Python: find the minimum in all rows

Python: find the minimum in all rows
# 1
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.

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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```CD-HIT-2D(1)							   User Commands						      CD-HIT-2D(1)

NAME
cdhit-2d - quickly group sequences in db1 or db2 format

SYNOPSIS
cdhit-2d [Options]

DESCRIPTION
====== CD-HIT version 4.6 (built on Apr 26 2012) ======

Options

-i     input filename for db1 in fasta format, required

-i2    input filename for db2 in fasta format, required

-o     output filename, required

-c     sequence	identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical
amino acids in alignment divided by the full length of the shorter sequence

-G     use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated as :  number  of  identical  amino
acids  in  alignment  divided  by  the length of the alignment NOTE!!! don't use -G 0 unless you use alignment coverage controls see
options -aL, -AL, -aS, -AS

-b     band_width of alignment, default 20

-M     memory limit (in MB) for the program, default 800; 0 for unlimitted;

-T     number of threads, default 1; with 0, all CPUs will be used

-n     word_length, default 5, see user's guide for choosing it

-l     length of throw_away_sequences, default 10

-t     tolerance for redundance, default 2

-d     length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space

-s     length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the	representative	of
the cluster

-S     length  difference  cutoff  in  amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the
representative of the cluster can not be bigger than 60

-s2    length difference cutoff for db1, default 1.0 by default, seqs in db1 >= seqs in db2 in a same cluster if set to 0.9,  seqs  in  db1
may just >= 90% seqs in db2

-S2    length  difference  cutoff,  default  0  by default, seqs in db1 >= seqs in db2 in a same cluster if set to 60, seqs in db2 may 60aa
longer than seqs in db1

-aL    alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence

-AL    alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length of the sequence is 400,  then  the
alignment must be >= 340 (400-60) residues

-aS    alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence

-AS    alignment  coverage control for the shorter sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the
alignment must be >= 340 (400-60) residues

-A     minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences

-uL    maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing
gaps) must not be more than 10% of the sequence

-uS    maximum  unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tail-
ing gaps) must not be more than 10% of the sequence

-U     maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be  more
than 10 bases

-B     1  or  0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive it is recommended to use
-B 1 for huge databases

-p     1 or 0, default 0 if set to 1, print alignment overlap in .clstr file

-g     1 or 0, default 0 by cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the  threshold  (fast  clus-
ter).  If  set  to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode) but
either 1 or 0 won't change the representatives of final clusters

-bak write backup cluster file (1 or 0, default 0)

-h     print this help

Questions, bugs, contact Weizhong Li at liwz@sdsc.edu

If you find cd-hit useful, please kindly cite:

"Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong  Li,  Lukasz  Jaroszewski  &  Adam
Godzik.  Bioinformatics,	(2001) 17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide
sequences", Weizhong Li & Adam Godzik. Bioinformatics, (2006) 22:1658-1659

cd-hit-2d 4.6-2012-04-25					    April 2012							      CD-HIT-2D(1)```