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_MASK_BY_SEARCH(1p)					User Contributed Perl Documentation				     BP_MASK_BY_SEARCH(1p)

NAME
mask_by_search - mask sequence(s) based on its alignment results SYNOPSIS
mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa DESCRIPTION
Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data which you want to mask. By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming you've provided the sequence file for the hit database. If you would like to do the reverse and mask the query sequence specify the -t/--type query flag. This is going to read in the whole sequence file into memory so for large genomes this may fall over. I'm using DB_File to prevent keeping everything in memory, one solution is to split the genome into pieces (BEFORE you run the DB search though, you want to use the exact file you BLASTed with as input to this program). Below the double dash (--) options are of the form --format=fasta or --format fasta or you can just say -f fasta By -f/--format I mean either are acceptable options. The =s or =n or =c specify these arguments expect a 'string' Options: -f/--format=s Search report format (fasta,blast,axt,hmmer,etc) -sf/--sformat=s Sequence format (fasta,genbank,embl,swissprot) --hardmask (booelean) Hard mask the sequence with the maskchar [default is lowercase mask] --maskchar=c Character to mask with [default is N], change to 'X' for protein sequences -e/--evalue=n Evalue cutoff for HSPs and Hits, only mask sequence if alignment has specified evalue or better -o/--out/ --outfile=file Output file to save the masked sequence to. -t/--type=s Alignment seq type you want to mask, the 'hit' or the 'query' sequence. [default is 'hit'] --minlen=n Minimum length of an HSP for it to be used in masking [default 0] -h/--help See this help information AUTHOR - Jason Stajich Jason Stajich, jason-at-bioperl-dot-org. perl v5.14.2 2012-03-02 BP_MASK_BY_SEARCH(1p)