def test_blastParser(self):
query = self.cwd + "/BLAST/queries_db1.fas"
blast_table = self.cwd + "/BLAST/queries_db1_blastn_out.csv"
sbj = self.cwd + "/BLAST/silkcds.fa"
out = self.cwd + "/BLAST/output.txt"
BLAST.blastn(query, sbj)
BLAST.blastParser(blast_table, sbj, out)
seqs = [i.id for i in SeqIO.parse(out, "fasta")]
self.assertEqual(2, len(seqs))
os.remove(out)
# with header row
query = self.cwd + "/BLAST/queries_db1.fas"
blast_table = self.cwd + "/BLAST/queries_db2_blastn_out.csv"
sbj = self.cwd + "/BLAST/silkcds.fa"
out = self.cwd + "/BLAST/output.txt"
BLAST.blastn(query, sbj)
BLAST.blastParser(blast_table, sbj, out)
seqs = [i.id for i in SeqIO.parse(out, "fasta")]
self.assertEqual(2, len(seqs))
os.remove(out)
#!/usr/bin/env python
from pyphylogenomics import BLAST
BLAST.blastn("grefs/Bombyx_exons.fas", "grefs/Dp_genome_v2.fasta")
BLAST.blastParser("grefs/Bombyx_exons_blastn_out.csv",
"grefs/Dp_genome_v2.fasta",
"grefs/Danaus_exons.fasta",
sp_name = "Danaus")
#!/usr/bin/env python from pyphylogenomics import BLAST import sys blast_output = sys.argv[1].strip() model_genome = sys.argv[2].strip() output_file = sys.argv[3].strip() species_name = sys.argv[4].strip() BLAST.blastParser(blast_output, model_genome, output_file, species_name)
