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Scan Through Txt, Append Certain Data To An Empty List In Python

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:

enter image description here

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

python programming
• 21,292 views • link
updated by Biostar Biostar • written by hicsuntdrac0nis • hicsuntdrac0nis

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!

• 0 views • link
written by Haibao Tang Haibao Tang

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] )
• 2 views • link
updated by Ram Ram • written by Chris • Chris

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']
• 2 views • link
updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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.

• 2 views • link
updated by Ram Ram • written by Damian Kao Damian Kao

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