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Nicolas MAILLET authored
core.py 11.65 KiB
# -*- coding: utf-8 -*-
########################################################################
# Author: Nicolas Maillet #
# Copyright © 2018 Institut Pasteur, Paris. #
# See the COPYRIGHT file for details #
# #
# This file is part of Rapid Peptide Generator (RPG) software. #
# #
# RPG is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# any later version. #
# #
# RPG is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public license #
# along with RPG (LICENSE file). #
# If not, see <http://www.gnu.org/licenses/>. #
########################################################################
"""Contains generic functions and global variables used by RPG"""
import sys
import gzip
AMINOACIDS = ["A", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N",
"O", "P", "Q", "R", "S", "T", "U", "V", "W", "Y", "B", "X", "Z",
"#", "*"]
"""All character accepted in a peptide."""
AA_MASS_AVERAGE = {"*" : 0.0,
"A" : 71.0788,
"C" : 103.1388,
"D" : 115.0886,
"E" : 129.1155,
"F" : 147.1766,
"G" : 57.0519,
"H" : 137.1411,
"I" : 113.1594,
"J" : 113.1594,
"K" : 128.1741,
"L" : 113.1594,
"M" : 131.1926,
"N" : 114.1038,
"O" : 237.3018,
"P" : 97.1167,
"Q" : 128.1307,
"R" : 156.1875,
"S" : 87.0782,
"T" : 101.1051,
"U" : 150.0388,
"V" : 99.1326,
"W" : 186.2132,
"Y" : 163.1760,
"B" : 0.0,
"X" : 0.0,
"Z" : 0.0,
"#" : 0.0}
"""Mass of all amino acids."""
WATER_MASS = 18.01528
"""Mass of a water molecule."""
# Biochemistry Stryer 7th
AA_PKA_S = {"Nterm" : 8.0,
"C" : 8.3,
"D" : 4.1,
"E" : 4.1,
"H" : 6.0,
"K" : 10.8,
"R" : 12.5,
"Y" : 10.9,
"Cterm" : 3.1}
"""pKa of important amino acid to compute pI (from Stryer)."""
# IPC_peptide
AA_PKA_IPC = {"Nterm" : 9.564,
"C" : 8.297,
"D" : 3.887,
"E" : 4.317,
"H" : 6.018,
"K" : 10.517,
"R" : 12.503,
"Y" : 10.071,
"Cterm" : 2.383}
"""pKa of important amino acid to compute pI (from IPC_peptide. See http://isoelectric.org/theory.html for details)."""
def handle_errors(message="", err=1, error_type=""):
"""Custom handling of errors and warnings.
:param message: error message to print
:param err: Type of message
:param error_type: header of error to print
:type message: str
:type err: int
:type error_type: str
*Type of message* is:\n
- **0** for critical error (exit)\n
- **1** for warning (no exit, default)\n
- **2** for print in stderr
"""
if err == 0:
print(error_type + "Error: " + message, file=sys.stderr)
sys.exit(1)
elif err == 2:
print(error_type + message, file=sys.stderr)
else:
print(error_type + "Warning: " + message, file=sys.stderr)
def get_header(fmt="fasta"):
"""Construct a header for output file in `csv` or `tsv`.
:param fmt: format of header
:type fmt: str
:return: formatted header
:rtype: str or None
Informations on the header are:\n
Original_header No_pep Enzyme Cleav_pos Pep_size Pep_mass pI Seq\n
No header for `fasta` or other format.
"""
ret = None
if fmt == "csv":
separator = ","
elif fmt == "tsv":
separator = "\t"
if fmt == "csv" or fmt == "tsv":
ret = "Original_header" + separator + "No_peptide" + separator + \
"Enzyme" + separator + "Cleaving_pos" + separator + \
"Peptide_size" + separator + "Peptide_mass" + separator + "pI" +\
separator + "Sequence"
return ret
def output_results(output_file, all_seq_digested, fmt, quiet, verbose):
"""Output results of digestion in file and optionally in `stdout`.
:param output_file: the file where to print results, if exist
:param all_seq_digested: results of digestions
:param fmt: output format (`csv`, `tsv` or `fasta`)
:param quiet: quiet mode, no `stdout` message
:param verbose: verbosity level
:type output_file: str
:type all_seq_digested: list(list(:py:class:`~rpg.digest.ResultOneDigestion`))
:type fmt: str
:type quiet: bool
:type verbose: int
"""
# Not output file
if not output_file:
# Header
header = get_header(fmt)
# If we have a header to print (csv/tsv)
if header:
# Stdout if small verbose
if verbose < 2 and not quiet:
print(header)
# Print all peptides
for one_seq in all_seq_digested: # list of list of ResultOneDig
# For all ResultOneDigestion
for one_enz_res in one_seq:
# Print on stdout
if verbose >= 2:
# Big verbose
print(one_enz_res.get_more_info())
if header:
print(header)
# Default stdout
if not quiet:
print(format(one_enz_res, fmt), end='')
# Output file exist
else:
try:
with open(output_file, 'w') as outfile:
# Header
header = get_header(fmt)
# If we have a header to print (csv/tsv)
if header:
# Print it in file
outfile.write(header + "\n")
# Stdout if small verbose
if verbose < 2 and not quiet:
print(header)
# Print all peptides
for one_seq in all_seq_digested: # list of list of ResultOneDi
# For all ResultOneDigestion
for one_enz_res in one_seq:
# Print results in file
outfile.write(format(one_enz_res, fmt))
# Print on stdout
if verbose >= 2:
# Big verbose
print(one_enz_res.get_more_info())
if header:
print(header)
# Default stdout
if not quiet:
print(format(one_enz_res, fmt), end='')
except IOError:
handle_errors(output_file + " can't be open in 'w' mode", 0,
"File ")
def next_read(file, offset_start, offset_end):
""" Return each sequence between offsets range of a file
as a tuple (header, seq) using a generator.
Can be fasta or fastq, gzipped or not.
:param file: fasta/fastq file to read
:param offset_start: offset in the file from where to read
:param offset_end: offset in the file until where to read
:type file: str
:type offset_start: int
:type offset_end: int
"""
# Is it a GZIP file?
test_file = open(str(file), "rb")
# Get the first values
magic = test_file.read(2)
# Close the file
test_file.close()
# Open the file, GZIP or not
with (gzip.open(file, "rb") if magic == b"\x1f\x8b"
else open(file, "rb")) as in_file:
first_line = in_file.readline().decode('utf-8')
# FASTQ file
if first_line.startswith("@"):
# Go to starting offset
in_file.seek(offset_start)
# Set current offset
beg_line_offset = offset_start
# Read each line from this point
for line in in_file:
# Consider this line as a header
header = line.decode('utf-8').strip()
# It is a proper fastq header
if header.startswith("@"):
# The beginning of header is in the offset range
if beg_line_offset < offset_end:
# Get the sequence
sequence = in_file.readline().decode('utf-8').strip()
# Skip the two next lines
in_file.readline()
in_file.readline()
# Return header and sequence and wait for the next one
yield (header, sequence.upper())
# Out of offset, stop this loop
else:
break
# Current offset
beg_line_offset = in_file.tell()
# (multi?)FASTA file
elif first_line.startswith(">"):
# Go to starting offset
in_file.seek(offset_start)
# Set current offset
beg_line_offset = offset_start
# Read each line from this point
for line in in_file:
# Consider this line as a header
header = line.decode('utf-8').strip()
# It is a proper fasta header
if header.startswith(">"):
# The beginning of header is in the offset range
if beg_line_offset < offset_end:
# Get the sequence
sequence = in_file.readline().decode('utf-8').strip()
# Get current offset
current_offset = in_file.tell()
# Get next line
next_l = in_file.readline().decode('utf-8').strip()
# While this next line is not a fasta header...
while next_l and not next_l.startswith(">"):
# Add this to the Sequence
sequence += next_l
# Get current offset
current_offset = in_file.tell()
# Get next line
next_l = in_file.readline().decode('utf-8').strip()
# Next line is a fasta header, go back to its beginning
in_file.seek(current_offset)
# Return header and sequence and wait for the next one
yield (header, sequence.upper())
# Out of offset, stop this loop
else:
break
# Current offset
beg_line_offset = in_file.tell()
# Not a valid file
else:
# Stop the generator with the error to show
raise ValueError("input file format not recognized (%s)"\
"." % first_line[0])