I have looked through all of the tagged Fasta posts, none seem to address this particular issue.
I have the following format for my headers:
>GeneDB|LinJ.35.4080 | organism=Leishmania_infantum | product=ATP-dependent RNA helicase, putative | location=LinJ.35:1596105-1598177(+) | length=690
I would like to learn how to retrieve the "LinJ.35.4080" (let's call this proteinID) as well as the "product=ATP-dependent RNA helicase, putative" (call this proteindescription) fields for all the records in my file and create a two column text file (proteinID, proteindescription).
If known, it would be helpful to remove the "product=" from the field as well.
I have searched through all of the online tutorials (that I could find) related to FASTA, Biopython, Python, etc., and thought (foolishly) my first attempt at this would go a bit smoother.
Thank you in advance for your help and time, this is something that will be used often. I'm hoping I didn't overlook someone else's solution to this.
Import regular expression in Python here:
$ python
>>> import re
>>> s = ">GeneDB|LinJ.35.4080 | organism=Leishmania_infantum | product=ATP-dependent RNA helicase, putative | location=LinJ.35:1596105-1598177(+) | length=690"
>>> m = re.search(r'(?m)\>GeneDB\|([^|]*)\s\|.*product=([^|]*)\s\|', s)
>>> if m:
... pro_id = m.group(1)
... pro_de = m.group(2)
...
>>> pro_id, pro_de
('LinJ.35.4080', 'ATP-dependent RNA helicase, putative')
No need for Python or any complicated programming. Assuming that all your FASTA headers are of the same form with fields separated by "|" in file myfile.fa, just use grep + awk + sed:
grep "^>" myfile.fa | awk 'BEGIN {FS="|"} {print $2, $4}' | sed 's/product=//'
Result:
LinJ.35.4080 ATP-dependent RNA helicase, putative
Agree, but if you really want to use python, you can use .split -> http://docs.python.org/library/string.html#string.split
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