Revert "move check_fastq to ubiquerg"

This reverts commit 5612d74.

pypiper/ngstk.py

@@ -4,10 +4,10 @@
 import re
 import subprocess
 import errno
+from attmap import AttMapEcho
 from .exceptions import UnsupportedFiletypeException
 from .utils import is_fastq, is_gzipped_fastq, is_sam_or_bam
-from attmap import AttMapEcho
-from ubiquerg import check_fastq
+
 
 
 class NGSTk(AttMapEcho):
@@ -457,6 +457,65 @@ def input_to_fastq(
         return [cmd, fastq_prefix, output_file]
 
 
+    def check_fastq(self, input_files, output_files, paired_end):
+        """
+        Returns a follow sanity-check function to be run after a fastq conversion.
+        Run following a command that will produce the fastq files.
+
+        This function will make sure any input files have the same number of reads as the
+        output files.
+        """
+
+        # Define a temporary function which we will return, to be called by the
+        # pipeline.
+        # Must define default parameters here based on the parameters passed in. This locks
+        # these values in place, so that the variables will be defined when this function
+        # is called without parameters as a follow function by pm.run.
+
+        # This is AFTER merge, so if there are multiple files it means the
+        # files were split into read1/read2; therefore I must divide by number
+        # of files for final reads.
+        def temp_func(input_files=input_files, output_files=output_files,
+                      paired_end=paired_end):
+
+            if type(input_files) != list:
+                input_files = [input_files]
+            if type(output_files) != list:
+                output_files = [output_files]
+
+            print(input_files)
+            print(output_files)
+
+            n_input_files = len(filter(bool, input_files))
+
+            total_reads = sum([int(self.count_reads(input_file, paired_end))
+                               for input_file in input_files])
+            raw_reads = total_reads / n_input_files
+            self.pm.report_result("Raw_reads", str(raw_reads))
+
+            total_fastq_reads = sum(
+                [int(self.count_reads(output_file, paired_end))
+                 for output_file in output_files])
+            fastq_reads = total_fastq_reads / n_input_files
+
+            self.pm.report_result("Fastq_reads", fastq_reads)
+            input_ext = self.get_input_ext(input_files[0])
+            # We can only assess pass filter reads in bam files with flags.
+            if input_ext == ".bam":
+                num_failed_filter = sum(
+                    [int(self.count_fail_reads(f, paired_end))
+                     for f in input_files])
+                pf_reads = int(raw_reads) - num_failed_filter
+                self.pm.report_result("PF_reads", str(pf_reads))
+            if fastq_reads != int(raw_reads):
+                raise Exception("Fastq conversion error? Number of reads "
+                                "doesn't match unaligned bam")
+
+            return fastq_reads
+
+        return temp_func
+
+
     def check_trim(self, trimmed_fastq, paired_end, trimmed_fastq_R2=None, fastqc_folder=None):
         """
         Build function to evaluate read trimming, and optionally run fastqc.