coalispr.resources.share.gtf_frm_tsv

Create a gtf for counting reads as reference using ‘features’, from a tabulated file with self-annotated siRNA-segments. The tsv file was built by copying locations straight from the IGB browser to create an index of chr:[start-stop](size).

Attributes

exts
prefix
headers

Functions

clean_igb(row)	Function to convert genome coordinates copy-pasted from IGB to a tsv file,
create_siRNA_GTF_line(row)	Function to create GTF from self-annotated file with peak regions.
get_GTF_comment()
tsv2gtf(file_name, prefix, cryp, gtf_name)	Function to convert tsv input to gtf output
main(args)

Module Contents

coalispr.resources.share.gtf_frm_tsv.exts = ['.tsv', '.tab', '.csv']

coalispr.resources.share.gtf_frm_tsv.prefix = '@'

coalispr.resources.share.gtf_frm_tsv.headers

coalispr.resources.share.gtf_frm_tsv.clean_igb(row)

Function to convert genome coordinates copy-pasted from IGB to a tsv file, loaded into dataframe that needs cleaning up; use via apply.

coalispr.resources.share.gtf_frm_tsv.create_siRNA_GTF_line(row)

Function to create GTF from self-annotated file with peak regions.

coalispr.resources.share.gtf_frm_tsv.get_GTF_comment()

coalispr.resources.share.gtf_frm_tsv.tsv2gtf(file_name, prefix, cryp, gtf_name)

Function to convert tsv input to gtf output

file_namestr

Name input file

prefixstr (default: ‘@’)

Prefix for gene_id to express ‘anti’

crypint (default: 1)

Use headers for 1: JEC21; 2: H99

gtf_namestr

Output filename

coalispr.resources.share.gtf_frm_tsv.main(args)