Python: find the minimum in all rows


 
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Old 05-16-2013
Python: find the minimum in all rows

I am using Biopython to process an alignment in fasta format. I need to slice the sequences where there is the first stop codon. So I divided my alignment in codons and found the stop.
I then found the first codon position using enumerate().
But I found the minimum for each row. However I need to find the minimum (storing it where it won't be reset when it does the next row), determine which of those is smallest. So that I can slice all the sequences in the same place.

Code:
from Bio import AlignIO
stop = ["TAA"]
alignment = AlignIO.read('/Users/....', 'fasta')
for row in alignment:
	codons=[]
	codons = [str(row.seq[i:i+3]) for i in range(0,len(row.seq),3)]
	pstop = min([x for x,y in enumerate(codons) if y in stop])
	print pstop

pstop gives me the min for each row and I want to get the min of those min
to slice everything according to that min.
Thanks you very much for your help!
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ddi_dma_devalign(9F)					   Kernel Functions for Drivers 				      ddi_dma_devalign(9F)

NAME
ddi_dma_devalign - find DMA mapping alignment and minimum transfer size SYNOPSIS
#include <sys/conf.h> #include <sys/ddi.h> #include <sys/sunddi.h> int ddi_dma_devalign(ddi_dma_handle_t handle, uint_t *alignment, uint_t *minxfr); INTERFACE LEVEL
Solaris DDI specific (Solaris DDI). PARAMETERS
handle The DMA handle filled in by a successful call to ddi_dma_setup(9F). alignment A pointer to an unsigned integer to be filled in with the minimum required alignment for DMA. The alignment is guaranteed to be a power of two. minxfr A pointer to an unsigned integer to be filled in with the minimum effective transfer size (see ddi_iomin(9F), ddi_dma_lim_sparc(9S) and ddi_dma_lim_x86(9S)). This also is guaranteed to be a power of two. DESCRIPTION
ddi_dma_devalign() determines after a successful DMA mapping (see ddi_dma_setup(9F)) the minimum required data alignment and minimum DMA transfer size. RETURN VALUES
ddi_dma_devalign() returns: DDI_SUCCESS The alignment and minxfr values have been filled. DDI_FAILURE The handle was illegal. CONTEXT
ddi_dma_devalign() can be called from user or interrupt context. SEE ALSO
ddi_dma_setup(9F), ddi_iomin(9F), ddi_dma_lim_sparc(9S), ddi_dma_lim_x86(9S), ddi_dma_req(9S) Writing Device Drivers SunOS 5.10 1 Feb 1994 ddi_dma_devalign(9F)

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