I have a text file that I am reading in python . I'm trying to extract certain elements from the text file that follow keywords to append them into empty lists . The file looks like this:
so I want to make two empty lists
. 1st list will append the sequence names
. 2nd list will be a list of lists which will include be in the format [Bacteria,Phylum,Class,Order, Family, Genus, Species]
most of the organisms will be Uncultured bacterium . I am trying to add the Uncultured bacterium with the following IDs that are separated by ;
Is there anyway to scan for a certain word and when the word is found, take the word that is after it [separated by a '\t'] ?
I need it to create a dictionary of the Sequence Name to be translated to the taxonomic data .
I know i will need an empty list to append the names to:
seq_names=[ ]
a second list to put the taxonomy lists into
taxonomy=[ ]
and a 3rd list that will be reset after every iteration
temp = [ ]
I'm sure it can be done in Biopython but i'm working on my python skills
4 answers
In general, this is a typical problem that could be approached by iterating over each line while splitting each line into tokens.
Try something like
seq_names = []
taxonomy = []
for line in file('/path/to/file'):
if line.startswith('query name'): continue #omit the header
tokens = line.split('\t') #tokens is a list containing words separated by '\t'
#Store specific tokens in your arrays, e.g.
seq_names.append( tokens[0] )
taxonomy.append( tokens[9] )
You can also use the csv module.
Example CSV file:
seq id strand taxon
seq1 1 + Bacteria
seq2 2 - Bacteria
seq3 3 + Archaea
seq4 4 + Archaea
Extract all the 'bacteria' rows:
>>> import csv
>>> import re
>>> reader = csv.reader(open("sample_csv.txt", "r"), delimiter='\t')
>>> [row[0] for row in reader if re.match('bacteria', row[3], re.IGNORECASE)]
['seq1', 'seq2']
You can do all of this with python's parsing functions. So here is a basic template to parse a tab delimited file:
inFile = open('yourFile','r')
headers = inFile.next() #skip your header line
for line in inFile:
data = line.strip().split('\t') #data is now an array of your columns
if data[0] == "query": #if the first column is equal to something
seq_names.append(data[0]) #add first column into seq_names array
But you should really study up on the python language itself. There are probably better data structures to store the information you want.
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Hi, I am sure you will get an answer here, but you will benefit more by learning python a bit longer. A good place is (http://www.diveintopython.net/). This problem is a good practice for your python skills!