Extraction of information from stringtie output for selected gene ids

Question

[kuntalasb]

I have stringtie abundance estimation output (.gtf and .tab) files for a set of genes and the gtf looks something like this:

MKYO02000001.1  StringTie   transcript  29543   31126   1000    -   .   gene_id "XLOC_000054"; transcript_id "TCONS_00000371"; cov "0.744585"; FPKM "0.133896"; TPM "0.234692";
MKYO02000001.1  StringTie   exon    29543   30439   1000    -   .   gene_id "XLOC_000054"; transcript_id "TCONS_00000371"; exon_number "1"; cov "0.716216";
MKYO02000001.1  StringTie   exon    30816   31126   1000    -   .   gene_id "XLOC_000054"; transcript_id "TCONS_00000371"; exon_number "2"; cov "0.826408";
MKYO02000001.1  StringTie   transcript  29543   30277   1000    -   .   gene_id "XLOC_000054"; transcript_id "TCONS_00001565"; cov "0.037965"; FPKM "0.006827"; TPM "0.011966";
MKYO02000001.1  StringTie   exon    29543   30277   1000    -   .   gene_id "XLOC_000054"; transcript_id "TCONS_00001565"; exon_number "1"; cov "0.037965";
MKYO02000001.1  StringTie   transcript  29547   33508   1000    -   .   gene_id "XLOC_000054"; transcript_id "TCONS_00000108"; cov "1.023863"; FPKM "0.184118"; TPM "0.322719";
MKYO02000001.1  StringTie   exon    29547   30439   1000    -   .   gene_id "XLOC_000054"; transcript_id "TCONS_00000108"; exon_number "1"; cov "1.049466";
MKYO02000001.1  StringTie   exon    30816   31078   1000    -   .   gene_id "XLOC_000054"; transcript_id "TCONS_00000108"; exon_number "2"; cov "1.306955";
MKYO02000001.1  StringTie   exon    31235   31320   1000    -   .   gene_id "XLOC_000054"; transcript_id "TCONS_00000108"; exon_number "3"; cov "1.382869";

How to I extract information for some selected transcript ids from this file? Since it will be impossible to manually extract 10000 transcripts information from a file of 30000 transcripts, any command based solution would be very helpful. However, I have a text file with all the selected transcript ids and it looks like this: TCONS_00000101 TCONS_00000102 TCONS_00000103 . . .

Is there any grep/cut command for extracting information for my required ids through the text file? Any response would be of great help. Thank you.

[marina.v.yurieva]

What if you just

grep -f file_TCON_ids.txt stringtie.gtf

That should give you all the info about your TCONS of interest.

[kuntalasb]

Thank you so much. It worked for me!