Hi all,
I have a gff file like:
gn|nvit|C3905550 assmcg CDS 68 646 . - . asmbl_401
gn|nvit|C3905550 assmcg exon 68 646 . - . asmbl_401
gn|nvit|C3918365 assmcg CDS 42 252 . + . asmbl_443
gn|nvit|C3918365 assmcg CDS 522 705 . + . asmbl_443
gn|nvit|C3918365 assmcg exon 522 705 . + . asmbl_443
gn|nvit|C3930535 assmcg exon 64 888 . - . asmbl_465
gn|nvit|C3930535 assmcg three_prime_utr 64 393 . - . asmbl_465
gn|nvit|C3930535 assmcg CDS 394 699 . - . asmbl_465
gn|nvit|C3930535 assmcg five_prime_utr 700 888 . - . asmbl_465
gn|nvit|C3935122 assmcg exon 4 567 . + . asmbl_476
gn|nvit|C3938828 assmcg CDS 293 745 . + . asmbl_481
gn|nvit|C3938828 assmcg exon 293 745 . + . asmbl_481
gn|nvit|C3942486 assmcg CDS 244 942 . - . asmbl_489
gn|nvit|C3942486 assmcg exon 244 942 . - . asmbl_489
gn|nvit|C3950921 assmcg exon 40 80 . + . asmbl_506
gn|nvit|C3950921 assmcg three_prime_utr 40 80 . + . asmbl_506
gn|nvit|C3950921 assmcg exon 172 253 . + . asmbl_506
gn|nvit|C3950921 assmcg five_prime_utr 172 190 . + . asmbl_506
I want to create a list writing all the 'transcript id that have both the three_prime_utr and five_prime_utr corndinates' like
asmbl_465
asmbl_506
I used cat final1.gff | perl -ne 's/.*\t(\S+_prime_utr)\t.*transcript_id \"(\S+)\".*/$2\t$1/; print;' | sort -u | perl -ne 'split; print "$_[0]\n" if ($g eq $_[0]); $g = $_[0];' > myutr_list.txt
but it did not worked for me.
Thanks!
I have a gff file like:
gn|nvit|C3905550 assmcg CDS 68 646 . - . asmbl_401
gn|nvit|C3905550 assmcg exon 68 646 . - . asmbl_401
gn|nvit|C3918365 assmcg CDS 42 252 . + . asmbl_443
gn|nvit|C3918365 assmcg CDS 522 705 . + . asmbl_443
gn|nvit|C3918365 assmcg exon 522 705 . + . asmbl_443
gn|nvit|C3930535 assmcg exon 64 888 . - . asmbl_465
gn|nvit|C3930535 assmcg three_prime_utr 64 393 . - . asmbl_465
gn|nvit|C3930535 assmcg CDS 394 699 . - . asmbl_465
gn|nvit|C3930535 assmcg five_prime_utr 700 888 . - . asmbl_465
gn|nvit|C3935122 assmcg exon 4 567 . + . asmbl_476
gn|nvit|C3938828 assmcg CDS 293 745 . + . asmbl_481
gn|nvit|C3938828 assmcg exon 293 745 . + . asmbl_481
gn|nvit|C3942486 assmcg CDS 244 942 . - . asmbl_489
gn|nvit|C3942486 assmcg exon 244 942 . - . asmbl_489
gn|nvit|C3950921 assmcg exon 40 80 . + . asmbl_506
gn|nvit|C3950921 assmcg three_prime_utr 40 80 . + . asmbl_506
gn|nvit|C3950921 assmcg exon 172 253 . + . asmbl_506
gn|nvit|C3950921 assmcg five_prime_utr 172 190 . + . asmbl_506
I want to create a list writing all the 'transcript id that have both the three_prime_utr and five_prime_utr corndinates' like
asmbl_465
asmbl_506
I used cat final1.gff | perl -ne 's/.*\t(\S+_prime_utr)\t.*transcript_id \"(\S+)\".*/$2\t$1/; print;' | sort -u | perl -ne 'split; print "$_[0]\n" if ($g eq $_[0]); $g = $_[0];' > myutr_list.txt
but it did not worked for me.
Thanks!
Comment