Parse command string

misopy/cluster_utils.py

@@ -228,6 +228,7 @@ def launch_job(cluster_cmd, cmd_name):
     # submission system
     output = proc.communicate()
     job_id = None
+    cmd_name = cmd_name.split(" ")[0]
     if cmd_name == "qsub":
         if "." in output[0][:-1] and ">" not in output[0]:
             job_id = int(output[0].split(".")[0])
@@ -281,6 +282,7 @@ def wait_on_jobs(job_ids, cluster_cmd,
     """
     if len(job_ids) == 0:
         return
+    cluster_cmd = cluster_cmd.split(" ")[0]
     if cluster_cmd not in supported_cmds:
         return 
     num_jobs = len(job_ids)

misopy/run_events_analysis.py

@@ -168,28 +168,28 @@ def check_gff_and_bam(gff_dir, bam_filename, main_logger,
     if bam_starts_with_chr != gff_starts_with_chr:
         mismatch_found = True
     if mismatch_found:
-        miso_logger.warning("It looks like your GFF annotation file and your BAM " \
+        main_logger.warning("It looks like your GFF annotation file and your BAM " \
                             "file might not have matching headers (chromosome names.) " \
                             "If this is the case, your run will fail as no reads from " \
                             "the BAM could be matched up with your annotation.")
-        miso_logger.warning("Please see:\n\t%s\n for more information." %(manual_url))
+        main_logger.warning("Please see:\n\t%s\n for more information." %(manual_url))
         # Default: assume BAM starts with chr headers
         chr_containing = "BAM file (%s)" %(bam_filename)
         not_chr_containing = "GFF annotation (%s)" %(gff_dir)
         if not bam_starts_with_chr:
             # BAM does not start with chr, GFF does
             chr_containing, not_chr_containing = \
                 not_chr_containing, chr_containing
-        miso_logger.warning("It looks like your %s contains \'chr\' chromosomes (UCSC-style) " \
+        main_logger.warning("It looks like your %s contains \'chr\' chromosomes (UCSC-style) " \
                             "while your %s does not." %(chr_containing,
                                                         not_chr_containing))
-        miso_logger.warning("The first few BAM chromosomes were: %s" \
+        main_logger.warning("The first few BAM chromosomes were: %s" \
                             %(",".join(bam_chroms.keys())))
         print "BAM references: "
         print bam_file.references
-        miso_logger.warning("The first few GFF chromosomes were: %s" \
+        main_logger.warning("The first few GFF chromosomes were: %s" \
                             %(",".join(gff_chroms.keys())))
-        miso_logger.warning("Run is likely to fail or produce empty output. Proceeding " \
+        main_logger.warning("Run is likely to fail or produce empty output. Proceeding " \
                             "anyway...")
         time.sleep(15)
 

misopy/samples_utils.py

@@ -303,7 +303,7 @@ def summarize_sampler_results(samples_dir, summary_filename,
         counts_info = samples_results[5]
         shape_len = len(shape(samples))
         if shape_len < 2:
-            print "WARNING: Skipping %s -- mishaped file" %(samples_filename)
+            print "WARNING: Skipping %s -- mishaped file" %(event_name)
             continue
         num_samples, num_isoforms = shape(samples)
         output_fields = format_credible_intervals(event_name, samples)

setup.py

@@ -1,4 +1,4 @@
-from distutils.core import setup, Extension
+from setuptools import setup, Extension
 import distutils.ccompiler
 import glob
 import os