read_genbank

A module to read and parse the features of a genbank file

To output a tab separated file:

$ read_genbank.py tests/phiX174.gbk
'phiX174'	'CDS'	(('100', '627'),)	{'gene': 'G'}
'phiX174'	'CDS'	(('636', '1622'),)	{'gene': 'H'}
'phiX174'	'CDS'	(('1659', '3227'),)	{'gene': 'A'}
'phiX174'	'CDS'	(('2780', '3142'),)	{'gene': 'B'}
'phiX174'	'CDS'	(('3142', '3312'),)	{'gene': 'K'}
'phiX174'	'CDS'	(('3224', '3484'),)	{'gene': 'C'}
'phiX174'	'CDS'	(('3481', '3939'),)	{'gene': 'D'}
'phiX174'	'CDS'	(('3659', '3934'),)	{'gene': 'E'}
'phiX174'	'CDS'	(('3939', '4055'),)	{'gene': 'J'}
'phiX174'	'CDS'	(('4092', '5375'),)	{'gene': 'F'}

To output the amino-acid translations in fasta format

$ read_genbank.py tests/phiX174.gbk -f faa
>phiX174[100..627]
MLQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK
>phiX174[636..1622]
MFGAIAGGIASALAGGAMSKLFGGGQKAASGGIQGDVLATDNNTVGMGDAGIKSAIQGSNVPNPDEAAPSFVSGAMAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNAWERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQNEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASGVVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK
>phiX174[1659..3227]
MPPNLGGFFMVRSYYPSECHADYFDFERIEALKPAIEACGISTLSQSPMLGFHKQMDNRIKLLEEILSFRMQGVEFDNGDMYVDGHKAASDVRDEFVSVTEKLMDELAQCYNVLPQLDINNTIDHRPEGDEKWFLENEKTVTQFCRKLAAERPLKDIRDEYNYPKKKGIKDECSRLLEASTMKSRRGFAIQRLMNAMRQAHADGWFIVFDTLTLADDRLEAFYDNPNALRDYFRDIGRMVLAAEGRKANDSHADCYQYFCVPEYGTANGRLHFHAVHFMRTLPTGSVDPNFGRRVRNRRQLNSLQNTWPYGYSMPIAVRYTQDAFSRSGWLWPVDAKGEPLKATSYMAVGFYVAKYVNKKSDMDLAAKGLGAKEWNNSLKTKLSLLPKKLFRIRMSRNFGMKMLTMTNLSTECLIQLTKLGYDATPFNQILKQNAKREMRLRLGKVTVADVLAAQPVTTNLLKFMRASIKMIGVSNLQSFIASMTQKLTLSDISDESKNYLDKAGITTACLRIKSKWTAGGK
>phiX174[2780..3142]
MEQLTKNQAVATSQEAVQNQNEPQLRDENAHNDKSVHGVLNPTYQAGLRRDAVQPDIEAERKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQPAEFYRFHDAEVNTFGYF
>phiX174[3142..3312]
MSRKIILIKQELLLLVYELNRSGLLAENEKIRPILAQLEKLLLCDLSPSTNDSVKN
>phiX174[3224..3484]
MRKFDLSLRSSRSSYFATFRHQLTILSKTDALDEEKWLNMLGTFVKDWFRYESHFVHGRDSLVDILKERGLLSESDAVQPLIGKKS
>phiX174[3481..3939]
MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM
>phiX174[3659..3934]
MVRWTLWDTLAFLLLLSLLLPSLLIMFIPSTFKRPVSSWKALNLRKTLLMASSVRLKPLNCSRLPCVYAQETLTFLLTQKKTCVKNYVRKE
>phiX174[3939..4055]
MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF
>phiX174[4092..5375]
MSNIQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEMDAVGALRLSPLRRGLAIDSTVDIFTFYVPHRHVYGEQWIKFMKDGVNATPLPTVNTTGYIDHAAFLGTINPDTNKIPKHLFQGYLNIYNNYFKAPWMPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS