Skip to content

Add checkpoint filtering spkgs with excessive off-target sequences #249

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wwood wants to merge 1 commit into
base: ben_lyrebird_metapackage_fixes
Choose a base branch
from
Open

Add checkpoint filtering spkgs with excessive off-target sequences #249

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 33 additions & 5 deletions extras/lyrebird_metapackage_creation/2_concatenate_and_build.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ Run `snakemake --cores 64 --use-conda --retries 2`
"""

localrules:
all, acquire_and_concat_hmms, hmmsearch_off_target, concat_fscores, resolve_fscores, roundrobin, shorten_vcontact_taxonomy, off_target_dup_rename
all, acquire_and_concat_hmms, hmmsearch_off_target, concat_fscores, resolve_fscores, roundrobin, shorten_vcontact_taxonomy, off_target_dup_rename, filter_off_target_ratio

import pandas as pd
import os
Expand All @@ -25,10 +25,16 @@ scripts_dir = output_dir + "/qsub_scripts"
hmms_and_names = pd.read_csv(output_dir + "/hmms_and_names_noconflict.tsv", sep="\t").set_index("gene", drop=False)
gtdb_proviruses = config["gtdb_proviruses"]

def get_filtered_spkgs(wildcards):
"""Return spkgs that pass the off-target ratio filter."""
filtered = checkpoints.filter_off_target_ratio.get().output.spkgs
with open(filtered) as f:
return [line.strip() for line in f if line.strip()]

rule all:
input:
output_dir + "/roundrobin.done",
expand(output_dir + "/regenerate/{spkg}.spkg", spkg=hmms_and_names.index),
expand(output_dir + "/regenerate/{spkg}.spkg", spkg=get_filtered_spkgs),
output_dir + "/cleanup.done",

#########################################
Expand Down Expand Up @@ -331,6 +337,28 @@ rule off_target_dup_rename:
script:
"scripts/rename_off_target_dups.py"

checkpoint filter_off_target_ratio:
"""Exclude spkgs with excessive off-target sequences."""
input:
rename_done = expand(output_dir + "/hmmseq_concat/off_target_renamed_dups/{spkg}.done", spkg=hmms_and_names.index),
output:
spkgs = output_dir + "/filtered_spkgs.txt"
run:
def count_seqs(fp):
with open(fp) as handle:
return sum(1 for line in handle if line.startswith('>'))

with open(output.spkgs, "w") as out:
for spkg in hmms_and_names.index:
viral = os.path.join(output_dir, "hmmseq_concat", "viral", f"{spkg}.faa")
off = os.path.join(output_dir, "hmmseq_concat", "off_target_renamed_dups", f"{spkg}.faa")
if not os.path.exists(off):
continue
viral_count = count_seqs(viral)
off_count = count_seqs(off)
if viral_count >= 100 * off_count:
out.write(f"{spkg}\n")

rule singlem_regenerate:
"""
Add off-target sequences to the initial SingleM packages.
Expand Down Expand Up @@ -437,8 +465,8 @@ rule get_fscore:

rule concat_fscores:
input:
fscores = expand(output_dir + "/fscore/{spkg}.fscore", spkg=hmms_and_names.index),
done = expand(output_dir + "/fscore/{spkg}.done", spkg=hmms_and_names.index)
fscores = lambda wildcards: expand(output_dir + "/fscore/{spkg}.fscore", spkg=get_filtered_spkgs(wildcards)),
done = lambda wildcards: expand(output_dir + "/fscore/{spkg}.done", spkg=get_filtered_spkgs(wildcards))
output:
fscore_list = output_dir + "/fscore_list.tsv",
done = output_dir + "/concat_fscores.done"
Expand Down Expand Up @@ -468,7 +496,7 @@ rule roundrobin:
Outputs a TSV file of the selected SingleM packages and their coverages.
"""
input:
spkgs = expand(output_dir + "/regenerate/{spkg}.spkg", spkg=hmms_and_names.index),
spkgs = lambda wildcards: expand(output_dir + "/regenerate/{spkg}.spkg", spkg=get_filtered_spkgs(wildcards)),
match_directory = output_dir + "/resolved_matches",
resolved_trees_list = output_dir + "/resolved_trees_list.tsv",
done = output_dir + "/resolved_trees.done"
Expand Down