From e8f8acc93b03f3e91cad3acfd8100cfa9ba1641a Mon Sep 17 00:00:00 2001
From: garion0000 <michele.garioni@unibas.ch>
Date: Wed, 17 Nov 2021 10:54:53 +0100
Subject: [PATCH] feat: add sampling from transcript file
---
requirements_dev.txt | 1 +
src/sampleinput.py | 73 +++++++++++++++++++++++++++++++++
tests/resources/Transcript1.csv | 7 ++++
tests/resources/Transcript2.tsv | 7 ++++
tests/test_dummy.py | 20 ++++++++-
5 files changed, 107 insertions(+), 1 deletion(-)
create mode 100644 src/sampleinput.py
create mode 100644 tests/resources/Transcript1.csv
create mode 100644 tests/resources/Transcript2.tsv
diff --git a/requirements_dev.txt b/requirements_dev.txt
index a382a35..61e56cc 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -3,3 +3,4 @@ flake8-docstrings
pytest
mypy
coverage
+pandas
\ No newline at end of file
diff --git a/src/sampleinput.py b/src/sampleinput.py
new file mode 100644
index 0000000..a6cc7e7
--- /dev/null
+++ b/src/sampleinput.py
@@ -0,0 +1,73 @@
+"""Samples transcripts from input.
+
+Samples a defined number of transcript following
+the relative RNA abundance per gene of a given input.
+"""
+import logging
+from pathlib import Path
+from random import choices
+
+LOG = logging.getLogger(__name__)
+
+
+def sample_from_input(
+ input_file: Path,
+ output_file: Path = Path.cwd() / 'sampled_cell.csv',
+ n: int = 10000,
+ sep: str = ',',
+) -> None:
+ """Samples transcripts from input.
+
+ Samples a defined number of transcript per gene following
+ the relative RNA abundance per gene of a given input and
+ writes the simulated results in a csv file.
+
+ Args:
+ input_file (string): name of the input gene expression file.
+ output_file (string): name of the sampled gene expression file.
+ n (int): number of total transcripts to be sampled.
+ sep (str): separator of the input file.
+ """
+ myfile = open(input_file, 'r')
+ # initialize empty dictionary
+ input_dc = {}
+
+ # read line, split key-value and assign key and value to the
+ # dictionary after stripping \n character.
+ LOG.info('reading file...')
+ for myline in myfile:
+ gene = myline.split(sep)
+ input_dc[gene[0].strip()] = int(gene[1].strip())
+ myfile.close()
+ LOG.debug(input_dc)
+ LOG.info('file read.')
+
+ # extract count numbers and calculate relative abundance
+ counts = list(input_dc.values())
+ tot_counts = sum(counts)
+ relative_value = [x / tot_counts for x in counts]
+
+ # sampling
+ LOG.info('sampling reads...')
+ sampled_genes = choices(list(input_dc.keys()), weights=relative_value, k=n)
+
+ # initialize empty dictionary
+ sampled_dc = dict()
+
+ # count the genes occurence from the sampled list
+ for i in sampled_genes:
+ if i not in sampled_dc:
+ sampled_dc[i] = 1
+ else:
+ sampled_dc[i] += 1
+ LOG.info('reads sampled.')
+
+ # write sample dictionary to a csv file, joining the
+ # key value pairs with a comma
+ myfile = open(output_file, 'w')
+ LOG.info('writing output...')
+ for (k, v) in sampled_dc.items():
+ line = ','.join([str(k), str(v)])
+ myfile.write(line + '\n')
+ myfile.close()
+ LOG.info('output written.')
diff --git a/tests/resources/Transcript1.csv b/tests/resources/Transcript1.csv
new file mode 100644
index 0000000..4ae4a98
--- /dev/null
+++ b/tests/resources/Transcript1.csv
@@ -0,0 +1,7 @@
+GENE1,92
+GENE2,13
+GENE3,73
+GENE4,83
+GENE5,32
+GENE6,136
+GENE7,36
\ No newline at end of file
diff --git a/tests/resources/Transcript2.tsv b/tests/resources/Transcript2.tsv
new file mode 100644
index 0000000..727c652
--- /dev/null
+++ b/tests/resources/Transcript2.tsv
@@ -0,0 +1,7 @@
+GENE1 92
+GENE2 13
+GENE3 73
+GENE4 83
+GENE5 32
+GENE6 136
+GENE7 36
\ No newline at end of file
diff --git a/tests/test_dummy.py b/tests/test_dummy.py
index 73a5117..d15a71f 100644
--- a/tests/test_dummy.py
+++ b/tests/test_dummy.py
@@ -1,10 +1,28 @@
"""Placeholder test for pipeline."""
+import pytest
import src
import re
-
+from src import sampleinput as si
+import pandas as pd
def test_version():
"""Assert that version matches semantic versioning format."""
assert re.match(r'\d\.\d\.\d', src.__version__)
+
+def test_sampleinput(tmpdir):
+ """Tests the output, input file name and separator."""
+
+ si.sample_from_input(
+ input_file='./tests/resources/Transcript2.tsv',
+ output_file=tmpdir / 'test1.csv',
+ sep='\t',
+ n=142958
+ )
+ t1=pd.read_table(tmpdir / 'test1.csv', header=None, sep=',')
+ assert t1[1].sum()==142958
+ with pytest.raises(IndexError):
+ si.sample_from_input(input_file='./tests/resources/Transcript2.tsv')
+ with pytest.raises(IOError):
+ si.sample_from_input(input_file='file_not_existing.txt')
\ No newline at end of file
--
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