Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow

[htsworkflow.git] / htsworkflow / pipelines / desplit_fastq.py

diff --git a/htsworkflow/pipelines/desplit_fastq.py b/htsworkflow/pipelines/desplit_fastq.py
new file mode 100644 (file)
index 0000000..0624aaa
--- /dev/null
+++ b/htsworkflow/pipelines/desplit_fastq.py
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+"""Write fastq data from multiple compressed files into a single file
+"""
+
+from glob import glob
+import os
+from optparse import OptionParser
+import sys
+
+from htsworkflow.version import version
+from htsworkflow.util.opener import autoopen
+from htsworkflow.util.conversion import parse_slice
+
+SEQ_HEADER = 0
+SEQUENCE = 1
+QUAL_HEADER = 2
+QUALITY = 3
+INVALID = -1
+
+
+def main(cmdline=None):
+    """Command line driver: [None, 'option', '*.fastq.bz2']
+    """
+    parser = make_parser()
+    opts, args = parser.parse_args(cmdline)
+
+    if opts.version:
+        print (version())
+        return 0
+
+    if opts.output is not None:
+        output = open(opts.output, 'w')
+    else:
+        output = sys.stdout
+
+    desplitter = DesplitFastq(file_generator(args), output)
+    desplitter.trim = parse_slice(opts.slice)
+    desplitter.run()
+
+    return 0
+
+
+def make_parser():
+    """Generate an option parser for above main function"""
+
+    usage = '%prog: [options] *.fastq.gz'
+    parser = OptionParser(usage)
+
+    parser.add_option('-o', '--output', default=None,
+                      help='output fastq file')
+    parser.add_option('-s', '--slice',
+                      help="specify python slice, e.g. 0:75, 0:-1",
+                      default=None)
+    parser.add_option("--version", default=False, action="store_true",
+                      help="report software version")
+    return parser
+
+
+def file_generator(pattern_list):
+    """Given a list of glob patterns return decompressed streams
+    """
+    for pattern in pattern_list:
+        for filename in glob(pattern):
+            yield autoopen(filename, 'r')
+
+
+class DesplitFastq(object):
+    """Merge multiple fastq files into a single file"""
+    def __init__(self, sources, destination):
+        self.sources = sources
+        self.destination = destination
+
+        self.making_fastq = True
+        self.trim = slice(None)
+
+    def run(self):
+        """Do the conversion
+
+        This is here so we can run via threading/multiprocessing APIs
+        """
+        state = SEQ_HEADER
+        for stream in self.sources:
+            for line in stream:
+                line = line.rstrip()
+                if state == SEQ_HEADER:
+                    self.destination.write(line)
+                    state = SEQUENCE
+                elif state == SEQUENCE:
+                    self.destination.write(line[self.trim])
+                    state = QUAL_HEADER
+                elif state == QUAL_HEADER:
+                    self.destination.write(line)
+                    state = QUALITY
+                elif state == QUALITY:
+                    self.destination.write(line[self.trim])
+                    state = SEQ_HEADER
+                self.destination.write(os.linesep)
+
+
+if __name__ == "__main__":
+    main()