Displaying the Length of Individual Sequences in File

Question

I have a file that contains two sequences. I have a program that could read all sequences, combine them together, and display the length of both sequences together. Now I want to display the length individually. The two sequences are separated by the symbol >.

Example:

SEQ1 >ATGGGACTAGCAGT

SEQ2  >AGGATGATGAGTGA

Program:

#!usr/bin/python
import re
fh=open('clostp1.fa','r')
count=0
content=fh.readlines()
fh.close()
seq=''
patt=re.compile('>(.*?)')
for item in content:
    m=patt.match(item)
    if not m:
        s=item.replace('\n','')
        seq=seq+s
seq=seq.replace('\s','')       
print seq
print 'The length of the coding sequence of the bacillus' 
print len(seq)

Answer 1

for line in open("clostp1.fa"):
    name, sequence = map(str.strip,line.split('>'))
    print "The length of %s is %s"%(name, len(sequence))

Answer 2

If I understood correctly, you want to print out each individual sequence followed by its length, right? I believe you just have a function to return the sequences and later do what ever yuo want with them.

#!usr/bin/python
import re

def get_content(file):
    """
    Returns a dict with the name of the seq and its value
    """
    result = {}
    for current_line in open(file):
        name, value = line.strip().split(">")
        result[name] = value
    return result

You get the dict and then print what ever you need to print.

Answer 3

for line in open("clostp1.fa"):
    name, _, seq = line.partition('>')
    name, seq = name.rstrip(), seq.rstrip()
    print("The length of {} is {}".format(name, len(seq)))

partition is more appropriate here then split. you need to rstrip each individual part, and formatting syntax will work in py3.1, use

print("The length of {0} is {1}".format(name, len(seq)))

to make it work in py2.6.

Answer 4

import re
pattern = re.compile('(?P<seqname>\w*)\s*>\s*(?P<seqval>\w*)')
for item in open('clostp1.fa','r').readlines():
    m = pattern.match(item)
    if m:
       print "sequence name: %s - %s length" % (m.groupdict()['seqname'],len(m.groupdict()['seqval']))