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terdon ♦
terdon ♦
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What ImI'm trying to do now is im replacingreplace the gene_ID with transcript_ID and the gene_name with transcript_name but imI'm doing something wrong as imI'm not getting the transcript ID rathertranscript_ID but the gene ensemblEnsembl ID ,notinstead. I'm not sure if imI'm choosing the right column for parsing the transcript_ID and name.....

So imI'm expecting to get this

What Im trying now is im replacing the gene_ID with transcript_ID and gene_name with transcript_name but im doing something wrong as im not getting the transcript ID rather gene ensembl ID ,not sure if im choosing the right column for parsing the transcript_ID and name.....

So im expecting to get this

What I'm trying to do now is replace the gene_ID with transcript_ID and the gene_name with transcript_name but I'm doing something wrong as I'm not getting the transcript_ID but the gene Ensembl ID instead. I'm not sure if I'm choosing the right column for parsing the transcript_ID and name.

So I'm expecting to get this

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terdon ♦
terdon ♦
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awk '{                                
    for (i = 1; i <= NF; i++) {
        if ($i ~ /gene_id|gene_name/) {
            printf "%s ", $(i+1)
        }
    }
    print ""
}' Homo_sapiens.GRCh37.70.gtf | sed -e 's/"//g' -e 's/;//g' -e 's/ /\t/' | sort -k1,1 | uniq > Homo_sapiens.GRCh37.70.txt

 

And the input file:

##description: evidence-based annotation of the human genome (GRCh38), version 21 (Ensembl 77)
##provider: GENCODE
##contact: [email protected]
##format: gtf
##date: 2014-09-29
chr1    HAVANA  gene    11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1    HAVANA  transcript  11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    11869   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    12613   12721   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    13221   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  transcript  12010   13670   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12010   12057   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12179   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12613   12697   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 3; exon_id "ENSE00001758273.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12975   13052   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 4; exon_id "ENSE00001799933.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";

awk '{                                
    for (i = 1; i <= NF; i++) {
        if ($i ~ /gene_id|gene_name/) {
            printf "%s ", $(i+1)
        }
    }
    print ""
}' Homo_sapiens.GRCh37.70.gtf | sed -e 's/"//g' -e 's/;//g' -e 's/ /\t/' | sort -k1,1 | uniq > Homo_sapiens.GRCh37.70.txt

 
    ##description: evidence-based annotation of the human genome (GRCh38), version 21 (Ensembl 77)
##provider: GENCODE
##contact: [email protected]
##format: gtf
##date: 2014-09-29
chr1    HAVANA  gene    11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1    HAVANA  transcript  11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    11869   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    12613   12721   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    13221   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  transcript  12010   13670   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12010   12057   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12179   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12613   12697   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 3; exon_id "ENSE00001758273.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12975   13052   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 4; exon_id "ENSE00001799933.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";

awk '{                                
    for (i = 1; i <= NF; i++) {
        if ($i ~ /gene_id|gene_name/) {
            printf "%s ", $(i+1)
        }
    }
    print ""
}' Homo_sapiens.GRCh37.70.gtf | sed -e 's/"//g' -e 's/;//g' -e 's/ /\t/' | sort -k1,1 | uniq > Homo_sapiens.GRCh37.70.txt

And the input file:

##description: evidence-based annotation of the human genome (GRCh38), version 21 (Ensembl 77)
##provider: GENCODE
##contact: [email protected]
##format: gtf
##date: 2014-09-29
chr1    HAVANA  gene    11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1    HAVANA  transcript  11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    11869   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    12613   12721   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    13221   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  transcript  12010   13670   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12010   12057   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12179   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12613   12697   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 3; exon_id "ENSE00001758273.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12975   13052   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 4; exon_id "ENSE00001799933.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
edited the question with input
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kcm
kcm
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awk '{                                
    for (i = 1; i <= NF; i++) {
        if ($i ~ /gene_id|gene_name/) {
            printf "%s ", $(i+1)
        }
    }
    print ""
}' Homo_sapiens.GRCh37.70.gtf | sed -e 's/"//g' -e 's/;//g' -e 's/ /\t/' | sort -k1,1 | uniq > Homo_sapiens.GRCh37.70.txt 


    ##description: evidence-based annotation of the human genome (GRCh38), version 21 (Ensembl 77)
##provider: GENCODE
##contact: [email protected]
##format: gtf
##date: 2014-09-29
chr1    HAVANA  gene    11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1    HAVANA  transcript  11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    11869   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    12613   12721   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    13221   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  transcript  12010   13670   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12010   12057   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12179   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12613   12697   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 3; exon_id "ENSE00001758273.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12975   13052   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 4; exon_id "ENSE00001799933.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";

What Im trying now is im replacing the gene_ID with transcript_ID and gene_name with transcript_name but im doing something wrong as im not getting the transcript ID rather gene ensembl ID ,not sure if im choosing the right column for parsing the transcript_ID and name.....

So im expecting to get this

transcript_id "ENST00000450305.2";  gene_name "DDX11L1";transcript_name "DDX11L1-001"

awk '{                                
    for (i = 1; i <= NF; i++) {
        if ($i ~ /gene_id|gene_name/) {
            printf "%s ", $(i+1)
        }
    }
    print ""
}' Homo_sapiens.GRCh37.70.gtf | sed -e 's/"//g' -e 's/;//g' -e 's/ /\t/' | sort -k1,1 | uniq > Homo_sapiens.GRCh37.70.txt

What Im trying now is im replacing the gene_ID with transcript_ID and gene_name with transcript_name but im doing something wrong as im not getting the transcript ID rather gene ensembl ID ,not sure if im choosing the right column for parsing the transcript_ID and name.....

awk '{                                
    for (i = 1; i <= NF; i++) {
        if ($i ~ /gene_id|gene_name/) {
            printf "%s ", $(i+1)
        }
    }
    print ""
}' Homo_sapiens.GRCh37.70.gtf | sed -e 's/"//g' -e 's/;//g' -e 's/ /\t/' | sort -k1,1 | uniq > Homo_sapiens.GRCh37.70.txt 


    ##description: evidence-based annotation of the human genome (GRCh38), version 21 (Ensembl 77)
##provider: GENCODE
##contact: [email protected]
##format: gtf
##date: 2014-09-29
chr1    HAVANA  gene    11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1    HAVANA  transcript  11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    11869   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    12613   12721   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    13221   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  transcript  12010   13670   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12010   12057   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12179   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12613   12697   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 3; exon_id "ENSE00001758273.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12975   13052   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 4; exon_id "ENSE00001799933.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";

What Im trying now is im replacing the gene_ID with transcript_ID and gene_name with transcript_name but im doing something wrong as im not getting the transcript ID rather gene ensembl ID ,not sure if im choosing the right column for parsing the transcript_ID and name.....

So im expecting to get this

transcript_id "ENST00000450305.2";  gene_name "DDX11L1";transcript_name "DDX11L1-001"
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