Script to extract reads from bam from bed regions.

libhts/__init__.py

 __copyright__ = "Copyright (C) 2020 Blaise Li"
 __licence__ = "GNU GPLv3"
-__version__ = 0.3
+__version__ = 0.4
 from .libhts import (
     aligner2min_mapq,
     gtf_2_genes_exon_lengths,

requirements.txt

 Cython
+libbamutils @ git+https://gitlab.pasteur.fr/bli/libbamutils.git@66879fb7e917dfa00e13da230310bb3b257766db
 libworkflows @ git+https://gitlab.pasteur.fr/bli/libworkflows.git@b29b854ff1db6c87386007808286207b8af11b9d
 matplotlib
 networkx

scripts/bed_bam2fq.py

+#!/usr/bin/env python3
+# Copyright (C) 2020 Blaise Li
+#
+# This program 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
+# (at your option) any later version.
+#
+# This program 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 this program.  If not, see <https://www.gnu.org/licenses/>.
+"""Extracts the fastq reads from a bam file
+corresponding to the annotations provided in a bed file.
+"""
+
+from argparse import (
+    ArgumentParser,
+    ArgumentDefaultsHelpFormatter)
+import sys
+
+from libbamutils import BamFile
+
+
+def main():
+    """Run the command-line script."""
+    parser = ArgumentParser(
+        description=__doc__,
+        formatter_class=ArgumentDefaultsHelpFormatter)
+    parser.add_argument(
+        "-b", "--bedfile",
+        required=True,
+        help="Input bed file.")
+    parser.add_argument(
+        "-a", "--bamfile",
+        required=True,
+        help="Input bam file.")
+    args = parser.parse_args()
+
+    bamfile = BamFile(args.bamfile)
+    for fastq in bamfile.bed_to_fastq(args.bedfile):
+        print(fastq, end="")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

setup.py

@@ -34,9 +34,11 @@ setup(
     packages=find_packages(),
     scripts=[
         "scripts/bam2bigwig.sh", "scripts/sam2indexedbam.sh",
+        "scripts/bed_bam2fq.py",
         "scripts/copypaste_bigwig_regions.py",
         "scripts/extract_annot_start.py"],
     install_requires=[
+        "libbamutils @ git+https://gitlab.pasteur.fr/bli/libbamutils.git@66879fb7e917dfa00e13da230310bb3b257766db",
         #"libworkflows @ git+https://gitlab+deploy-token-31:isEzpsgbNf2sJMdUDy2g@gitlab.pasteur.fr/bli/libworkflows.git@744dd79b579577cb6e131653260d7990946be3ad#egg=libworkflows-0.1",
         #"libworkflows @ git+https://gitlab+deploy-token-31:isEzpsgbNf2sJMdUDy2g@gitlab.pasteur.fr/bli/libworkflows.git#egg=libworkflows-0.1",
         #"libworkflows @ git+https://gitlab+deploy-token-31:isEzpsgbNf2sJMdUDy2g@gitlab.pasteur.fr/bli/libworkflows.git",