从txt文件中提取字符串到CSV

Question

I'm trying to extract strings from a .txt file with a few thousand sequences and write a CSV with these strings. I have deleted all of the irrelevant information from the original .txt file and this is the format of the document I have now:

DEFINITION  Homo sapiens haplogroup HV5 mitochondrion, complete genome.
ACCESSION   DQ377992
/haplogroup="HV5"
/pop_variant="Ashkenazi Jew"
/note="ethnicity:Ashkenazi Jew; origin_locality:Belarus:Homel' Volast', Vyetka; origin_coordinates:52.51 N 31.17 E"
DEFINITION  Homo sapiens haplotype U5b1c mitochondrion, complete genome.
ACCESSION   DQ661681
/haplotype="U5b1c"
/note="Native American (Cherokee)"

I am trying to extract the accession numbers, haplotype or haplogroup, ethnicity, location (origin_locality), coordinates (origin_coordinates) and any additional information that might have been put in /note= to a csv. One of the problems I am facing is that not every sequence has all of the information and not all of the strings are in their own quotation marks.

How do I extract the accession numbers, the strings between quotation marks and make sure that I am extracting the right strings to the right sequence? Also how would I deal with the strings that are only separated by semicolons?

edit: The other question does not address missing information or the resulting alignment in a CSV which was my primary concern.

Answer 1

You can create a class with all possible parameters as attributes. Then loop through all lines, with creating a new object whenever required (ie, when line starts with 'Definition') and filling up attribute values of that object. After that you can reference that object and write its atrributes' value in the csv.