Back to index

python-biopython  1.60
Variables
clustal_run Namespace Reference

Variables

tuple cline = ClustalwCommandline(infile='opuntia.fasta', outfile='test.aln')
tuple return_code = subprocess.call(str(cline), shell=(sys.platform!="win32"))
tuple alignment
tuple summary_align = AlignInfo.SummaryInfo(alignment)
tuple consensus = summary_align.dumb_consensus()
tuple my_pssm
dictionary expect_freq
tuple freq_table_info
tuple info_content

Variable Documentation

Initial value:
00001 AlignIO.read("test.aln", "clustal",
00002                          alphabet=Gapped(IUPAC.unambiguous_dna))

Definition at line 28 of file clustal_run.py.

tuple clustal_run.cline = ClustalwCommandline(infile='opuntia.fasta', outfile='test.aln')

Definition at line 21 of file clustal_run.py.

tuple clustal_run.consensus = summary_align.dumb_consensus()

Definition at line 44 of file clustal_run.py.

Initial value:
00001 {
00002     'A' : .3,
00003     'G' : .2,
00004     'T' : .3,
00005     'C' : .2}

Definition at line 52 of file clustal_run.py.

Initial value:
00001 FreqTable.FreqTable(expect_freq, FreqTable.FREQ,
00002                                       IUPAC.unambiguous_dna)

Definition at line 58 of file clustal_run.py.

Initial value:
00001 summary_align.information_content(5, 30,
00002                                                  chars_to_ignore = ['N'],
00003                                                  e_freq_table = \
00004                                                  freq_table_info)

Definition at line 61 of file clustal_run.py.

Initial value:
00001 summary_align.pos_specific_score_matrix(consensus,
00002                                                   chars_to_ignore = ['N'])

Definition at line 47 of file clustal_run.py.

tuple clustal_run.return_code = subprocess.call(str(cline), shell=(sys.platform!="win32"))

Definition at line 24 of file clustal_run.py.

tuple clustal_run.summary_align = AlignInfo.SummaryInfo(alignment)

Definition at line 42 of file clustal_run.py.