Docs::Project::PySAT

Module: checkembl

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Functions:: intron : testembl : maketrembl

function intron (dbs='intron')
function testembl (dbs)
function maketrembl (dbs)

Module: classseq

Makes a sequence objects from a string. Prints in a variety of formats Can do a simple translation from dna->protein sequence. See maketrembl module.

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Classes:: SeqFormat : Seq
Functions:: trans : gcgchecksum : stringSplit : between : _printString : printStringGcg : test : test2 : ttest

class SeqFormat ()
Methods: __init__ : format : error : fmt_gcg : fmt_genbank : fmt_fasta : fmt_staden : fmt_raw : fmt_pir : fmt_asn : fmt_nbrf : fmt_embl : fmt_swiss : fmt_ig : fmt_stdpir
class Seq (SeqFormat)
Methods: __init__ : __repr__ : GetFormats : Len : SetFormat : WhichFormat : SeqPrint : SubSeq : Subseq : Get : SetName : SeqInfo : translate

function trans (s, letter=None)
function gcgchecksum (str)
function stringSplit (s, n)
function between (j, a, b)
function _printString (s, numchars, ncols=1, printlineno=None, prefix='')
function printStringGcg (s, numchars=10, ncols=5)
function test ()
function test2 ()
function ttest ()

Module: database

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Classes:: ReadLine : DBParser : database
Functions:: dbInformation : testembl : testswissprot : testpdbfinder : testenzyme : testgenbank

class ReadLine ()
Methods: __init__ : __getitem__
class DBParser ()
Methods: __init__ : Init : Parse : Field : PrintFields : ReParse
class database ()
Methods: __init__ : tell : seek : Info : Init : OpenFile : ActiveFile : NextFile : Close : NextEntry : _NextEntry

function dbInformation (dbName)
function testembl ()
function testswissprot ()
function testpdbfinder ()
function testenzyme ()
function testgenbank ()

Module: embl_parser

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Module: enzyme_parser

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Module: feat

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Classes:: ftobj : findob
Functions:: test

class ftobj ()
Methods: __init__ : ftmake : printft
class findob ()
Methods: __init__ : _search : search : empty : printf : ftgetfor : next : ftget_keyval

function test (filename)

Module: genbank_parser

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Module: generate_dbs

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Functions:: intron : testembl : maketrembl

function intron (dbs='intron')
function testembl (dbs)
function maketrembl (dbs)

Module: jo

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Classes:: expfeat
Functions:: replint : replacc

class expfeat ()
Methods: __init__ : getfeature : join : complement

function replint (match)
function replacc (match)

Module: pdbfinder_parser

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Functions:: CheckConflict : testpdbfinder

function CheckConflict ()
function testpdbfinder ()

Module: prosite_parser

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Functions:: testprosite : testprosite2

function testprosite ()
function testprosite2 ()

Module: readfasta

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Functions:: fasta

function fasta ()

Module: swissprot_parser

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Created by Doc-Tool V0.9 on Thu Oct 19 14:08:07 2000