Commands from section ‘information’¶
In this section we will require the following datasets:
$ gtftk get_example -q -d simple -f '*'
$ gtftk get_example -q -d mini_real -f '*'
apropos¶
Description: Search in all command description files those related to a user-defined keyword.
Example: Search all commands related to promoters.
$ gtftk apropos -k promoter
|-- 10:51-INFO-apropos : >> Keyword 'promoter' was found in the following command:
- coverage.
- ologram.
- divergent.
Arguments:
$ gtftk apropos -h
Usage: gtftk apropos -k keyword [-n] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Search in all command description files those related to a user-defined keyword.
Arguments:
-k, --keyword The keyword (default: None)
-n, --notes Look also for the keywords in notes associated to each command. (default: False)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
retrieve¶
Description: Retrieves a GTF file from ensembl.
Example: List the available GTF files in ensembl FTP. Bacteria are not listed at the moment.
$ # gtftk retrieve -l | head -5
Example: Perform basic statistics on Vicugna pacos genomic annotations.
$ # gtftk retrieve -s vicugna_pacos -c -d | gtftk count -t vicugna_pacos
Arguments:
$ gtftk retrieve -h
Usage: gtftk retrieve [-s SPECIES] [-o GTF.GZ] [-e {vertebrate,protists,fungi,plants,metazoa}] [-r RELEASE] [-l] [-hs] [-c] [-d] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Retrieve a GTF file from ensembl.
Arguments:
-s, --species-name The species name. (default: homo_sapiens)
-o, --outputfile Output file (gtf.gz). (default: None)
-e, --ensembl-collection Which ensembl collection to interrogate('vertebrate', 'protists', 'fungi', 'plants', 'metazoa'). (default: vertebrate)
-r, --release Release number. By default, the latest. (default: None)
-l, --list-only If selected, list available species. (default: False)
-hs, --hide-species-name If selected, hide species names upon listing. (default: False)
-c, --to-stdout This option specifies that output will go to the standard output stream, leaving downloaded files intact (or not, see -d). (default: False)
-d, --delete Delete the gtf file after processing (e.g if -c is used). (default: False)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
get_example¶
Description: Get an example GTF file (or any other kind of example available in the installation directory). This command is only provided for demonstration purpose.
We can see from the example below that this gtf file follows the ensembl format and contains the transcript and gene features (column 3).
Example: The very basic (and artificial) example.
$ gtftk get_example | head -2
chr1 gtftk gene 125 138 . + . gene_id "G0001";
chr1 gtftk transcript 125 138 . + . gene_id "G0001"; transcript_id "G0001T002";
let’s get all files from the simple dataset.
$ gtftk get_example -q -d simple -f '*'
Arguments:
$ gtftk get_example -h
Usage: gtftk get_example [-d {simple,mini_real,mini_real_noov_rnd_tx,tiny_real,hg38_chr1,simple_02,simple_03,simple_04,simple_05,simple_06,simple_07,mini_real_10M,control_list,ologram_1,ologram_2,mini_real_ens}] [-f {*,gtf,bed,bw,bam,join,join_mat,chromInfo,tsv,fa,fa.idx,genes,geneList,2.bw,genome}] [-o OUTPUT] [-l] [-a] [-q] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Print example files including GTF.
Notes:
* Use format '*' to get all files from a dataset.
Arguments:
-d, --dataset Select a dataset. (default: simple)
-f, --format The dataset format. (default: gtf)
-o, --outputfile Output file. (default: <stdout>)
-l, --list Only list files of a dataset. (default: False)
-a, --all-dataset Get the list of all datasets. (default: False)
-q, --quiet Don't write any message when copying files. (default: False)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
add_exon_nb¶
Description: Add exon number transcript-wise (based on 5’ to 3’ orientation).
Example:
$ gtftk add_exon_nb -i simple.gtf -k exon_number | gtftk select_by_key -k feature -v exon | gtftk tabulate -k chrom,start,end,exon_number,transcript_id | head -n 20
seqid start end exon_number transcript_id
chr1 125 138 1 G0001T002
chr1 125 138 1 G0001T001
chr1 180 189 1 G0002T001
chr1 50 54 2 G0003T001
chr1 57 61 1 G0003T001
chr1 65 68 1 G0004T002
chr1 71 71 2 G0004T002
chr1 74 76 3 G0004T002
chr1 65 68 1 G0004T001
chr1 71 71 2 G0004T001
chr1 74 76 3 G0004T001
chr1 33 35 2 G0005T001
chr1 42 47 1 G0005T001
chr1 22 25 3 G0006T001
chr1 28 30 2 G0006T001
chr1 33 35 1 G0006T001
chr1 28 30 2 G0006T002
chr1 33 35 1 G0006T002
chr1 107 116 1 G0007T001
Arguments:
$ gtftk add_exon_nb -h
Usage: gtftk add_exon_nb [-i GTF] [-o GTF] [-k exon_numbering_key] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Add exon number transcript-wise (based on 5' to 3' orientation).
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
-k, --exon-numbering-key The name of the key containing the exon numbering. (default: exon_nbr)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
count¶
Description: Count the number of features (transcripts, genes, exons, introns).
Example:
$ gtftk count -i simple.gtf -t example_gtf
gene 10 example_gtf
transcript 15 example_gtf
exon 25 example_gtf
CDS 20 example_gtf
Arguments:
$ gtftk count -h
Usage: gtftk count [-i GTF] [-o TXT] [-d header] [-t TEXT] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Count the number of each features in the gtf file.
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN. (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
-d, --header A comma-separated list of string to use as header. (default: None)
-t, --additional-text A facultative text to be printed in the third column (e.g species name). (default: None)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
count_key_values¶
Description: Count the number of values for a set of keys.
Example: Count the number of non-redondant entries for chromosomes and transcript_id.
$ gtftk count_key_values -i simple.gtf -k chrom,transcript_id -u
chrom 1
transcript_id 15
Arguments:
$ gtftk count_key_values -h
Usage: gtftk count_key_values [-i GTF] [-o TXT] [-k keys] [-t TEXT] [-u] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Count the number of values/levels for a set of keys.
Notes:
* Use --uniq to get the count of non-redondant values.
* Not available values ('.') are not taken into account.
* Use "*" as the key to get the counts for all keys.
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN. (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
-k, --keys The set of keys of interest. (default: *)
-t, --additional-text A facultative text to be printed in the third column (e.g species name). (default: None)
-u, --uniq Ask for the count of non redondant values. (default: False)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
get_attr_list¶
Description: Get the list of attributes from a GTF file.
Example: Get the list of attributes in the “simple” dataset.
$ gtftk get_attr_list -i simple.gtf
gene_id
transcript_id
exon_id
ccds_id
Arguments:
$ gtftk get_attr_list -h
Usage: gtftk get_attr_list [-i GTF] [-o TXT] [-s SEP] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Get the list of attributes from a GTF file.
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
-s, --separator The separator to be used for separating key names. (default: )
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
get_attr_value_list¶
Description: Get the list of values observed for an attributes.
Example: Get the number of time each gene_id is used.
$ gtftk get_attr_value_list -i simple.gtf -k gene_id -c -s ';'
G0001;7
G0002;4
G0003;5
G0004;13
G0005;5
G0006;13
G0007;7
G0008;5
G0009;7
G0010;4
Arguments:
$ gtftk get_attr_value_list -h
Usage: gtftk get_attr_value_list [-i GTF] [-o TXT] -k key_name [-s separator] [-c] [-p] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Get the list of values observed for an attributes.
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
-k, --key-name The comma separated list of key name. (default: None)
-s, --separator The separator used if -c or -p are true. (default: )
-c, --count Add the counts for each key (separator will be set to ' ' by default). (default: False)
-p, --print-key-name Also print the key name in the first column. (default: False)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
get_feature_list¶
Description: Get the list of features enclosed in the GTF.
Example: Get the list of features enclosed in the GTF.
$ gtftk get_feature_list -i simple.gtf
gene
transcript
exon
CDS
Arguments:
$ gtftk get_feature_list -h
Usage: gtftk get_feature_list [-i GTF] [-o TXT] [-s SEP] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Get the list of features enclosed in the GTF.
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
-s, --separator The separator to be used for separating key names. (default: )
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
nb_exons¶
Description: Count the number of exons and add it as a novel key/value. Output may also be in text format if requested.
Example:
$ gtftk nb_exons -i simple.gtf | head -n 5
chr1 gtftk gene 125 138 . + . gene_id "G0001";
chr1 gtftk transcript 125 138 . + . gene_id "G0001"; transcript_id "G0001T002"; nb_exons "1";
chr1 gtftk exon 125 138 . + . gene_id "G0001"; transcript_id "G0001T002"; exon_id "G0001T002E001";
chr1 gtftk CDS 125 130 . + . gene_id "G0001"; transcript_id "G0001T002"; ccds_id "CDS_G0001T002";
chr1 gtftk transcript 125 138 . + . gene_id "G0001"; transcript_id "G0001T001"; nb_exons "1";
Arguments:
$ gtftk nb_exons -h
Usage: gtftk nb_exons [-i GTF] [-o TXT/GTF] [-f] [-a key_name] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Returns the transcript name and number of exons with nb_exons as a novel key for each transcript
feature.
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
-f, --text-format Return a text format. (default: False)
-a, --key-name The name of the key. (default: nb_exons)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
nb_transcripts¶
Description: Count the number of transcript per gene.
Example: Count the number of transcript per gene.
$ gtftk nb_transcripts -i simple.gtf | gtftk select_by_key -g
chr1 gtftk gene 125 138 . + . gene_id "G0001"; nb_tx "2";
chr1 gtftk gene 180 189 . + . gene_id "G0002"; nb_tx "1";
chr1 gtftk gene 50 61 . - . gene_id "G0003"; nb_tx "1";
chr1 gtftk gene 65 76 . + . gene_id "G0004"; nb_tx "2";
chr1 gtftk gene 33 47 . - . gene_id "G0005"; nb_tx "1";
chr1 gtftk gene 22 35 . - . gene_id "G0006"; nb_tx "2";
chr1 gtftk gene 107 116 . + . gene_id "G0007"; nb_tx "2";
chr1 gtftk gene 210 222 . - . gene_id "G0008"; nb_tx "1";
chr1 gtftk gene 3 14 . - . gene_id "G0009"; nb_tx "2";
chr1 gtftk gene 176 186 . + . gene_id "G0010"; nb_tx "1";
Arguments:
$ gtftk nb_transcripts -h
Usage: gtftk nb_transcripts [-i GTF] [-o GTF/TXT] [-f] [-a key_name] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Compute the number of transcript per gene.
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
-f, --text-format Return a text format. (default: False)
-a, --key-name If gtf format is requested, the name of the key. (default: nb_tx)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
seqid_list¶
Description: Return the chromosome list.
Example: Return the chromosome list.
$ gtftk seqid_list -i simple.gtf
chr1
Arguments:
$ gtftk seqid_list -h
Usage: gtftk seqid_list [-i GTF] [-o TXT] [-s SEP] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Select the seqid/chromosomes
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
-s, --separator The separator to be used for separating key names. (default: )
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
tss_dist¶
Description: Compute the distance between TSSs of pairs of gene transcripts. The tss_num_1 and tss_num_2 columns contains the TSSs number (for transcript_id_1 and transcript_id_2 respectively). Numering starts from 1 (most 5’ TSS for a gene) to the number of different TSS coordinates. Two or more transcripts will have the same tss_num if they share a TSS.
Example: An example on the mini_real dataset.
$ gtftk random_list -i mini_real.gtf.gz -t gene -n 1 -s 2 | gtftk tss_dist
gene_id transcript_id_1 transcript_id_2 dist tss_num_1 tss_num_2
ENSG00000107829 ENST00000457105 ENST00000331272 36 1 2
ENSG00000107829 ENST00000331272 ENST00000470093 68360 2 4
ENSG00000107829 ENST00000331272 ENST00000482428 82106 2 5
ENSG00000107829 ENST00000331272 ENST00000489578 18545 2 3
ENSG00000107829 ENST00000457105 ENST00000470093 68396 1 4
ENSG00000107829 ENST00000457105 ENST00000482428 82142 1 5
ENSG00000107829 ENST00000457105 ENST00000489578 18581 1 3
ENSG00000107829 ENST00000470093 ENST00000482428 13746 4 5
ENSG00000107829 ENST00000489578 ENST00000470093 49815 3 4
ENSG00000107829 ENST00000489578 ENST00000482428 63561 3 5
Arguments:
$ gtftk tss_dist -h
Usage: gtftk tss_dist [-i GTF] [-o TXT] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Computes the distance between TSSs of pairs of gene transcripts.
Notes:
* The tss_num_1/tss_num_1 columns contains the numbering of TSSs (transcript_id_1 and
transcript_id_2 respectively) for each gene.
* Numering starts from 1 (most 5' TSS) to the number of different TSS coordinates.
* Thus two or more transcripts will have the same tss_num if they share a TSS.
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN. (default: <stdin>)
-o, --outputfile Output file. (default: <stdout>)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)
feature_size¶
Description: Get the size and limits (start/end) of features enclosed in the GTF. If bed format is requested returns the limits in bed format and the size as a score. Otherwise output GTF file with ‘feat_size’ as a new key and size as value
Example: Add trancript size (mature RNA) to the gtf.
$ gtftk feature_size -i simple.gtf -t mature_rna | gtftk select_by_key -k feature -v transcript | head -n 5
chr1 gtftk transcript 125 138 . + . gene_id "G0001"; transcript_id "G0001T002"; feat_size "14";
chr1 gtftk transcript 125 138 . + . gene_id "G0001"; transcript_id "G0001T001"; feat_size "14";
chr1 gtftk transcript 180 189 . + . gene_id "G0002"; transcript_id "G0002T001"; feat_size "10";
chr1 gtftk transcript 50 61 . - . gene_id "G0003"; transcript_id "G0003T001"; feat_size "10";
chr1 gtftk transcript 65 76 . + . gene_id "G0004"; transcript_id "G0004T002"; feat_size "8";
Arguments:
$ gtftk feature_size -h
Usage: gtftk feature_size [-i GTF] [-o GTF/BED] [-t ft_type] [-n NAME] [-k KEY_NAME] [-s SEP] [-b] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
Description:
Get the size and limits (start/end) of features enclosed in the GTF. The feature can be of any
type (as found in the 3rd column of the GTF) or 'mature_rna' to get transcript size (i.e
without introns). If bed format is requested returns the limits in bed format and the size as a
score. Otherwise output GTF file with 'feat_size' as a new key and size as value.
Arguments:
-i, --inputfile Path to the GTF file. Default to STDIN (default: <stdin>)
-o, --outputfile Output file (BED). (default: <stdout>)
-t, --ft-type A target feature (as found in the 3rd column of the GTF) or 'mature_rna' to get transcript size (without introns). (default: transcript)
-n, --names The key(s) that should be used as name if bed is requested. (default: transcript_id)
-k, --key-name Name for the new key if GTF format is requested. (default: feat_size)
-s, --separator The separator to be used for separating name elements (see -n). (default: |)
-b, --bed Output bed format. (default: False)
Command-wise optional arguments:
-h, --help Show this help message and exit.
-V, --verbosity Set output verbosity ([0-3]). (default: 0)
-D, --no-date Do not add date to output file names. (default: False)
-C, --add-chr Add 'chr' to chromosome names before printing output. (default: False)
-K, --tmp-dir Keep all temporary files into this folder. (default: None)
-A, --keep-all Try to keep all temporary files even if process does not terminate normally. (default: False)
-L, --logger-file Stores the arguments passed to the command into a file. (default: None)
-W, --write-message-to-file Store all message into a file. (default: None)