3 b: @sJdddZdddZdddZdddZdd d Zdd d ZdddZdS)I@cCst|||\}}|S)a8 Abstract: Returns the NG50 value of the passed list of numbers. Comments: Works for any percentage (e.g. NG60, NG70) with optional argument Usage: NG50(numlist, reference_length) Based on the definition from this SEQanswers post http://seqanswers.com/forums/showpost.php?p=7496&postcount=4 (modified Broad Institute's definition https://www.broad.harvard.edu/crd/wiki/index.php/N50) See SEQanswers threads for details: http://seqanswers.com/forums/showthread.php?t=2857 http://seqanswers.com/forums/showthread.php?t=2332 ) NG50_and_LG50)numlistreference_length percentageng50lg50r8/home/psgendb/BIRCHDEV/pkg/quast-5.2.0/quast_libs/N50.pyNG50sr cCst|||\}}|S)z Abstract: Returns the LG50 value of the passed list of numbers. Comments: Works for any percentage (e.g. LG60, LG70) with optional argument Usage: LG50(numlist, reference_length) )r)rrrrrrrr LG50sr cCst|t||S)z Abstract: Returns the N50 value of the passed list of numbers. Comments: Works for any percentage (e.g. N60, N70) with optional argument Usage: N50(numlist) )r sum)rrrrr N50%sr cCst|t||S)z Abstract: Returns the L50 value of the passed list of numbers. Comments: Works for any percentage (e.g. L60, L70) with optional argument Usage: L50(numlist) )r r )rrrrr L50.srFc Csv|dks t|dkst|r(|jdd|}|d|d}d}x0|D](}||8}|d7}||krF|}||fSqFWdS)NggY@T)reverse)NN)AssertionErrorsort) rrrZ need_sortslimitrlrrrr r7s     rcCst|t||S)N)rr )rrrrr N50_and_L50IsrNc Csyrt|dkstdtdd|Ds0td|r>t|}n tt|}|dksZtdttdd|D|Stk rd SXd S) z numlist - length of contigs metric explanation http://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity rzEmpty list as inputcSsg|]}t|tttfqSr) isinstanceintfloatcomplex).0irrr Tszau_metric..zNon-numerical inputgzall contigs are 0cSsg|] }|dqS)r)rnrrr rZsN)lenrallrr )rrZdenumrrr au_metricMs  r#)r)r)r)r)rF)r)N)r r r rrrr#rrrr s