Additing gtf file
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I had to get only ENSEMBLE non-chromosomal pseudogenes from given gtf file
add additional attribute field "filtered" with value "manually" for each of the annotated pseudogenes and save as new file. So I had to filter the given file by containing "ENSEMBLY" "pseudogenes" and not containing "Chr" save it in new file and add to the last column additional property(filter-manually). Could you tell me how can I do this using awk or sed preferably?
##description: evidence-based annotation of the human genome (GRCh38), version 29 (Ensembl 94)
##provider: GENCODE
##contact: gencode-help@ebi.ac.uk
##format: gtf
##date: 2018-08-30
chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name
"DDX11L1-202"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; tr
anscript_name "DDX11L1-201"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unp
regex bash awk sed bioinformatics
edited Nov 19 at 14:29
zx8754
28.9k76395
asked Nov 19 at 13:25
Sergei
31
|
show 1 more comment
up vote
0
down vote
favorite
I had to get only ENSEMBLE non-chromosomal pseudogenes from given gtf file
add additional attribute field "filtered" with value "manually" for each of the annotated pseudogenes and save as new file. So I had to filter the given file by containing "ENSEMBLY" "pseudogenes" and not containing "Chr" save it in new file and add to the last column additional property(filter-manually). Could you tell me how can I do this using awk or sed preferably?
##description: evidence-based annotation of the human genome (GRCh38), version 29 (Ensembl 94)
##provider: GENCODE
##contact: gencode-help@ebi.ac.uk
##format: gtf
##date: 2018-08-30
chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name
"DDX11L1-202"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; tr
anscript_name "DDX11L1-201"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unp
regex bash awk sed bioinformatics
edited Nov 19 at 14:29
zx8754
28.9k76395
asked Nov 19 at 13:25
Sergei
31
What have you already tried?
– Didier Trosset
Nov 19 at 13:46
1
What is the expected output?
– zx8754
Nov 19 at 14:30
Which lines in the example do describe aENSEMBLE non-chromosomal pseudogene? and why (what are the related strings) ?
– Jay jargot
Nov 19 at 14:35
This are lines that match patterns:ENSEMBL exon 169224 169502 . - . gene_id "ENSG00000284215.2"; transcript_id "ENST00000639764.2"; gene_type "pseudogene"; gene_name "AC245056.4"; transcript_type "pseudogene"; transcript_name "AC245056.4-201"; exon_number 2; exon_id "ENSE00003804365.1"; level 3; tag "basic"; Filtered: manually;
– Sergei
Nov 19 at 15:05
Actually I have managed to do this but maybe there is better solution using only awk?
– Sergei
Nov 19 at 15:05
|
show 1 more comment
up vote
0
down vote
favorite
up vote
0
down vote
favorite
I had to get only ENSEMBLE non-chromosomal pseudogenes from given gtf file
add additional attribute field "filtered" with value "manually" for each of the annotated pseudogenes and save as new file. So I had to filter the given file by containing "ENSEMBLY" "pseudogenes" and not containing "Chr" save it in new file and add to the last column additional property(filter-manually). Could you tell me how can I do this using awk or sed preferably?
##description: evidence-based annotation of the human genome (GRCh38), version 29 (Ensembl 94)
##provider: GENCODE
##contact: gencode-help@ebi.ac.uk
##format: gtf
##date: 2018-08-30
chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name
"DDX11L1-202"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; tr
anscript_name "DDX11L1-201"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unp
regex bash awk sed bioinformatics
edited Nov 19 at 14:29
zx8754
28.9k76395
asked Nov 19 at 13:25
Sergei
31
I had to get only ENSEMBLE non-chromosomal pseudogenes from given gtf file
add additional attribute field "filtered" with value "manually" for each of the annotated pseudogenes and save as new file. So I had to filter the given file by containing "ENSEMBLY" "pseudogenes" and not containing "Chr" save it in new file and add to the last column additional property(filter-manually). Could you tell me how can I do this using awk or sed preferably?
##description: evidence-based annotation of the human genome (GRCh38), version 29 (Ensembl 94)
##provider: GENCODE
##contact: gencode-help@ebi.ac.uk
##format: gtf
##date: 2018-08-30
chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name
"DDX11L1-202"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; tr
anscript_name "DDX11L1-201"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; 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_name "DDX11L1"; transcript_type "transcribed_unp
regex bash awk sed bioinformatics
regex bash awk sed bioinformatics
edited Nov 19 at 14:29
zx8754
28.9k76395
asked Nov 19 at 13:25
Sergei
31
edited Nov 19 at 14:29
zx8754
28.9k76395
asked Nov 19 at 13:25
Sergei
31
edited Nov 19 at 14:29
zx8754
28.9k76395
edited Nov 19 at 14:29
zx8754
28.9k76395
edited Nov 19 at 14:29
zx8754
28.9k76395
28.9k76395
asked Nov 19 at 13:25
Sergei
31
asked Nov 19 at 13:25
Sergei
31
asked Nov 19 at 13:25
Sergei
31
31
What have you already tried?
– Didier Trosset
Nov 19 at 13:46
1
What is the expected output?
– zx8754
Nov 19 at 14:30
Which lines in the example do describe aENSEMBLE non-chromosomal pseudogene? and why (what are the related strings) ?
– Jay jargot
Nov 19 at 14:35
This are lines that match patterns:ENSEMBL exon 169224 169502 . - . gene_id "ENSG00000284215.2"; transcript_id "ENST00000639764.2"; gene_type "pseudogene"; gene_name "AC245056.4"; transcript_type "pseudogene"; transcript_name "AC245056.4-201"; exon_number 2; exon_id "ENSE00003804365.1"; level 3; tag "basic"; Filtered: manually;
– Sergei
Nov 19 at 15:05
Actually I have managed to do this but maybe there is better solution using only awk?
– Sergei
Nov 19 at 15:05
|
show 1 more comment
What have you already tried?
– Didier Trosset
Nov 19 at 13:46
1
What is the expected output?
– zx8754
Nov 19 at 14:30
Which lines in the example do describe aENSEMBLE non-chromosomal pseudogene? and why (what are the related strings) ?
– Jay jargot
Nov 19 at 14:35
This are lines that match patterns:ENSEMBL exon 169224 169502 . - . gene_id "ENSG00000284215.2"; transcript_id "ENST00000639764.2"; gene_type "pseudogene"; gene_name "AC245056.4"; transcript_type "pseudogene"; transcript_name "AC245056.4-201"; exon_number 2; exon_id "ENSE00003804365.1"; level 3; tag "basic"; Filtered: manually;
– Sergei
Nov 19 at 15:05
Actually I have managed to do this but maybe there is better solution using only awk?
– Sergei
Nov 19 at 15:05
What have you already tried?
– Didier Trosset
Nov 19 at 13:46
What have you already tried?
– Didier Trosset
Nov 19 at 13:46
1
1
What is the expected output?
– zx8754
Nov 19 at 14:30
What is the expected output?
– zx8754
Nov 19 at 14:30
Which lines in the example do describe a
ENSEMBLE non-chromosomal pseudogene? and why (what are the related strings) ?– Jay jargot
Nov 19 at 14:35
Which lines in the example do describe a
ENSEMBLE non-chromosomal pseudogene? and why (what are the related strings) ?– Jay jargot
Nov 19 at 14:35
This are lines that match patterns:ENSEMBL exon 169224 169502 . - . gene_id "ENSG00000284215.2"; transcript_id "ENST00000639764.2"; gene_type "pseudogene"; gene_name "AC245056.4"; transcript_type "pseudogene"; transcript_name "AC245056.4-201"; exon_number 2; exon_id "ENSE00003804365.1"; level 3; tag "basic"; Filtered: manually;
– Sergei
Nov 19 at 15:05
This are lines that match patterns:ENSEMBL exon 169224 169502 . - . gene_id "ENSG00000284215.2"; transcript_id "ENST00000639764.2"; gene_type "pseudogene"; gene_name "AC245056.4"; transcript_type "pseudogene"; transcript_name "AC245056.4-201"; exon_number 2; exon_id "ENSE00003804365.1"; level 3; tag "basic"; Filtered: manually;
– Sergei
Nov 19 at 15:05
Actually I have managed to do this but maybe there is better solution using only awk?
– Sergei
Nov 19 at 15:05
Actually I have managed to do this but maybe there is better solution using only awk?
– Sergei
Nov 19 at 15:05
|
show 1 more comment
1 Answer
1
active
oldest
votes
up vote
1
down vote
accepted
If you are using Awk anyway, you don't need grep at all.
Also, less crucially, modifying $0 is mildly wasteful. print lets you specify precisely what you want to print.
awk '!/##/ && !/chr/ && /pseudogene/ && /ENSEMBL/ {
print $0" Filtered: manually;"}' gencode.v29.chr_patch_hapl_scaff.basic.annotation.gtf > gencode.v29.filtered.gtf
answered Nov 19 at 15:36
tripleee
87.4k12122177
Thanks, yes this is much better)
– Sergei
Nov 19 at 16:25
add a comment |
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
1
down vote
accepted
If you are using Awk anyway, you don't need grep at all.
Also, less crucially, modifying $0 is mildly wasteful. print lets you specify precisely what you want to print.
awk '!/##/ && !/chr/ && /pseudogene/ && /ENSEMBL/ {
print $0" Filtered: manually;"}' gencode.v29.chr_patch_hapl_scaff.basic.annotation.gtf > gencode.v29.filtered.gtf
answered Nov 19 at 15:36
tripleee
87.4k12122177
Thanks, yes this is much better)
– Sergei
Nov 19 at 16:25
add a comment |
up vote
1
down vote
accepted
If you are using Awk anyway, you don't need grep at all.
Also, less crucially, modifying $0 is mildly wasteful. print lets you specify precisely what you want to print.
awk '!/##/ && !/chr/ && /pseudogene/ && /ENSEMBL/ {
print $0" Filtered: manually;"}' gencode.v29.chr_patch_hapl_scaff.basic.annotation.gtf > gencode.v29.filtered.gtf
answered Nov 19 at 15:36
tripleee
87.4k12122177
Thanks, yes this is much better)
– Sergei
Nov 19 at 16:25
add a comment |
up vote
1
down vote
accepted
up vote
1
down vote
accepted
If you are using Awk anyway, you don't need grep at all.
Also, less crucially, modifying $0 is mildly wasteful. print lets you specify precisely what you want to print.
awk '!/##/ && !/chr/ && /pseudogene/ && /ENSEMBL/ {
print $0" Filtered: manually;"}' gencode.v29.chr_patch_hapl_scaff.basic.annotation.gtf > gencode.v29.filtered.gtf
answered Nov 19 at 15:36
tripleee
87.4k12122177
If you are using Awk anyway, you don't need grep at all.
Also, less crucially, modifying $0 is mildly wasteful. print lets you specify precisely what you want to print.
awk '!/##/ && !/chr/ && /pseudogene/ && /ENSEMBL/ {
print $0" Filtered: manually;"}' gencode.v29.chr_patch_hapl_scaff.basic.annotation.gtf > gencode.v29.filtered.gtf
answered Nov 19 at 15:36
tripleee
87.4k12122177
answered Nov 19 at 15:36
tripleee
87.4k12122177
answered Nov 19 at 15:36
tripleee
87.4k12122177
answered Nov 19 at 15:36
tripleee
87.4k12122177
87.4k12122177
Thanks, yes this is much better)
– Sergei
Nov 19 at 16:25
add a comment |
Thanks, yes this is much better)
– Sergei
Nov 19 at 16:25
Thanks, yes this is much better)
– Sergei
Nov 19 at 16:25
Thanks, yes this is much better)
– Sergei
Nov 19 at 16:25
add a comment |
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What have you already tried?
– Didier Trosset
Nov 19 at 13:46
1
What is the expected output?
– zx8754
Nov 19 at 14:30
Which lines in the example do describe a
ENSEMBLE non-chromosomal pseudogene? and why (what are the related strings) ?– Jay jargot
Nov 19 at 14:35
This are lines that match patterns:ENSEMBL exon 169224 169502 . - . gene_id "ENSG00000284215.2"; transcript_id "ENST00000639764.2"; gene_type "pseudogene"; gene_name "AC245056.4"; transcript_type "pseudogene"; transcript_name "AC245056.4-201"; exon_number 2; exon_id "ENSE00003804365.1"; level 3; tag "basic"; Filtered: manually;
– Sergei
Nov 19 at 15:05
Actually I have managed to do this but maybe there is better solution using only awk?
– Sergei
Nov 19 at 15:05