
limit the list to a specific tool type (blastn, tblast, blastp, blastx, diamond) |
None
|
blast2galaxy.tblastn
tblastn(profile='default', query='', query_str=None, task=ChoicesTaskTblastn.tblastn, db=None, evalue='0.001', out='', outfmt='6', html=False, seg=ChoicesYesNo.yes.value, db_gencode=None, matrix=None, max_target_seqs=500, num_descriptions=None, num_alignments=None, threshold=None, max_hsps=None, word_size=None, ungapped=False, parse_deflines=False, qcov_hsp_perc=0.0, window_size=None, gapopen=None, gapextend=None, comp_based_stats='2')
tblastn
search translated nucleotide databases using a protein query
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
profile |
str
|
the profile ID from .blast2galaxy.toml or runtime configuration |
'default'
|
query |
str
|
file path with your query sequence |
''
|
query_str |
str
|
Python string containing the query sequence, can be used instead of |
None
|
task |
Optional[ChoicesTaskTblastn]
|
the blastn task: megablast or something |
tblastn
|
db |
Optional[str]
|
the BLAST database to search in |
None
|
evalue |
Optional[str]
|
Expectation value cutoff |
'0.001'
|
out |
str
|
Path / filename of file to store the BLAST result |
''
|
outfmt |
Optional[str]
|
Output format |
'6'
|
html |
Optional[bool]
|
Format output as HTML document |
False
|
seg |
Optional[ChoicesYesNo]
|
Filter out low complexity regions (with SEG) |
yes.value
|
db_gencode |
Optional[int]
|
Genetic code to use to translate database/subjects (see user manual for details) |
None
|
matrix |
Optional[str]
|
Scoring matrix name (normally BLOSUM62) |
None
|
max_target_seqs |
Optional[int]
|
Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = 500 |
500
|
num_descriptions |
Optional[int]
|
Number of database sequences to show one-line descriptions for. Not applicable for outfmt > 4. Default = 500 * Incompatible with: max_target_seqs |
None
|
num_alignments |
Optional[int]
|
Number of database sequences to show alignments for. Default = 250 * Incompatible with: max_target_seqs |
None
|
threshold |
Optional[float]
|
Minimum word score such that the word is added to the BLAST lookup table |
None
|
max_hsps |
Optional[int]
|
Maximum number of HSPs (alignments) to keep for any single query-subject pair |
None
|
word_size |
Optional[int]
|
Word size for wordfinder algorithm |
None
|
ungapped |
Optional[bool]
|
Perform ungapped alignment only? |
False
|
parse_deflines |
Optional[bool]
|
Should the query and subject defline(s) be parsed? |
False
|
qcov_hsp_perc |
Optional[float]
|
Minimum query coverage per hsp (percentage, 0 to 100) |
0.0
|
window_size |
Optional[int]
|
Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default |
None
|
gapopen |
Optional[int]
|
Cost to open a gap |
None
|
gapextend |
Optional[int]
|
Cost to extend a gap |
None
|
comp_based_stats |
Optional[str]
|
Use composition-based statistics: D or d: default (equivalent to 2 ); 0 or F or f: No composition-based statistics; 1: Composition-based statistics as in NAR 29:2994-3005, 2001; 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties; 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally |
'2'
|
Configuration via API during runtime
blast2galaxy.config.add_default_profile
add_default_profile(server, tool)
add a default profile to the configuration settings
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
server |
str
|
Server ID |
required |
tool |
str
|
Tool-ID (e.g. |
required |
blast2galaxy.config.add_default_server
add_default_server(server_url, api_key)
add a server to the configuration settings
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
server_url |
str
|
URL of the Galaxy server (e.g. |
required |
api_key |
str
|
Galaxy API key |
required |
blast2galaxy.config.add_profile
add_profile(profile, server, tool)
add a profile to the configuration settings
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
profile |
str
|
Profile ID (must be unique) |
required |
server |
str
|
Server ID (one of the server IDs you have defined with |
required |
tool |
str
|
Tool-ID (e.g. |
required |
blast2galaxy.config.add_server
add_server(server, server_url, api_key)
add a server to the configuration settings
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
server |
str
|
the Server ID (must be unique) that is referenced in profiles |
required |
server_url |
str
|
URL of the Galaxy server (e.g. |
required |
api_key |
str
|
Galaxy API key |
required |