From 30ca7f20184b6c9e804fc89d27ca2864ddbfbb9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= <mate.balajti@unibas.ch>
Date: Mon, 4 Sep 2023 17:07:48 +0200
Subject: [PATCH] refactor: remove tqdm, update cli and main
---
requirements.txt | 1 -
requirements_dev.txt | 1 -
tsg/cli.py | 4 +-
tsg/main.py | 93 ++++++++++++++++++++++++--------------------
4 files changed, 53 insertions(+), 46 deletions(-)
diff --git a/requirements.txt b/requirements.txt
index bf93cc4..babdd14 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,2 @@
matplotlib
pandas
-tqdm
diff --git a/requirements_dev.txt b/requirements_dev.txt
index 558b809..f973661 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -1,7 +1,6 @@
matplotlib
pandas
pip
-tqdm
mypy
flake8
flake8-docstrings
diff --git a/tsg/cli.py b/tsg/cli.py
index fcc0e71..30a2dec 100644
--- a/tsg/cli.py
+++ b/tsg/cli.py
@@ -30,8 +30,8 @@ def setup_logging(loglevel: str) -> None:
raise
logging.basicConfig(
- format='[%(asctime)s: %(levelname)s] \
- %(message)s (module "%(module)s")',
+ format=('[%(asctime)s: %(levelname)s] '
+ '%(message)s (module "%(module)s")'),
level=numeric_level,
)
diff --git a/tsg/main.py b/tsg/main.py
index 8307b79..d2c1bb6 100644
--- a/tsg/main.py
+++ b/tsg/main.py
@@ -4,8 +4,6 @@ import logging
import numpy as np
import pandas as pd # type: ignore
-from tqdm import tqdm # type: ignore
-
LOG = logging.getLogger(__name__)
@@ -31,15 +29,17 @@ def read_abundances(transcripts_file: str) -> pd.DataFrame:
def filter_df(gtf_df: pd.DataFrame, transcripts: list) -> pd.DataFrame:
- """Filter annotations to include only exons \
- with the highest transcript support level, i.e. TSL1.
+ """Filter dataframe.
+
+ Filter annotations to include only exons
+ with the highest transcript support level, i.e. TSL1.
`feature` column is filtered on value "exon" and
- `free_text` column is filtered to include the string \
+ `free_text` column is filtered to include the string
denoting the highest transcript support level
('transcript_support_level "1"').
- If a list of transcript IDs is given, `free_text` column \
+ If a list of transcript IDs is given, `free_text` column
is filtered to include one of the IDs.
Args:
@@ -47,7 +47,7 @@ def filter_df(gtf_df: pd.DataFrame, transcripts: list) -> pd.DataFrame:
transcript: list of transcript IDs
Returns:
- A pd.DataFrame containing only rows with exon annotations \
+ A pd.DataFrame containing only rows with exon annotations
of highest transcript support level and,
if provided, belonging to one of the given transcripts
"""
@@ -68,7 +68,7 @@ def filter_df(gtf_df: pd.DataFrame, transcripts: list) -> pd.DataFrame:
def str_to_dict(gene_string: str) -> dict:
"""Split between key/value pairs.
- Split string based on delimiter ';' into items, remove empty items and \
+ Split string based on delimiter ';' into items, remove empty items and
split items on delimiter ' ' into
key/value pairs. Remove quotes from value strings and create a dictionary.
@@ -92,9 +92,9 @@ def dict_to_str(gene_dict: dict) -> str:
Takes e.g. dictionary {'gene_id': 'GENE1', 'transcript_id': 'TRANSCRIPT1'}
and returns string 'gene_id "GENE1"; transcript_id "TRANSCRIPT1";'.
- Key/value pairs are joined by space to form an item and items are \
+ Key/value pairs are joined by space to form an item and items are
joinded by ';' to form a string.
- If a value is Not a Number (nan), the key/value pair is omitted \
+ If a value is Not a Number (nan), the key/value pair is omitted
from the string.
Args:
@@ -115,13 +115,15 @@ def dict_to_str(gene_dict: dict) -> str:
def reverse_parse_free_text(df_all: pd.DataFrame) -> pd.DataFrame:
- """Reverse parsing of gtf based pd.DataFrame to include only columns that \
- are well defnined by gtf-file standards.
+ """Reverse parse a gtf based pd.DataFrame.
+
+ The data frame will include only columns that
+ are well defnined by gtf-file standards.
The first 8 defined columns are constant as defined by gtf-file standards.
- Further columns are assumed to be parsed free-text columns \
+ Further columns are assumed to be parsed free-text columns
(see Gtf.parse_free_text()).
- The parsed free-text columns are aggregated as a dictionary and \
+ The parsed free-text columns are aggregated as a dictionary and
the dictionry is parsed as a string in gtf format.
Args:
@@ -165,8 +167,9 @@ def write_gtf(gtf_df: pd.DataFrame, filename: str) -> None:
def write_header(annotations_file: str) -> None:
- """Write the header of an annotations file, consisting of the \
- tab delimited column names.
+ """Write the header of an annotations file.
+
+ It consists of the tab delimited column names.
Args:
annotations_file: Filename to write header to.
@@ -182,7 +185,7 @@ class Gtf:
dtypes: A dictionary containing column names and respective data types.
parsed: A boolean indicating if the pd.DataFrame is parsed.
original_columns: A list of columns not touched by parsing.
- free_text_columns: A list of columns created during parsing \
+ free_text_columns: A list of columns created during parsing
of column `free_text`.
"""
@@ -240,7 +243,7 @@ class Gtf:
Part of initialization is:
Set dataframe attribute
Check which columns belong to the free-text part of the gtf-file.
- Check if there are no columns called free-text and if so, sets \
+ Check if there are no columns called free-text and if so, sets
the value of parsed attribute to TRUE.
Args:
@@ -254,11 +257,11 @@ class Gtf:
self.parsed = True
def parse_key_value(self):
- """Parse key/value pairs from `free_text` column into column `key` \
- with row entry `value`.
+ """Parse key/value pairs.
- Creates a dataframe with columns for keys in the free-text column \
- instead of `free_text` column.
+ From `free_text` column into column `key` with row entry `value`.
+ Creates a dataframe with columns for keys in the free-text column
+ instead of `free_text` column.
Saves it to Gtf.df attribute.
"""
assert self.parsed is False
@@ -316,15 +319,15 @@ class TranscriptGenerator:
strands = transcript_df["strand"].unique()
if len(transcript_df) == 0:
LOG.warning(
- "Transcript %s can't be sampled. "
+ "Transcript \"%s\" can't be sampled: "
"Annotation is missing or TSL is not 1.", transcript_id
)
instance = None
elif len(strands) > 1:
LOG.warning(
- "Transcript %s can't be sampled. Transcript generator is "
+ "Transcript \"%s\" can't be sampled: Transcript generator is "
"not implemented for transcripts with exons annotated on "
- "different strands", transcript_id,
+ "different strands.", transcript_id,
)
instance = None
else:
@@ -350,8 +353,8 @@ class TranscriptGenerator:
def get_inclusions(self) -> np.ndarray:
"""Generate inclusions array.
- Each column corresponds to one sample and the number of columns \
- corresponds to the number of samples.
+ Each column corresponds to one sample and the number of columns
+ corresponds to the number of samples.
Returns:
A boolean np.array, where True means intron inclusion.
@@ -367,16 +370,18 @@ class TranscriptGenerator:
return inclusion_arr
def get_unique_inclusions(self) -> tuple[list, np.ndarray, np.ndarray]:
- """Inclusion of unique intron inclusion via arrays and counts and \
- name generation of each unique count.
+ """Get unique inclusions.
+
+ Inclusion of unique intron inclusion via arrays and counts and
+ name generation of each unique count.
Args:
Returns:
- List of names for generated exons.
- - A boolean np.array where columns correspond to generated \
+ - A boolean np.array where columns correspond to generated
transcripts and rows to intron inclusion.
- - A np.array containing sample number per generated inclusions, \
+ - A np.array containing sample number per generated inclusions,
i.e. transcript.
"""
inclusion_arr = self.get_inclusions()
@@ -397,8 +402,10 @@ class TranscriptGenerator:
def get_df(
self, inclusions: np.ndarray, transcript_id: str
) -> pd.DataFrame:
- """Take as input a dataframe filtered to one transcript and \
- a boolean vector denoting intron inclusions.
+ """Get dataframe.
+
+ Take as input a dataframe filtered to one transcript and
+ a boolean vector denoting intron inclusions.
Args:
inclusions: A boolean vector denoting intron inclusion.
@@ -466,7 +473,7 @@ class TranscriptGenerator:
data_frame = reverse_parse_free_text(data_frame)
write_gtf(data_frame, filename)
- LOG.debug("Transcript %s sampled", self.ts_id)
+ LOG.debug("Transcript \"%s\" sampled.", self.ts_id)
def sample_transcripts(
@@ -476,19 +483,21 @@ def sample_transcripts(
output_transcripts_file: str,
output_annotations_file: str,
):
- """Read input files, iterate over transcript IDs, \
- sample each transcript and save results.
+ """Sample transcripts.
+
+ Read input files, iterate over transcript IDs,
+ sample each transcript and save results.
Args:
- input_transcripts_file: Filename of transcript abundances, \
+ input_transcripts_file: Filename of transcript abundances,
needs to be csv or tsv.
- input_annotations_file: Filename of annotations, \
+ input_annotations_file: Filename of annotations,
needs to be gtf.
- prob_inclusion: Probability of intron inclusion, \
+ prob_inclusion: Probability of intron inclusion,
needs to be float in range [0,1].
- output_transcripts_file: Filename of file to write \
+ output_transcripts_file: Filename of file to write
sampled transcripts to.
- output_annotations_file: Filename of file to write \
+ output_annotations_file: Filename of file to write
generated annotations to.
"""
LOG.info("Probability of intron inclusion: %s", str(prob_inclusion))
@@ -508,7 +517,7 @@ def sample_transcripts(
# Set up output file, write header once and append data in loop
write_header(output_annotations_file)
- for _, row in tqdm(transcripts.iterrows()):
+ for _, row in transcripts.iterrows():
transcript_id = row["id"]
transcript_count = row["count"]
--
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