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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BP_PAIRWISE_KAKS(1p)					User Contributed Perl Documentation				      BP_PAIRWISE_KAKS(1p)

NAME
pairwise_kaks - script to calculate pairwise Ka,Ks for a set of sequences SYNOPSIS
pairwise_kaks.PLS -i t/data/worm_fam_2785.cdna [-f fasta/genbank/embl...] [-msa tcoffee/clustal] [-kaks yn00/codeml] DESCRIPTION
This script will take as input a dataset of cDNA sequences verify that they contain no stop codons, align them in protein space, project the alignment back into cDNA and estimate the Ka (non-synonymous) and Ks (synonymous) substitutions based on the ML method of Yang with the PAML package. Requires: * bioperl-run package * PAML program codeml or yn00 * Multiple sequence alignment programs Clustalw OR T-Coffee Often there are specific specific parameters you want to run when you a computing Ka/Ks ratios so consider this script a starting point and do not rely it on for every situation. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR
Jason Stajich jason-at-bioperl-dot-org perl v5.14.2 2012-03-02 BP_PAIRWISE_KAKS(1p)