BLAST

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The BLAST program can be determined from the provided input (will assign either blastn or blastp) and the appropriate database will be used: nt and nr respectively.

You may override these though by using their argument flags. Keep in mind that there is no logic built into validating your inputs. All non-default arguments will be passed to the BLAST API as is.

Arguments

Name	Short	Long	Description
Program	`-p`	`--program`	blast program to use [possible values: blastn, blastp, blastx, tblastn, tblastx]
Database	`-d`	`--database`	blast database to use [possible values: nt, nr, refseq-rna, refseq-protein, swissprot, pdbaa, pdbnt]
Limit	`-l`	`--limit`	Number of hits to return [default: 50]
Expect	`-e`	`--expect`	Minimum expected value to consider [default: 10.0]
Low Complexity Filter	`-f`	`--low-comp-filter`	Include flag to use a complexity filter [default = false]
MEGABLAST	`-m`	`--megablast`	Whether to use MEGABLAST (default = false)
Output	`-o`	`--output`	optional filepath to write output to [default=stdout]

Command Line Interface

# Perform BLAST with a nucleotide sequence
ggetrs blast ATACTCAGTCACACAAGCCATAGCAGGAAACAGCGAGCTTGCAGCCTCACCGACGAGTCTCAACTAAAAGGGACTCCCGGAGCTAGGGGTGGGGACTCGGCCTCACACAGTGAGTGCCGG

# Perform BLAST with an amino acid sequence
ggetrs blast MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE

# Perform BLAST with an amino acid sequence using the PDBAA database
ggetrs blast -d pdbaa MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE

Python

import ggetrs

# Perform BLAST with a nucleotide sequence
ggetrs.blast(
  "ATACTCAGTCACACAAGCCATAGCAGGAAACAGCGAGCTTGCAGCCTCACCGACGAGTCTCAACTAAAAGGGACTCCCGGAGCTAGGGGTGGGGACTCGGCCTCACACAGTGAGTGCCGG"
)

# Perform BLAST with an amino acid sequence
ggetrs.blast(
  "MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE"
)

# Perform BLAST with an amino acid sequence using the PDBAA database
ggetrs.blast(
  "MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE",
  database = "pdbaa"
)

# Perform BLAST with an amino acid sequence using the PDBAA database with a low complexity filter and a limit
ggetrs.blast(
  "MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE",
  database = "pdbaa",
  limit = 10,
  low_comp_filter=True,
)