lapa.link

Module Contents

Functions

_read_alignment_reads(alignment, mapq=10, min_read_length=100)	Read read_name and locus of reads from alignment file.
_link_reads_to_tes(df_tes_cluster, df_reads, distance=50)	Link reads to transcript end sites
_link_reads_to_tss(df_tss_cluster, df_reads, distance=50)	Link reads to transcript start sites
link_tss_to_tes(alignment, lapa_dir, lapa_tss_dir, distance=50, mapq=10, min_read_length=100, dataset='all')	Link transcript site sites to transcript end sites using

Attributes

_reads_cols

lapa.link._reads_cols = ['read_name', 'Chromosome', 'read_Start', 'read_End', 'Strand']

lapa.link._read_alignment_reads(alignment, mapq=10, min_read_length=100)

Read read_name and locus of reads from alignment file.

lapa.link._link_reads_to_tes(df_tes_cluster, df_reads, distance=50)

Link reads to transcript end sites

lapa.link._link_reads_to_tss(df_tss_cluster, df_reads, distance=50)

Link reads to transcript start sites

lapa.link.link_tss_to_tes(alignment, lapa_dir, lapa_tss_dir, distance=50, mapq=10, min_read_length=100, dataset='all')

Link transcript site sites to transcript end sites using long-read from the alignment file.

Parameters

• alignment (str) – Path to bam file or TALON read_annot file.

• lapa_dir (str) – Path to lapa output directory generated with lapa command

• lapa_tss_dir (str) – Path to lapa tss directory with lapa_tss command