o Rŀg!@sNdZddlmZddlmZGdddeZedkr%ddlmZedSdS) zGCommand line wrapper for the short read aligner Novoalign by Novocraft.)_Option)AbstractCommandlinec@seZdZdZdddZdS)NovoalignCommandlinea.Command line wrapper for novoalign by Novocraft. See www.novocraft.com - novoalign is a short read alignment program. Examples -------- >>> from Bio.Sequencing.Applications import NovoalignCommandline >>> novoalign_cline = NovoalignCommandline(database='some_db', ... readfile='some_seq.txt') >>> print(novoalign_cline) novoalign -d some_db -f some_seq.txt As with all the Biopython application wrappers, you can also add or change options after creating the object: >>> novoalign_cline.format = 'PRBnSEQ' >>> novoalign_cline.r_method='0.99' # limited valid values >>> novoalign_cline.fragment = '250 20' # must be given as a string >>> novoalign_cline.miRNA = 100 >>> print(novoalign_cline) novoalign -d some_db -f some_seq.txt -F PRBnSEQ -r 0.99 -i 250 20 -m 100 You would typically run the command line with novoalign_cline() or via the Python subprocess module, as described in the Biopython tutorial. Last checked against version: 2.05.04 novoalignc sgdgdgdtddgdddd td d gd ddd td dgddfddddtddgdddddtddgdddddtddgdddddtd d!gd"d#dddtd$d%gd&d'dddtd(d)gd*d+dddtd,d-gd.d/dddtd0d1gd2d3dddtd4d5gd6d7dddtd8d9gd:d;dddtddfd?dddtd@dAgdBdCdddtdDdEgdFdGdddtdHdIgdJdfdKdddtdLdMgdNdOdddtdPdQgdRdSdddtdTdUgdVdWdddtdXdYgdZd[dddtd\d]gd^d_dddtd`dagdbdcdddtdddegdfdgdddtdhdigdjdkdddg|_tj||fi|dlS)mzInitialize the class.)FASLXFQSTDFQILMFQPRBPRBnSEQ)NativePairwiseSAM)NoneRandomAll Exhaustivez0.99z-ddatabasezdatabase filenameTF)filenameequatez-freadfilez read filez-Fformatz'Format of read files. Allowed values: z, c|vSNx) READ_FORMATrZ/var/www/html/myenv/lib/python3.10/site-packages/Bio/Sequencing/Applications/_Novoalign.py:z/NovoalignCommandline.__init__..)checker_functionrz-t thresholdzThreshold for alignment scorecS t|tSr isinstanceintrrrrrA z-ggap_openz!Gap opening penalty [default: 40]cSr#rr$rrrrrGr'z-x gap_extendz Gap extend penalty [default: 15]cSr#rr$rrrrrMr'z-u unconvertedzRExperimental: unconverted cytosines penalty in bisulfite mode Default: no penaltycSr#rr$rrrrrTr'z-l good_basesz?Minimum number of good quality bases [default: log(N_g, 4) + 5]cSr#rr$rrrrr[r'z-h homopolymerz>Homopolymer read filter [default: 20; disable: negative value]cSr#rr$rrrrrar'z-aadapter3z`Strips a 3' adapter sequence prior to alignment. With paired ends two adapters can be specifiedcSr#rr%strrrrrrir'z-ntruncatez,Truncate to specific length before alignmentcSr#rr$rrrrror'z-strimmingzWIf fail to align, trim by s bases until they map or become shorter than l. Ddefault: 2cSr#rr$rrrrrvr'z-5adapter5zKStrips a 5' adapter sequence. Similar to -a (adaptor3), but on the 5' end.cSr#rr.rrrrr}r'z-oreportz@Specifies the report format. Allowed values: %s Default: Nativecrrrr) REPORT_FORMATrrrr z-Qqualityzs  I