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python-biopython  1.60
Variables
www_blast Namespace Reference

Variables

tuple file_for_blast = open('m_cold.fasta', 'r')
tuple f_iterator = Fasta.Iterator(file_for_blast)
tuple f_record = f_iterator.next()
tuple result_handle = NCBIWWW.qblast('blastn', 'nr', f_record)
tuple save_file = open('m_cold_blast.out', 'w')
tuple blast_results = result_handle.read()
tuple b_parser = NCBIWWW.BlastParser()
tuple string_result_handle = cStringIO.StringIO(blast_results)
tuple b_record = b_parser.parse(string_result_handle)
float E_VALUE_THRESH = 0.1

Variable Documentation

tuple www_blast.b_parser = NCBIWWW.BlastParser()

Definition at line 30 of file www_blast.py.

tuple www_blast.b_record = b_parser.parse(string_result_handle)

Definition at line 37 of file www_blast.py.

tuple www_blast.blast_results = result_handle.read()

Definition at line 25 of file www_blast.py.

Definition at line 40 of file www_blast.py.

tuple www_blast.f_iterator = Fasta.Iterator(file_for_blast)

Definition at line 16 of file www_blast.py.

tuple www_blast.f_record = f_iterator.next()

Definition at line 18 of file www_blast.py.

tuple www_blast.file_for_blast = open('m_cold.fasta', 'r')

Definition at line 15 of file www_blast.py.

tuple www_blast.result_handle = NCBIWWW.qblast('blastn', 'nr', f_record)

Definition at line 21 of file www_blast.py.

tuple www_blast.save_file = open('m_cold_blast.out', 'w')

Definition at line 24 of file www_blast.py.

tuple www_blast.string_result_handle = cStringIO.StringIO(blast_results)

Definition at line 36 of file www_blast.py.