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python-biopython  1.60
Variables
test_NCBI_qblast Namespace Reference

Variables

list tests
tuple handle
tuple record = NCBIXML.read(handle)
 found_result = False

Variable Documentation

Definition at line 100 of file test_NCBI_qblast.py.

Initial value:
00001 NCBIWWW.qblast(program, database, query, \
00002                                     alignments=10, descriptions=10, \
00003                                     hitlist_size=10, \
00004                                     entrez_query=entrez_filter,
00005                                     expect=e_value, megablast="FALSE")

Definition at line 63 of file test_NCBI_qblast.py.

tuple test_NCBI_qblast.record = NCBIXML.read(handle)

Definition at line 77 of file test_NCBI_qblast.py.

Initial value:
00001 [ \
00002     #Simple protein blast filtered for rat only, using protein GI:160837788
00003     #the actin related protein 2/3 complex, subunit 1B [Mus musculus]
00004     ("blastp", "nr", "160837788", 0.001,
00005      "rat [ORGN]", ['9506405','13592137','37589612','149064087','56912225']),
00006     #This next example finds PCR primer matches in Chimpanzees, e.g. BRCA1:
00007     ("blastn", "nr", "GTACCTTGATTTCGTATTC"+("N"*30)+"GACTCTACTACCTTTACCC",
00008      10, "pan [ORGN]", ["37953274","51104367","51104367","51104367"]),
00009     #Try an orchid EST (nucleotide) sequence against NR using BLASTX
00010     ("blastx", "nr", """>gi|116660609|gb|EG558220.1|EG558220 CR02019H04 Leaf CR02 cDNA library Catharanthus roseus cDNA clone CR02019H04 5', mRNA sequenceCTCCATTCCCTCTCTATTTTCAGTCTAATCAAATTAGAGCTTAAAAGAATGAGATTTTTAACAAATAAAAAAACATAGGGGAGATTTCATAAAAGTTATATTAGTGATTTGAAGAATATTTTAGTCTATTTTTTTTTTTTTCTTTTTTTGATGAAGAAAGGGTATATAAAATCAAGAATCTGGGGTGTTTGTGTTGACTTGGGTCGGGTGTGTATAATTCTTGATTTTTTCAGGTAGTTGAAAAGGTAGGGAGAAAAGTGGAGAAGCCTAAGCTGATATTGAAATTCATATGGATGGAAAAGAACATTGGTTTAGGATTGGATCAAAAAATAGGTGGACATGGAACTGTACCACTACGTCCTTACTATTTTTGGCCGAGGAAAGATGCTTGGGAAGAACTTAAAACAGTTTTAGAAAGCAAGCCATGGATTTCTCAGAAGAAAATGATTATACTTCTTAATCAGGCAACTGATATTATCAATTTATGGCAGCAGAGTGGTGGCTCCTTGTCCCAGCAGCAGTAATTACTTTTTTTTCTCTTTTTGTTTCCAAATTAAGAAACATTAGTATCATATGGCTATTTGCTCAATTGCAGATTTCTTTCTTTTGTGAATG""",
00011      0.0000001, None, ["21554275","18409071","296087288"]),
00012 ]

Definition at line 35 of file test_NCBI_qblast.py.