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Bartosz Jan Bartmanski
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#!/usr/bin/env python3
import argparse
from pathlib import Path
from tempfile import TemporaryDirectory
import matplotlib.pyplot as plt
import streamlit as st
from plotting_on_genome import Pipeline, plot_insert, plot_insert_dists, plot_on_genome
# st.set_page_config(layout="wide")
if "stage" not in st.session_state:
st.session_state.stage = 0
if "filter_threshold" not in st.session_state:
st.session_state.filter_threshold = None
if "insert_types" not in st.session_state:
st.session_state.insert_types = "both"
if "workdir" not in st.session_state:
st.session_state.workdir = None
class TempDirManager:
def __init__(self, dirpath=None):
self.dirpath = dirpath
def __enter__(self):
if self.dirpath is None:
self.temp_dir = TemporaryDirectory()
return self.temp_dir.name
else:
Path(self.dirpath).mkdir(exist_ok=True)
return self.dirpath
def __exit__(self, exc_type, exc_value, traceback):
if self.dirpath is None:
self.temp_dir.cleanup()
@st.cache_data
def run_pipeline(
seq_fh, genome_fh, email, search_term, retmax, fwd_suf, rev_suf, workdir=None
):
with st.spinner("Processing..."), TempDirManager(workdir) as work_dir:
dirpath = Path(work_dir)
if genome_fh is not None:
genome_path = str(dirpath / genome_fh.name)
with open(genome_path, "wb") as fh:
fh.write(genome_fh.getbuffer())
else:
genome_path = None
seq_path = str(dirpath / seq_fh.name)
with open(seq_path, "wb") as fh:
fh.write(seq_fh.getbuffer())
return Pipeline(
seq_path,
dirpath,
genome_path,
email,
search_term,
retmax,
fwd_suf,
rev_suf,
)
def submit(*args):
st.session_state.pipeline = run_pipeline(*args)
st.session_state.stage = 1
def get_main_inputs():
parser = argparse.ArgumentParser("PlottingOnGenome")
parser.add_argument("--workdir", action="store_true")
args = parser.parse_args()
# Radio buttons to switch between text input and file upload
genome_src = st.radio("Genome:", ("NCBI", "File"))
# Text inputs
genome_fh = None
search_term = None
email = None
retmax = None
if genome_src == "NCBI":
search_term = st.text_input("Search term:", key="search_term")
email = st.text_input("Email:", key="email")
retmax = st.text_input(
"Retmax (Max. # of records from NCBI)", 200, key="retmax"
)
else:
genome_fh = st.file_uploader("Upload genome:", type="gbk", key="genome")
seq_fh = st.file_uploader("Sequence file:", type=["fasta", "fna"], key="seqs")
fwd_suf = st.text_input("Forward suffix:", "_F", key="fwd_suf")
rev_suf = st.text_input("Reverse suffix:", "_R", key="rev_suf")
filter_threshold = st.text_input("Filter threshold:", None)
if filter_threshold is not None:
st.session_state.filter_threshold = int(filter_threshold)
st.session_state.insert_types = st.selectbox(
"insert types:", ["both", "matched", "unmatched"]
)
if args.workdir:
st.session_state.workdir = st.text_input("workdir", "Output")
st.button(
"Submit",
on_click=submit,
args=[
seq_fh,
genome_fh,
email,
search_term,
retmax,
fwd_suf,
rev_suf,
st.session_state.workdir,
],
)
def main():
st.title("PlottingOnGenome")
if st.session_state.stage == 0:
get_main_inputs()
if st.session_state.stage >= 1:
option = st.selectbox(
"plot type:",
["plot inserts", "plot all on genome", "plot insert dists", "show data"],
None,
)
p = st.session_state.pipeline
insert_types = st.session_state.insert_types
filter_threshold = st.session_state.filter_threshold
if option == "plot inserts":
seq_id = st.selectbox("Select sequence id:", p.seq_ids)
inserts = p.get_inserts(seq_id, insert_types, filter_threshold)
for insert in inserts:
fig, axs = plt.subplots(2, 1, figsize=(10, 10), height_ratios=[3, 5])
axs = plot_insert(insert, p.genome, axs=axs)
st.pyplot(fig)
plt.close()
elif option == "plot all on genome":
labels = st.radio("Labels:", (True, False))
inserts = p.get_all_inserts(insert_types, filter_threshold)
fig, ax = plt.subplots(figsize=(10, 10 * (1 + 2 * labels)))
ax = plot_on_genome(inserts, p.genome, labels=labels, ax=ax)
st.pyplot(fig, use_container_width=True)
elif option == "plot insert dists":
inserts = p.get_all_inserts(insert_types, filter_threshold)
fig, axs = plt.subplots(1, 3, figsize=(12, 5))
plot_insert_dists(inserts, axs)
st.pyplot(fig)
elif option == "show data":
st.write(p.to_dataframe(insert_types, filter_threshold))
if st.button("Reset"):
st.session_state.stage = 0
st.rerun()
if __name__ == "__main__":
main()