How to delete everything after a certain point in GFF3 file - PYTHON

Question

[caseyd7]

I have a GFF3 file and at the bottom of the file there is a FASTA report of the genome.

I want to delete everything below the line that says '##FASTA' - including that line so that all i have left is the regular GFF report with out the FASTA.

I need to do this for multiple files. Please help.

Answer 1

[James Ashmore]

Lets try with an example file (using line numbers instead of actual GFF content):

$ cat test.gff
1
2
3
4
5
6
7
8
9
##FASTA
11
12
13
14
15

Find the line number which the pattern first '##FASTA' appears (for example say line 10):

egrep -n -m 1 '##FASTA' test.gff

Find the total number of lines in your file (for example say line 15):

wc -l test.gff | awk '{print $1}'

Delete the lines starting at the line number where your pattern first appears and ending at the end of the file:

sed '15,30d' test.gff > result.gff

Package this up into a small shell script and run on each file.

[colindaven]

True, but it would be even easier to just use head instead of wc -l and sed.

egrep -n -m 1 '##FASTA' test.gff

head -n 15 test.gff > result.gff