Entering edit mode
5.6 years ago
madzayasodara
•
0
I have a gtf file like:
scaffold_0 maker exon 9496 9623 . + . transcript_id "RHOH"; transcript_id_full "RHOH"
scaffold_0 StringTie exon 11728 11971 . + . transcript_id "RHOH"; transcript_id_full "RHOH"
scaffold_0 maker exon 12077 12144 . + . transcript_id "RHOH"; transcript_id_full "RHOH"
scaffold_0 StringTie exon 20708 23579 . + . transcript_id "RHOH"; transcript_id_full "RHOH"
scaffold_0 maker exon 39534 40131 . - . transcript_id "gene17"; transcript_id_full "gene17"
scaffold_0 maker exon 43071 43701 . + . transcript_id "gene1"; transcript_id_full "gene1"
scaffold_0 maker exon 57526 57640 . + . transcript_id "CHRNA9"; transcript_id_full "CHRNA9"
scaffold_0 maker exon 58475 58630 . + . transcript_id "CHRNA9"; transcript_id_full "CHRNA9"
scaffold_0 maker exon 59298 59831 . + . transcript_id "CHRNA9"; transcript_id_full "CHRNA9"
scaffold_0 maker exon 60967 61512 . + . transcript_id "CHRNA9"; transcript_id_full "CHRNA9"
and a .fa scaffold file:
>scaffold_0
agcagggctggagcaggagcagggctggagctggagcaaggctggagcag
gagcagggctggggctggagcagggctggagcaggagcaggagcagggct
ggagcagggctggagctagagcaggggctggagcagggctggggctggag
cagggctggagctggagcagggctggagctagagcaggggctggagcagg
agcagggctggagcaggagcagggctggagctagagcacgggctggagca
gggctggggctggagcagggctggagcaggagcaggggctggggctggag
caggggctggagcagggactggagcagggctggagcagggctggagcagg
gctggagcagggccggggctggagcGGGGTGCCGGCTCCCTCGTGGCTGG
CAGGCGGTGTGTGCTCGGCGAGcCCCCGGAGCCGGAGCCCCGGGGCGGGG
and would like to output the sequences for individual transcripts:
something maybe like (or similar to in some way):
>scaffold_0 maker exon 9496 9623 . + . transcript_id "RHOH"; transcript_id_full "RHOH"
GGTGCCGGCTCCCTCGTGGCTGGCAGGCGGTGTGTGCTCGGCGAGcCCCCGGAGCCGGAGCCCCGGG ...
>scaffold_0 StringTie exon 11728 11971 . + . transcript_id "RHOH"; transcript_id_full "RHOH"
GAGAGAGAAAACGGCAAAAGTCAGAGTTTAGAGAAACAGATGTGGGTTTGCACGTTCTGCACGTTCTCCCTTTG ...
and so on.
Do I have to code it up or there is a tool that would allow me to do this? If I do have to code for it. Would you have insights on how to do it in a easy way?
Take a look at
gffread
utility here.Indeed, a working example here: A: Cufflinks gffread utility