diff --git a/rpg/RapidPeptidesGenerator.py b/rpg/RapidPeptidesGenerator.py
index de07794dd5c93bcf9b5d395836a8dee777384ebc..378b897f004397f3fc5f194fd0c8ef6a1c7a1942 100644
--- a/rpg/RapidPeptidesGenerator.py
+++ b/rpg/RapidPeptidesGenerator.py
@@ -163,8 +163,6 @@ def get_enzymes_to_use(mode, id_enz_selected, miscleavage):
:return: list of enzyme's id with associated miscleavage values
:rtype: list(int)
-
- .. warning:: Not tested
"""
# Get the correct Enzymes inputed
@@ -217,10 +215,7 @@ def get_enzymes_to_use(mode, id_enz_selected, miscleavage):
return enzymes_to_use
# Not tested
def main():
- """Launcher of RapidPeptidesGenerator
-
- .. warning:: Not tested
- """
+ """Launcher of RapidPeptidesGenerator"""
parser = argparse.ArgumentParser(description="This software takes protein "
"sequences as input (-i optio"
"n). All sequences will be cl"
@@ -285,6 +280,8 @@ def main():
"to output result peptides.")
group_output.add_argument("-r", "--randomname", action="store_true",
help="Random (not used) output file name")
+ parser.add_argument("-c", "--processes", type=int, metavar="", default=1,
+ help="Number of parallel processes to use (default: 1)")
group_verbose = parser.add_mutually_exclusive_group()
group_verbose.add_argument("-q", "--quiet", action="store_true",
help="No standard output, only error(s)")
@@ -322,6 +319,10 @@ def main():
args.quiet = 1
args.verbose = 0
+ # Be sure to have at least 1 process
+ if args.processes <= 0:
+ parser.error("argument -c/--processes should be greater than 0")
+
# input data
input_data = None
input_type = None
@@ -394,13 +395,13 @@ def main():
# Make the actual digestion of input data
results_digestion = digest.digest_from_input(input_data, input_type,
- enzymes_to_use, mode, aa_pka)
+ enzymes_to_use, mode, aa_pka,
+ args.processes)
# Output results
core.output_results(output_file, results_digestion, args.fmt, args.quiet,
args.verbose)
-
### Let'z go ###
if __name__ == '__main__':
main()
diff --git a/rpg/core.py b/rpg/core.py
index 06509f7333365df7d5fcf4357a85970dfdd74c48..d9f55858a17474e177aafc7e178a757c4b1208e7 100644
--- a/rpg/core.py
+++ b/rpg/core.py
@@ -24,6 +24,7 @@
"""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",
@@ -204,3 +205,96 @@ def output_results(output_file, all_seq_digested, fmt, quiet, verbose):
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(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])