get_lncrna_overlaps_and_nearest.py

import pyranges_db as db
import pyranges as pr

gr = db.gencode.genes("human") # takes a while to download from ftp
# Wall time: 2min 1s

gr.to_gtf("gencode_human.gtf.gz") # takes a while to gzip and write to disk
# Wall time: 4min 3s

# subset for faster operations
gr = gr[["Feature", "gene_type", "gene_id", "gene_name"]]

gr = gr[gr.Feature == "transcript"].drop("Feature")

lncrna = gr[(gr.gene_type == "lncRNA")].drop("gene_type")
protein = gr[gr.gene_type == "protein_coding"].drop("gene_type")

_overlap = lncrna.join(protein, strandedness="same", suffix="_protein").drop(
  like="Start_protein|End_protein|Strand_protein")
_overlap.Distance = 0

no_overlap_protein = lncrna.overlap(protein, invert=True, strandedness="same")

_upstream = no_overlap_protein.nearest(protein, how="upstream", overlap=False, strandedness="same", suffix="_protein").drop(
  like="Start_protein|End_protein|Strand_protein")

_downstream = no_overlap_protein.nearest(protein, how="downstream", overlap=False, strandedness="same", suffix="_protein").drop(
  like="Start_protein|End_protein|Strand_protein|gene_type")
_downstream.Distance = -_downstream.Distance

outgr = pr.concat([_overlap, _downstream, _upstream])

outgr
# +--------------+-----------+-----------+--------------+-------------------+--------------+--------------------+---------------------+------------+
# | Chromosome   | Start     | End       | Strand       | gene_id           | gene_name    | gene_id_protein    | gene_name_protein   | Distance   |
# | (category)   | (int32)   | (int32)   | (category)   | (category)        | (category)   | (category)         | (category)          | (int64)    |
# |--------------+-----------+-----------+--------------+-------------------+--------------+--------------------+---------------------+------------|
# | chr1         | 1055032   | 1056116   | +            | ENSG00000242590.1 | AL645608.5   | ENSG00000188157.15 | AGRN                | 0          |
# | chr1         | 1055032   | 1056116   | +            | ENSG00000242590.1 | AL645608.5   | ENSG00000188157.15 | AGRN                | 0          |
# | chr1         | 1055032   | 1056116   | +            | ENSG00000242590.1 | AL645608.5   | ENSG00000188157.15 | AGRN                | 0          |
# | chr1         | 1055032   | 1056116   | +            | ENSG00000242590.1 | AL645608.5   | ENSG00000188157.15 | AGRN                | 0          |
# | ...          | ...       | ...       | ...          | ...               | ...          | ...                | ...                 | ...        |
# | chrY         | 22296797  | 22298876  | -            | ENSG00000215560.2 | TTTY5        | ENSG00000188120.14 | DAZ1                | 830479     |
# | chrY         | 22439592  | 22441458  | -            | ENSG00000131538.7 | TTTY6        | ENSG00000188120.14 | DAZ1                | 687897     |
# | chrY         | 23936726  | 23941622  | -            | ENSG00000280961.1 | TTTY3B       | ENSG00000172352.5  | CDY1B               | 103607     |
# | chrY         | 24183433  | 24187231  | -            | ENSG00000244231.1 | CSPG4P2Y     | ENSG00000187191.14 | DAZ3                | 575838     |
# +--------------+-----------+-----------+--------------+-------------------+--------------+--------------------+---------------------+------------+
# Stranded PyRanges object has 100,466 rows and 9 columns from 24 chromosomes.
# For printing, the PyRanges was sorted on Chromosome and Strand.


outgr.to_csv("lncrna_prot_join.csv", sep="\t", header=True)

# !head lncrna_prot_join.csv
# Chromosome	Start	End	Strand	gene_id	gene_name	gene_id_protein	gene_name_protein	Distance
# chr1	1055032	1056116	+	ENSG00000242590.1	AL645608.5	ENSG00000188157.15	AGRN	0
# chr1	1055032	1056116	+	ENSG00000242590.1	AL645608.5	ENSG00000188157.15	AGRN	0
# chr1	1055032	1056116	+	ENSG00000242590.1	AL645608.5	ENSG00000188157.15	AGRN	0
# chr1	1055032	1056116	+	ENSG00000242590.1	AL645608.5	ENSG00000188157.15	AGRN	0
# chr1	1055032	1056116	+	ENSG00000242590.1	AL645608.5	ENSG00000188157.15	AGRN	0
# chr1	7368941	7370270	+	ENSG00000237402.1	CAMTA1-IT1	ENSG00000171735.19	CAMTA1	0
# chr1	7776382	7776775	+	ENSG00000269925.1	Z98884.2	ENSG00000049245.13	VAMP3	0
# chr1	7776382	7776775	+	ENSG00000269925.1	Z98884.2	ENSG00000049245.13	VAMP3	0
# chr1	9942922	9949974	+	ENSG00000228150.1	AL357140.2	ENSG00000173614.14	NMNAT1	0