# HG changeset patch
# User davidvanzessen
# Date 1499955879 14400
# Node ID b00c257f0a671629e2c7b94e403d6188c832105b
Uploaded
diff -r 000000000000 -r b00c257f0a67 imgt_locus_split.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/imgt_locus_split.py Thu Jul 13 10:24:39 2017 -0400
@@ -0,0 +1,138 @@
+import argparse
+import logging
+import os
+import re
+import shutil
+import sys
+import tarfile
+import tempfile
+import zipfile
+
+import magic
+
+imgt_file_regex = re.compile("^\d+_[^P]")
+
+
+def sniff_imgt_type(input_file):
+ m = magic.Magic()
+ file_type = m.from_file(input_file)
+ logging.debug("File type of {0} is {1}".format(input_file, file_type))
+ return file_type.split(" ")[0]
+
+
+def unpack_imgt_zip(input_file, output_dir):
+ imgt_type = sniff_imgt_type(input_file)
+ if imgt_type == "Zip":
+ with zipfile.ZipFile(input_file) as inf:
+ inf.extractall(output_dir)
+ elif imgt_type == "XZ":
+ with tarfile.open(input_file) as inf:
+ inf.extractall(output_dir)
+ else:
+ raise IOError("Unsuppported file type: {0}".format(imgt_type))
+ logging.debug("Extracted {0} to {1}".format(input_file, output_dir))
+ check = os.listdir(output_dir)
+ if len(check) == 1:
+ check = os.path.join(output_dir, check[0])
+ if os.path.isdir(check):
+ logging.info("{0} is an older IMGT zip, removing extra dir".format(input_file))
+ files = os.listdir(check)
+ for file in files:
+ new_file = os.path.join(output_dir, file)
+ file = os.path.join(check, file)
+ shutil.move(file, new_file)
+ shutil.rmtree(check)
+
+
+def filter_tabular_file(old_file, new_file, column, regex):
+ logging.debug("Filtering {0} with {1}".format(old_file, regex.pattern))
+ first = True
+ total = 0
+ remain = 0
+ with open(old_file, 'r') as of, open(new_file, 'w') as nf:
+ column_index = -1
+ for line in of:
+ splt = line.split("\t")
+ if first:
+ column_index = splt.index(column)
+ first = False
+ nf.write(line)
+ continue
+ total += 1
+ if len(splt) >= column_index and regex.search(splt[column_index]):
+ remain += 1
+ nf.write(line)
+ return total, remain
+
+
+def all_same_in_list(l):
+ return all(l[0] == x for x in l[1:])
+
+
+def filter_imgt_dir(imgt_dir, loci):
+ logging.info("Filtering {0} with {1}".format(imgt_dir, loci))
+ imgt_files = [f for f in os.listdir(imgt_dir) if imgt_file_regex.match(f)]
+ tmp_file = os.path.join(imgt_dir, "tmp.txt")
+ totals = []
+ remains = []
+ loci_regex = re.compile("|".join(loci))
+ for imgt_file in imgt_files:
+ imgt_file = os.path.join(imgt_dir, imgt_file)
+ total, remain = filter_tabular_file(imgt_file, tmp_file, "V-GENE and allele", loci_regex)
+ totals.append(total)
+ remains.append(remain)
+ logging.debug("{0} rows, {1} after filtering".format(total, remain))
+ shutil.move(tmp_file, imgt_file)
+ if not (all_same_in_list(totals) and all_same_in_list(remains)):
+ logging.warning("Not all files had the same number of sequences remaining for {0}: {1}".format(imgt_dir, remains))
+ return totals[0], remains[0]
+
+
+def make_new_xz_file(input_dir, output_file):
+ logging.info("Creating new IMGT zip for {0} at {1}".format(input_dir, output_file))
+ imgt_files = [f for f in os.listdir(input_dir)]
+ with tarfile.open(output_file, 'w:xz') as out:
+ for imgt_file in imgt_files:
+ logging.debug("Writing {0} to new IMGT zip".format(imgt_file))
+ imgt_file = os.path.join(input_dir, imgt_file)
+ out.add(imgt_file, arcname=os.path.basename(imgt_file))
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument("-i", "--input", help="The input IMGT file", required=True)
+ parser.add_argument("-l", "--loci", help="The Loci to filter on", required=True)
+ parser.add_argument("-o", "--output", help="The output file for the new IMGT zip with just the filtered sequences", required=True)
+
+ logging.basicConfig(filename="./log.html", level=logging.DEBUG, format="%(asctime)s: %(message)s
",
+ datefmt='%Y/%m/%d %H:%M:%S')
+ logging.getLogger().addHandler(logging.StreamHandler(sys.stdout))
+ logging.info("Started IMGT locus split")
+
+ args = parser.parse_args()
+ input_file = args.input
+ loci = args.loci.split(",")
+ output_file = args.output
+
+ logging.debug("All Parameters:")
+ logging.debug("Input: {0}".format(input_file))
+ logging.debug("Loci: {0}".format(loci))
+ logging.debug("Output: {0}".format(output_file))
+
+ if len(loci) == 0:
+ raise Exception("No locus selected, nothing to do")
+
+ work_dir = tempfile.mkdtemp()
+ original_files_dir = os.path.join(work_dir, "original")
+ os.mkdir(original_files_dir)
+
+ unpack_imgt_zip(input_file, original_files_dir)
+
+ total, remain = filter_imgt_dir(original_files_dir, loci)
+ logging.info("{0}\t{1}".format(total, remain))
+
+ make_new_xz_file(original_files_dir, output_file)
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r b00c257f0a67 imgt_locus_split.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/imgt_locus_split.xml Thu Jul 13 10:24:39 2017 -0400
@@ -0,0 +1,34 @@
+
+
+ python-magic
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1093/nar/gku1056
+
+
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