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python-biopython  1.60
Variables
test_Clustalw_tool Namespace Reference

Variables

 clustalw_exe = None
list prog_files = os.environ["PROGRAMFILES"]
list likely_dirs
list likely_exes
tuple output = commands.getoutput("clustalw2 --version")
string input_file = "does_not_exist.fasta"
tuple cline = ClustalwCommandline(clustalw_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"))
 tree_file = newtree_file

Variable Documentation

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

Definition at line 196 of file test_Clustalw_tool.py.

tuple test_Clustalw_tool.cline = ClustalwCommandline(clustalw_exe, infile=input_file)

Definition at line 85 of file test_Clustalw_tool.py.

Definition at line 22 of file test_Clustalw_tool.py.

Definition at line 142 of file test_Clustalw_tool.py.

string test_Clustalw_tool.input_file = "does_not_exist.fasta"

Definition at line 83 of file test_Clustalw_tool.py.

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

Definition at line 169 of file test_Clustalw_tool.py.

Initial value:
00001 ["ClustalW2", "",
00002                    "Clustal","Clustalw","Clustalw183","Clustalw1.83",
00003                    r"CTCBioApps\clustalw\v1.83"]

Definition at line 44 of file test_Clustalw_tool.py.

Initial value:
00001 ["clustalw2.exe",
00002                    "clustalw.exe", "clustalw1.83.exe"]

Definition at line 47 of file test_Clustalw_tool.py.

tuple test_Clustalw_tool.output = commands.getoutput("clustalw2 --version")

Definition at line 61 of file test_Clustalw_tool.py.

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

Definition at line 200 of file test_Clustalw_tool.py.

string test_Clustalw_tool.prog_files = os.environ["PROGRAMFILES"]

Definition at line 27 of file test_Clustalw_tool.py.

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

Definition at line 153 of file test_Clustalw_tool.py.

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

Definition at line 141 of file test_Clustalw_tool.py.

string test_Clustalw_tool.temp_large_fasta_file = "temp_cw_prot.fasta"

Definition at line 151 of file test_Clustalw_tool.py.

tuple test_Clustalw_tool.tree_file = newtree_file

Definition at line 213 of file test_Clustalw_tool.py.