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python-biopython  1.60
Variables
test_ClustalOmega_tool Namespace Reference

Variables

 clustalo_exe = None
tuple output = commands.getoutput("clustalo --help")
string input_file = "does_not_exist.fasta"
tuple cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file)
string temp_filename_with_spaces = "Clustalw/temp horses.fasta"
tuple handle = open(temp_filename_with_spaces, "w")
string temp_large_fasta_file = "temp_cw_prot.fasta"
tuple records = list(SeqIO.parse("NBRF/Cw_prot.pir", "pir"))
tuple input_records
tuple align = AlignIO.read(output_file, "clustal")
tuple output_records = SeqIO.to_dict(SeqIO.parse(output_file,"clustal"))

Variable Documentation

tuple test_ClustalOmega_tool.align = AlignIO.read(output_file, "clustal")

Definition at line 147 of file test_ClustalOmega_tool.py.

tuple test_ClustalOmega_tool.cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file)

Definition at line 42 of file test_ClustalOmega_tool.py.

Definition at line 20 of file test_ClustalOmega_tool.py.

Definition at line 92 of file test_ClustalOmega_tool.py.

string test_ClustalOmega_tool.input_file = "does_not_exist.fasta"

Definition at line 40 of file test_ClustalOmega_tool.py.

Initial value:
00001 SeqIO.to_dict(SeqIO.parse(input_file,"fasta"),
00002                                   lambda rec : rec.id.replace(":","_"))

Definition at line 118 of file test_ClustalOmega_tool.py.

tuple test_ClustalOmega_tool.output = commands.getoutput("clustalo --help")

Definition at line 26 of file test_ClustalOmega_tool.py.

tuple test_ClustalOmega_tool.output_records = SeqIO.to_dict(SeqIO.parse(output_file,"clustal"))

Definition at line 151 of file test_ClustalOmega_tool.py.

tuple test_ClustalOmega_tool.records = list(SeqIO.parse("NBRF/Cw_prot.pir", "pir"))

Definition at line 103 of file test_ClustalOmega_tool.py.

string test_ClustalOmega_tool.temp_filename_with_spaces = "Clustalw/temp horses.fasta"

Definition at line 91 of file test_ClustalOmega_tool.py.

string test_ClustalOmega_tool.temp_large_fasta_file = "temp_cw_prot.fasta"

Definition at line 101 of file test_ClustalOmega_tool.py.