Parse the --readTypes option

Author: arteymix

rnaseq_pipeline/sources/sra.py

@@ -134,8 +134,12 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]:
         if loader == 'fastq-load.py':
             # parse options...
             # TODO: use argparse or something safer
+            fastq_load_read_types = None
             fastq_load_files = []
             if options:
+                if '--readTypes' in options and options['--readTypes'] is not None:
+                    fastq_load_read_types = list(str(options['--readTypes']))
+                    logger.warning(fastq_load_read_types)
                 opts = ['--read1PairFiles',
                         '--read2PairFiles',
                         '--read3PairFiles',
@@ -149,6 +153,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]:
                 issues |= SraRunIssue.NO_FASTQ_LOAD_OPTIONS
         else:
             issues |= SraRunIssue.NO_FASTQ_LOAD
+            fastq_load_read_types = None
             fastq_load_files = None
 
         statistics = run.find('Statistics')