Regular expression to parse sequence IDs

Question

I'm having a bit of trouble with using regular expressions to extract information from flat files (just text). The files are structured as such:

#

ID (eg >YAL001C)

Annotations/metadata (short phrases describing origin of ID)

Sequence (very long string of characters, eg KRHDE .... ~500 letters on average)

#

I am trying to extract only IDs and sequences (skip all the metadata). Unfortunately, list operations alone don't suffice, eg

with open("composition.in","rb") as all_info:
    all_info=all_info.read() 
    all_info=all_info.split(">")[1:]

because the metadata/annotation part of the text is littered with '>' characters that cause the list that is generated to be incorrectly structured. List comprehensions get very ugly after a certain point, so I am trying the following:

with open("composition.in","rb") as yeast_all:
yeast_all=yeast_all.read() # convert file to string

## Regular expression to clean up rogue ">" characters
## i.e. "<i>", "<sub>", etc which screw up
## the structure of the eveuntual list
import re
id_delimeter = r'^>{1}+\w{7,10}+\s' 
match=re.search(id_delimeter, yeast_all)
if match:
    print 'found', match.group()
else:
    print 'did not find'        
yeast_all=yeast_all.split(id_delimeter)[1:]

I get only an error message saying "error: multiple repeat"

The IDs are of type:

YAL001C

YGR103W

YKL068W-A

The first character is always ">", followed by capital letters and numbers and sometimes dashes (-). I would like a RE that could be used to find all such occurrences and split the text using the RE as a delimeter in order to get IDs and sequences and leave out metadata. I am new to regular expressions so have limited knowledge of the topic!

Note: Only a single newline between each of the three fields (ID, metadata, sequence)

Answer 1

Try

>(?P<id>[\w-]+)\s.*\n(?P<sequence>[\w\n]+)

You'll find the ID in the group id and the sequence in the group sequence .

Demo.

Explanation:

> # start with a ">" character
(?P<id> # capture the ID in group "id"
    [\w-]+ # this matches any number (>1) of word characters (A to Z, a to z, digits, and _) or dashes "-"
)
\s+ # after the ID, there must be at least one whitespace character
.* # consume the metadata part, we have no interest in this
\n # up to a newline
(?P<sequence> # finally, capture the sequence data in group "sequence"
    [\w\n]+ # this matches any number (>1) of word characters and newlines.
)

As python code:

text= '''>YKL068W-A
foo
ABCD

>XYZ1234
<><><><>><<<>
LMNOP'''

pattern= '>(?P<id>[\w-]+)\n.*\n(?P<sequence>\w+)'

for id, sequence in re.findall(pattern, text):
    print((id, sequence))