Python: find the minimum in all rows


 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Python: find the minimum in all rows
# 1  
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!
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Programming

Find the minimum value of the column with respect to other column

Hi All, I would like get the minimum value in the certain column with respect to other column. For example, I have a text file like this. ATOM 1 QSS SPH S 0 -2.790 -1.180 -2.282 2.28 2.28 ATOM 1 QSS SPH S 1 -2.915 -1.024 -2.032 2.31 2.31 ATOM 1 ... (4 Replies)
Discussion started by: bala06
4 Replies

2. Shell Programming and Scripting

awk to find maximum and minimum from column and store in other column

Need your support for below. Please help to get required output If column 5 is INV then only consider column1 and take out duplicates/identical rows/values from column1 and then put minimum value of column6 in column7 and put maximum value in column 8 and then need to do subtract values of... (7 Replies)
Discussion started by: as7951
7 Replies

3. Shell Programming and Scripting

Find minimum and maximum values based on column with associative array

Hello, I need to find out the minimum and maximum values based on specific column, and then print out the entire row with the max value. Infile.txt: scf6 290173 290416 . + X_047241 T_00113118-1 scf6 290491 290957 . + X_047241 T_00113118-2 scf6 290898 290957 . + X_047241 T_00113119-3 scf6... (2 Replies)
Discussion started by: yifangt
2 Replies

4. Shell Programming and Scripting

How to find a minimum value of a row?

input 1 2 3 4 5 2 8 2 1 1 1 4 2 1 5 4 4 4 2 1 3 2 2 6 7 4 5 4 5 5 5 4 3 3 5 I woud like to print a min of each row such that my output would look like 1 1 1 2 3 (5 Replies)
Discussion started by: johnkim0806
5 Replies

5. Shell Programming and Scripting

In a row, replace negative sign and find minimum value among four columns

Hi Friends, I have an input file like this chr1 100 200 1 2 3 4 chr1 150 200 4 5 6 7 chr2 300 400 9 6 7 1 chr2 300 410 -10 21 -11 13 chr3 700 900 -21 -22 130 165 Now, my output file is chr1 100 200 1 chr1 150 200 4 chr2 300 400 1 chr2 300 410 10 chr3 700 900 21 Remove... (5 Replies)
Discussion started by: jacobs.smith
5 Replies

6. Shell Programming and Scripting

Find minimum value different from zero

Hello, I have this file file1.csv Element1;23-10-2012;1,450;1,564;1,428 Element2;23-10-2012;1,448;1,565;1,427 Element3;23-10-2012;1,453;1,570;1,424 Element4;23-10-2012;1,428;1,542;1,405 Element5;23-10-2012;1,461;;1,453 Element6;23-10-2012;1,438;1,555;1,417... (6 Replies)
Discussion started by: saba01
6 Replies

7. Shell Programming and Scripting

Finding minimum value out of specific rows

Hi all, I am having multiple files with the pattern given below: I need to find the minimum value of 5th column if column 1 is x and 2nd column is awh or vbn or ... (20 different strings). the output must be like: Kindly help me to figure out this prob.... Thanks in... (4 Replies)
Discussion started by: CAch
4 Replies

8. Shell Programming and Scripting

Find the minimum value

Hi there I have generated a column containing 100.000 values. Sample: 94.971 101.468 73.120 100.601 102.329 I need to find the minimum value in this file and I must know which row it is in (no sorting). I hope you can help! Thanks! (16 Replies)
Discussion started by: cno
16 Replies

9. Shell Programming and Scripting

Find the minimum number

Input 10 8 20 8 10 9 20 9 10 12 20 19 10 10 20 40 Output1 10 8 2 20 8 12 10 9 1 20 9 11 10 12 -2 20 19 1 10 10 0 20 40 -20 Output2 10 9 ... (0 Replies)
Discussion started by: repinementer
0 Replies

10. Shell Programming and Scripting

Merge two rows using awk or python

Hi, Suppose I have a space delimited file like this: Serial# 1970 1971 1972 1973 1974 193532 21 2 X X X 200201 20 30 X X 40 200201 X X 13 15 X 393666 66 3 X X 5 ... (2 Replies)
Discussion started by: grossgermany
2 Replies
Login or Register to Ask a Question
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)