perl2python: Reading files

Table of Contents

File

Read files

HERE documents

File

Read files

•             perl

#!/usr/bin/perl -w
use strict;
open FILE, "data/test.fa" or die "$!";
while(my $line = <FILE> ){
    print "$line";
}

## >gene1
## ATGGCTAGCATCGTACGTCG
## >gene2
## ATGGCTAGCTACGTACGTAG

•             python

infile = open("data/test.fa", 'r')
for line in infile.readlines():
  line = line.rstrip('\n')
  print line

## >gene1
## ATGGCTAGCATCGTACGTCG
## >gene2
## ATGGCTAGCTACGTACGTAG

Here readline() reads one line character at a time, readlines() reads in the whole file at once and splits it by line.

The xreadlines() function should be used for big files:

infile = open("data/test.fa", 'r')
for line in infile.xreadlines():
  line = line.rstrip('\n')
  print line

## >gene1
## ATGGCTAGCATCGTACGTCG
## >gene2
## ATGGCTAGCTACGTACGTAG

HERE documents

•             Perl code

$len_gene1 = 100;
$len_gene2 = 200;
print <<OUT;
gene1\t$len_gene1
gene2\t$len_gene2
OUT

## gene1    100
## gene2    200

•             Python code

len_gene1 = 100
len_gene2 = 200
print '''
gene1\t%s
gene2\t%s
'''[1:-1] % (len_gene1, len_gene2)

## gene1    100
## gene2    200

Or so long as there's no indentation on the first line or trailing space on the last:

print '''
dog
cat
'''.strip()

## dog
## cat