BLASTquery

Performs a blast query online. As in https://ncbi.github.io/blast-cloud/

BLASTquery(query,database,program,filter=None, format_type=None, expect=None, nucl_reward=None, nucl_penalty=None, gapcosts=None, matrix=None, hitlist_size=None, descriptions=None, alignments=None, ncbi_gi=None, threshold=None, word_size=None, composition_based_statistics=None, organism=None, others=None, num_threads=None, baseURL="http://blast.ncbi.nlm.nih.gov", verbose=False)

  • query Search query. Allowed values: Accession, GI, or FASTA.
  • database BLAST database. Allowed values: nt, nr, refseq_rna, refseq_protein, swissprot, pdbaa, pdbnt
  • program BLAST program. Allowed values: blastn, megablast, blastp, blastx, tblastn, tblastx
  • filter Low complexity filtering. Allowed values: F to disable. T or L to enable. Prepend “m” for mask at lookup (e.g., mL)
  • format_type Report type. Allowed values: HTML, Text, XML, XML2, JSON2, or Tabular. HTML is the default.
  • expect Expect value. Allowed values: Number greater than zero.
  • nucl_reward Reward for matching bases (BLASTN and megaBLAST). Allowed values: Integer greater than zero.
  • nucl_penalty Cost for mismatched bases (BLASTN and megaBLAST). Allowed values: Integer less than zero.
  • gapcosts Gap existence and extension costs. Allowed values: Pair of positive integers separated by a space such as “11 1”.
  • matrix Scoring matrix name. Allowed values: One of BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, PAM250, PAM30 or PAM70. Default: BLOSUM62 for all applicable programs.
  • hitlist_size Number of databases sequences to keep. Allowed values: Integer greater than zero.
  • descriptions Number of descriptions to print (applies to HTML and Text). Allowed values: Integer greater than zero.
  • alignments Number of alignments to print (applies to HTML and Text). Allowed values: Integer greater than zero.
  • ncbi_gi Show NCBI GIs in report. Allowed values: T or F.
  • threshold Neighboring score for initial words. Allowed values: Positive integer (BLASTP default is 11). Does not apply to BLASTN or MegaBLAST).
  • word_size Size of word for initial matches. Allowed values: Positive integer.
  • composition_based_statistics Composition based statistics algorithm to use. Allowed values: One of 0, 1, 2, or 3. See comp_based_stats command line option in the BLAST+ user manual for details.
  • organism an organism as in https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
  • others here you can add other parameters as seen in a blast bookmarked page. Define you query in https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome Once your query is defined click on "Bookmark" on right upper side of the page. You can copy fragments of the URL which define the query. Eg. For organism "Homo sapiens (taxid:9606)" you will see the string "EQ_MENU=Homo%20sapiens%20%28taxid%3A9606%29" - this is the string you can use here in others.
  • num_threads Number of virtual CPUs to use. Allowed values: Integer greater than zero (default is 1). Supported only on the cloud.

  • verbose print more

  • returns BLAST search request identifier

>>> import AGEpy as age
>>> seq="CTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTAC"
>>> RID=age.BLASTquery(seq,"nt","blastn")
>>> print RID

4MS2JV8T014

BLASTcheck

Checks the status of a query.

BLASTcheck(rid,baseURL="http://blast.ncbi.nlm.nih.gov")

  • rid BLAST search request identifier. Allowed values: The Request ID (RID) returned when the search was submitted

  • baseURL server url. Default=http://blast.ncbi.nlm.nih.gov

  • returns status status for the query.

  • returns therearehist yes or no for existing hits on a finished query.
>>> import AGEpy as age
>>> status, therearehits=age.BLASTcheck(RID)

RID: 4MRYDZSC014; status:READY; hits: yes

>>> print status, therearehits

READY yes

BLASTresults

Retrieves results for an RID.

BLASTresults(rid, format_type="Tabular", hitlist_size= None, alignments=None, ncbi_gi = None, format_object=None, baseURL="http://blast.ncbi.nlm.nih.gov")

  • rid BLAST search request identifier. Allowed values: The Request ID (RID) returned when the search was submitted
  • format_type Report type. Allowed values: HTML, Text, XML, XML2, JSON2, or Tabular.
  • hitlist_size Number of databases sequences to keep. Allowed values: Integer greater than zero.
  • alignments Number of alignments to print (applies to HTML and Text). Allowed values: Integer greater than zero.
  • ncbi_gi Show NCBI GIs in report. Allowed values: T or F.
  • format_object Object type. Allowed values: SearchInfo (status check) or Alignment (report formatting).

  • baseURL server url. Default=http://blast.ncbi.nlm.nih.gov

  • returns the result of a BLAST query. If format_type="Tabular" it will parse the content into a Pandas dataframe.

>>> import AGEpy as age
>>> r=age.BLASTresults(RID)
>>> print r.head()

query id                                        subject ids  \
0  Query_17381                       gi|1012955506|gb|JN214348.1|   
1  Query_17381                       gi|631786534|tpe|HG975427.1|   
2  Query_17381                        gi|369762889|gb|JN900492.1|   
3  Query_17381                   gi|371502118|ref|NM_001126118.1|   
4  Query_17381  gi|371502115|ref|NM_001126112.2|;gi|454521556|...   

query acc.ver subject acc.ver % identity alignment length mismatches  \
0   Query_17381      JN214348.1    100.000             1190          0   
1   Query_17381      HG975427.1    100.000             1190          0   
2   Query_17381      JN900492.1    100.000             1190          0   
3   Query_17381  NM_001126118.1    100.000             1190          0   
4   Query_17381  NM_001126112.2    100.000             1190          0   

gap opens q. start q. end s. start s. end evalue bit scor  
0         0        1   1190      614   1803    0.0     2147  
1         0        1   1190      766   1955    0.0     2147  
2         0        1   1190      877   2066    0.0     2147  
3         0        1   1190      888   2077    0.0     2147  
4         0        1   1190      768   1957    0.0     2147