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src/c/o/cogent-1.5.3/cogent/app/muscle_v38.py   cogent(Download)
                 params=params)
    #Get results using int_map as input to app
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(MinimalFastaParser(res['MuscleOut'].readlines()))
 
    # Collect result
    result = app(int_map.toFasta())
 
    # Build tree
    seqs_filename = get_tmp_filename()
    seqs_out = open(seqs_filename,'w')
    seqs_out.write(seqs_int_map.toFasta())
    seqs_out.close()
 
    #save aln to tmp file
    aln_filename = get_tmp_filename()
    aln_out = open(aln_filename, 'w')
    aln_out.write(aln_int_map.toFasta())
    aln1_filename = get_tmp_filename()
    aln1_out = open(aln1_filename,'w')
    aln1_out.write(aln1_int_map.toFasta())
    aln1_out.close()
 

src/c/o/cogent-1.5.3/cogent/app/muscle.py   cogent(Download)
                 params=params)
    #Get results using int_map as input to app
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(MinimalFastaParser(res['MuscleOut'].readlines()))
 
    # Collect result
    result = app(int_map.toFasta())
 
    # Build tree
    seqs_filename = get_tmp_filename()
    seqs_out = open(seqs_filename,'w')
    seqs_out.write(seqs_int_map.toFasta())
    seqs_out.close()
 
    #save aln to tmp file
    aln_filename = get_tmp_filename()
    aln_out = open(aln_filename, 'w')
    aln_out.write(aln_int_map.toFasta())
    aln1_filename = get_tmp_filename()
    aln1_out = open(aln1_filename,'w')
    aln1_out.write(aln1_int_map.toFasta())
    aln1_out.close()
 

src/p/y/pycogent-HEAD/cogent/app/muscle_v38.py   pycogent(Download)
                 params=params)
    #Get results using int_map as input to app
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(MinimalFastaParser(res['MuscleOut'].readlines()))
 
    # Collect result
    result = app(int_map.toFasta())
 
    # Build tree
    seqs_filename = get_tmp_filename()
    seqs_out = open(seqs_filename,'w')
    seqs_out.write(seqs_int_map.toFasta())
    seqs_out.close()
 
    #save aln to tmp file
    aln_filename = get_tmp_filename()
    aln_out = open(aln_filename, 'w')
    aln_out.write(aln_int_map.toFasta())
    aln1_filename = get_tmp_filename()
    aln1_out = open(aln1_filename,'w')
    aln1_out.write(aln1_int_map.toFasta())
    aln1_out.close()
 

src/p/y/pycogent-HEAD/cogent/app/muscle.py   pycogent(Download)
                 params=params)
    #Get results using int_map as input to app
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(MinimalFastaParser(res['MuscleOut'].readlines()))
 
    # Collect result
    result = app(int_map.toFasta())
 
    # Build tree
    seqs_filename = get_tmp_filename()
    seqs_out = open(seqs_filename,'w')
    seqs_out.write(seqs_int_map.toFasta())
    seqs_out.close()
 
    #save aln to tmp file
    aln_filename = get_tmp_filename()
    aln_out = open(aln_filename, 'w')
    aln_out.write(aln_int_map.toFasta())
    aln1_filename = get_tmp_filename()
    aln1_out = open(aln1_filename,'w')
    aln1_out.write(aln1_int_map.toFasta())
    aln1_out.close()
 

src/c/o/cogent-1.5.3/cogent/app/clustalw.py   cogent(Download)
 
    # Collect result
    result = app(int_map.toFasta())
 
    # Build tree
 
    # Collect result
    result = app(int_map.toFasta())
 
    # Build tree
    app = Clustalw(InputHandler='_input_as_multiline_string',params=params)
    #Get results using int_map as input to app
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(ClustalParser(res['Align'].readlines()))
    #Add seq_int_map as profile2
    app.Parameters['-profile2'].on(\
        app._tempfile_as_multiline_string(seq_int_map.toFasta()))
    #Get results using int_map as input to app
    res = app()

src/p/y/pycogent-HEAD/cogent/app/clustalw.py   pycogent(Download)
 
    # Collect result
    result = app(int_map.toFasta())
 
    # Build tree
 
    # Collect result
    result = app(int_map.toFasta())
 
    # Build tree
    app = Clustalw(InputHandler='_input_as_multiline_string',params=params)
    #Get results using int_map as input to app
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(ClustalParser(res['Align'].readlines()))
    #Add seq_int_map as profile2
    app.Parameters['-profile2'].on(\
        app._tempfile_as_multiline_string(seq_int_map.toFasta()))
    #Get results using int_map as input to app
    res = app()

src/c/o/cogent-1.5.3/cogent/app/mafft.py   cogent(Download)
 
    #Get results using int_map as input to app
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(MinimalFastaParser(res['StdOut'].readlines()))
 
    #Get results using int_map as input to app
    res = app(seq_int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(MinimalFastaParser(res['StdOut'].readlines()))

src/p/y/pycogent-HEAD/cogent/app/mafft.py   pycogent(Download)
 
    #Get results using int_map as input to app
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(MinimalFastaParser(res['StdOut'].readlines()))
 
    #Get results using int_map as input to app
    res = app(seq_int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(MinimalFastaParser(res['StdOut'].readlines()))

src/c/o/cogent-1.5.3/cogent/app/cd_hit.py   cogent(Download)
 
    # grab result
    res = app(int_map.toFasta())
    clusters = parse_cdhit_clstr_file(res['CLSTR'].readlines())
 
 
    # grab result
    res = app(seqs.toFasta())
    new_seqs = dict(MinimalFastaParser(res['FASTA'].readlines()))
 

src/p/y/pycogent-HEAD/cogent/app/cd_hit.py   pycogent(Download)
 
    # grab result
    res = app(int_map.toFasta())
    clusters = parse_cdhit_clstr_file(res['CLSTR'].readlines())
 
 
    # grab result
    res = app(seqs.toFasta())
    new_seqs = dict(MinimalFastaParser(res['FASTA'].readlines()))
 

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