我如何获取python中的特定字段

Question

I have two rows like below

Tp1g00130_scaffold_1    blastn    exon    20495    20602    .    +    .    
Tp1g00130_scaffold_1    blastn    exon    20650    20804    .    +    .    

What i want to do is to merge the seq start (column 3 of row 1) and seq end (column 4 of row 2) of two lines if they have the same ID(column 1). For example, the output would look like

Tp1g00130_scaffold_1    blastn    exon    20495    20804    .    +    .    

I made a good start but cannot quite finish.

prev = None

with open("test_parse") as fh_in:
    for line in fh_in:
        line = line.strip()
        line = line.split()
        line_id = line[0]
        print line
        if prev is not None and prev == line_id:
            print "yes"
        prev = line_id

Any help?

Answer 1

You're almost there.

Instead of prev being just the id , make it the whole last line. This lets us check existance and id ( if prev and prev[0] == line[0]: ) and get the seq start and seq end ( print('{} -> {}'.format(prev[3], line[4])) ).

prev = None
with open("test_parse") as fh_in:
    for line in fh_in:
        line = line.strip().split()
        if prev and prev[0] == line[0]:
            print(' '.join(prev).replace(prev[4], line[4]).split())
        prev = line

Answer 2

If your file is small you can use a temporary dict.

records = {}

with open("test_parse") as fh_in:
    for line in fh_in:
        id_, f1, f2, start, end, f4, f5, f6 = line.strip().split()
        if id_ in records:
            records[id_][4] = end
        else:
            records[id_] = [id_, f1, f2, start, end, f4, f5, f6]

for line in records.values():
    print "\t".join(line)

Answer 3

If you have aa header row in your file you can use a DictReader .

For a file with headers for columns x, y, and z you can do:

import DictReader

reader = DictReader(open('sample.csv'))
for line in reader:
    print(line['x'], line['z'])

The csv module it is a part of is very helpful in general.