parse file and amend strings in python

Question

I have got a gene bank file .gbk from which I want to extract certain genes. My problem is the following: In order to process the file, the header for each locus must be in a specific format, and it is not in my file. I want to parse the file and replace the headers as following:

LOCUS       NODE_1_length_393688_cov_17.8554393688 bp   DNA linear
BCT22-MAY-2017
DEFINITION  Escherichia coli strain strain.
ACCESSION   
VERSION
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
            Escherichia.
....
>>Gene data here
....

LOCUS       NODE_2_length_278889_cov_17.85545278889 bp   DNA linear
BCT22-MAY-2017
DEFINITION  Escherichia coli strain strain.
ACCESSION   
VERSION
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
            Escherichia.
....
>>Gene data here
....

LOCUS       NODE_3_length_340008_cov_17.855432340008 bp   DNA linear
BCT22-MAY-2017
DEFINITION  Escherichia coli strain strain.
ACCESSION   
VERSION
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
            Escherichia.
....
>>Gene data here
....

The string commencing with NODE is too long for the file format convention and needs to be replaced so it looks like that:

LOCUS       NODE_1_393688 bp   DNA linear
....
LOCUS       NODE_2_278889 bp   DNA linear
....
LOCUS       NODE_3_340008 bp   DNA linear

The part that needs to be cut out is not necessary of the same lenght, so a fixed approach removing everything between certain positions of the string is not feasible. I have tried different approaches using re.compile() and r.sub() but have not been successful so far.

Any help would be highly appreciated. Thank you for your time!

Laurent LAPORTE · Accepted Answer · 2017-09-30 13:12:45Z

1

When you read the first line, you can read the fields and normalize the "node" field, as follow:

import operator

def normalize_name(name):
    parts = name.split("_")
    return "_".join(operator.itemgetter(0, 1, 3)(parts))

It splits the field name into parts; you get a list. Then, the operator.itemgetter(0, 1, 3) function, applied on parts will extract the items at index 0, 1 and 3, skipping the 2.

For instance:

for name in [
    "NODE_1_length_393688_cov_17.8554393688",
    "NODE_2_length_278889_cov_17.85545278889",
    "NODE_3_length_340008_cov_17.855432340008"
    ]:
    print(normalize_name(name))

You get:

NODE_1_393688
NODE_2_278889
NODE_3_340008

Demo

import operator
import textwrap


get_parts = operator.itemgetter(0, 1, 3)


def normalize_name(name):
    parts = name.split("_")
    return "_".join(get_parts(parts))


def normalize_header(header):
    fields = header.split()
    fields[1] = normalize_name(fields[1])
    return "{0:<11} {1} {2:<4} {3} {4}".format(*fields)


content = textwrap.dedent("""\
LOCUS       NODE_1_length_393688_cov_17.8554393688 bp   DNA linear
BCT22-MAY-2017
DEFINITION  Escherichia coli strain strain.
ACCESSION   
VERSION
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
            Escherichia.
....
>>Gene data here
....
""")

for line in content.splitlines():
    if line.startswith("LOCUS"):
        line = normalize_header(line)
    print(line)

edited Sep 30, 2017 at 13:12

answered Sep 30, 2017 at 12:54

Laurent LAPORTE

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1 Comment

kruemelprinz Over a year ago

OK thanks, that sounds good, I just need to implement this into a loop that parses multiple files in different subdirectories and amends all instances of a line beginning with 'LOCUS' in each file. In order to do that, I need instead of filling in the text into the content = textwrap.dedent function read in the whole file itself. Can textwrap.dedent do that?

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