extract transcrips_id and gene_id from output cuffcampare

Question

[yaghoub.amraei]

آHi all. I have a cuffcompare output and I want to extract the transcript_id andgene_id in column 9, which is a string, using grep or AWK. Thank you for your guidance

1   Cufflinks   exon    2899    3255    .   +   .   gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1";

1 Cufflinks exon 3354 3616 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 4357 4455 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "3"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 5457 5560 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "4"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 7136 7944 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "5"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 8028 8150 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "6"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 8408 8608 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "7"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 9210 9615 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "8"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 10102 10187 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "9"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 10274 10430 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "10"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 10504 10817 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "11"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1";

[yaghoub.amraei]

1 Cufflinks exon 2899 3255 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 3354 3616 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 4357 4455 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "3"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 5457 5560 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "4"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 7136 7944 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "5"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 8028 8150 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "6"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 8408 8608 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "7"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 9210 9615 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "8"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 10102 10187 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "9"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 10274 10430 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "10"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 10504 10817 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "11"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1";enter code here

[rpolicastro]

It's hard to tell the format of your file, but if it's in GTF format you can use this perl one liner.

perl -pe 's/.+gene_id\s\"(\w+)\".+transcript_id\s\"(\w+)\".+/$1\t$2/' file.txt

[yaghoub.amraei]

hello. amazing, as usual.