Parsing a file with Python

Question

I'm trying to parse an alignment output file using python, but I am having some problems with that.

The file has three main "blocks" of information, and I want to get the third block values, which have this structure:

 I J ILEN JLEN MATCH NGAPS NALIG NIDENT %IDENT NAS NASAL NRANS RMEAN STDEV SCORE
1 2 177 104 433.00 7 104 20 19.23 416.35 335.58 0 0.00 0.00 0.00 1
1 3 177 107 427.00 6 107 21 19.63 399.07 331.78 0 0.00 0.00 0.00 2
1 4 177 126 480.00 4 126 15 11.90 380.95 342.86 0 0.00 0.00 0.00 3

So I have written this:

infile=open('ig_pairs.out')
init=infile.readline()
while init[:6] !=' 1542':
 line=infile.readline()
colnames=['I', 'J', 'ILEN', 'JLEN', 'MATCH', 'NGAPS', 'NALIG', 'NIDENT', '%IDEN$
file=open('ig_file.txt', 'w')
for c in colnames:
 file.write(c + '\t')
for line in infile.readline():
 I=line[5:7]
 J=line[9:11]
 ILEN=line[14:16]
 JLEN=line[19:21]
 MATCH=line[26:31]
 NGAPS=line[37:38]
 NALIG=line[43:45]
 NIDENT=line[50:52]
 IDEN=line[58:62]
 NAS=line[68:72]
 NASAL=line[77:82]
 NRANS=line[87:89]
 RMEAN=line[93:99]
 STDEV=line[105:109]
 SCORE=line[114:119]
 NUMBER=line[120:126]
 file.write('\n' + I + '\t' + J + '\t' + ILEN + '\t' + JLEN + '\t' + MATCH + '\t' + NGAPS + '\t' + NALIG + '\t' + NIDENT + '\t' + IDEN + '\t' + NAS + '\t' + NASAL + '\t' + NRANS + '\t' + RMEAN + '\t' + STDEV + '\t' + SCORE + '\t' + NUMBER)
file.close()

But for some reason it is not working. I don't get back any error message, the terminal just get blocked and nothing happens.

Any idea of what's wrong?

• alvas: can you post a sample of your file?

Answer 1

It appears that this is creating an infinite loop:

while init[:6] !=' 1542':
 line=infile.readline()

You need to reset the init variable, else this could always evaluate to true.

Change line = infile.readline() to init = infile.readline().

Answer 2

I guess the problem is with:

for line in infile.readline()

You're reading just one line, not all lines, thus line will be a character not a single line, because python will think you're iterating on characters.

And thus line[5:7] won't amount to anything.

Use

for line in infile.readlines()

• user3368952: I can't believe I forget a "s". Thanks, of course that solved the problem, thank you!
• poke: You should just do for line in infile btw. (without readlines). The default behavior is to iterate over the lines of a file.