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[ .. KEMBALI ]
📄 0README.html
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📄 AcManForm.dfm
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📄 LAparser.py
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📄 Setup.ini
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📄 SimpleCalc.py
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📄 SingleForm.dfm
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📄 TAP.py
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📄 __init__.py
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📁 __pycache__/
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📄 adventureEngine.py
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📄 antlr_grammar.py
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📄 antlr_grammar_tests.py
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📄 apicheck.py
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📄 bigquery_view_parser.py
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📄 booleansearchparser.py
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📄 btpyparse.py
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📄 builtin_parse_action_demo.py
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📄 cLibHeader.py
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📄 chemicalFormulas.py
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📄 commasep.py
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📄 configParse.py
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📄 cpp_enum_parser.py
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📄 cuneiform_python.py
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📄 datetimeParseActions.py
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📄 decaf_parser.py
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📄 delta_time.py
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📄 dfmparse.py
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📄 dhcpd_leases_parser.py
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📄 dictExample.py
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📄 dictExample2.py
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📄 ebnf.py
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📄 ebnftest.py
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📄 eval_arith.py
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📄 excelExpr.py
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📄 fourFn.py
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📄 gen_ctypes.py
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📄 getNTPserversNew.py
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📄 greeting.py
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📄 greetingInGreek.py
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📄 greetingInKorean.py
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📄 groupUsingListAllMatches.py
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📄 holaMundo.py
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📄 htmlStripper.py
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📄 htmlTableParser.py
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📄 httpServerLogParser.py
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📄 idlParse.py
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📄 include_preprocessor.py
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📄 indentedGrammarExample.py
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📄 indented_block_example.py
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📄 invRegex.py
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📄 javascript_grammar.g
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📄 jsonParser.py
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📄 left_recursion.py
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📄 linenoExample.py
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📄 listAllMatches.py
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📄 lua_parser.py
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📄 lucene_grammar.py
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📄 macroExpander.py
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📄 make_diagram.py
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📄 matchPreviousDemo.py
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📄 mozilla.ics
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📄 mozillaCalendarParser.py
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📄 nested.py
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📄 nested_markup.py
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📄 number_words.py
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📄 numerics.py
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📄 oc.py
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📄 one_to_ninety_nine.py
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📄 parsePythonValue.py
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📄 parseResultsSumExample.py
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📄 parseTabularData.py
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📄 partial_gene_match.py
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📄 pgn.py
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📄 position.py
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📄 protobuf_parser.py
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📄 pymicko.py
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📄 pythonGrammarParser.py
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📄 railroad_diagram_demo.py
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📄 rangeCheck.py
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📄 readJson.py
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📄 removeLineBreaks.py
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📄 romanNumerals.py
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📄 rosettacode.py
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📄 scanExamples.py
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📄 searchParserAppDemo.py
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📄 searchparser.py
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📄 select_parser.py
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📄 sexpParser.py
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📄 shapes.py
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📄 simpleArith.py
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📄 simpleBool.py
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📄 simpleSQL.py
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📄 simpleWiki.py
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📄 snmp_api.h
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📄 sparser.py
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📄 sql2dot.py
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📄 stackish.py
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📁 statemachine/
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📄 test_bibparse.py
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📄 unicode_denormalizer.py
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📄 urlExtractor.py
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📄 urlExtractorNew.py
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📁 verilog/
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📄 verilogParse.py
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📄 withAttribute.py
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📄 wordsToNum.py
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SAVING...
BERHASIL DIUBAH!
EDITING: partial_gene_match.py
# partial_gene_match.py # # Example showing how to use the CloseMatch class, to find strings in a gene with up to 'n' mismatches # import pyparsing as pp from urllib.request import urlopen # read in a bunch of genomic data data_url = "http://toxodb.org/common/downloads/release-6.0/Tgondii/TgondiiApicoplastORFsNAs_ToxoDB-6.0.fasta" with urlopen(data_url) as datafile: fastasrc = datafile.read().decode() # define parser to extract gene definitions """ Sample header: >NC_001799-6-2978-2778 | organism=Toxoplasma_gondii_RH | location=NC_001799:2778-2978(-) | length=201 """ integer = pp.pyparsing_common.integer genebit = pp.Group( ">" + pp.Word(pp.alphanums.upper() + "-_")("gene_id") + "|" + pp.Word(pp.printables)("organism") + "|" + pp.Word(pp.printables)("location") + "|" + "length=" + integer("gene_len") + pp.LineEnd() + pp.Word("ACGTN")[1, ...].addParseAction("".join)("gene") ) # read gene data from .fasta file - takes just a few seconds # An important aspect of this parsing process is the reassembly of all the separate lines of the # gene into a single scannable string. Just searching the raw .fasta file could overlook matches # if the match is broken up across separate lines. The parse action in the genebit parser does # this reassembly work. genedata = genebit[1, ...].parseString(fastasrc) # using the genedata extracted above, look for close matches of a gene sequence searchseq = pp.CloseMatch("TTAAATCTAGAAGAT", 3) for g in genedata: show_header = True # scan for close matches, list out found strings, and mark mismatch locations for t, startLoc, endLoc in searchseq.scanString(g.gene, overlap=True): if show_header: # only need to show the header once print("%s/%s/%s (%d)" % (g.gene_id, g.organism, g.location, g.gene_len)) print("-" * 24) show_header = False matched = t[0] mismatches = t["mismatches"] print("MATCH:", searchseq.match_string) print("FOUND:", matched) if mismatches: print( " ", "".join( "*" if i in mismatches else " " for i, c in enumerate(searchseq.match_string) ), ) else: print("<exact match>") print("at location", startLoc) print()
SIMPAN PERUBAHAN