Combine runSubprocessN into a single function

.gitignore

@@ -5,3 +5,5 @@
 dockerbuild/
 sample_data/
 .DS_Store
+funannotate.egg-info
+.idea

funannotate/annotate.py

@@ -34,7 +34,7 @@ def MEROPSBlast(input, cpus, evalue, tmpdir, output, diamond=True):
         cmd = ['blastp', '-db', blastdb, '-outfmt', '5', '-out', blast_tmp, '-num_threads', str(cpus),
                '-max_target_seqs', '1', '-evalue', str(evalue), '-query', input]
     if not os.path.isfile(blast_tmp):
-        lib.runSubprocess4(cmd, '.', lib.log)
+        lib.runSubprocess(cmd, '.', lib.log, only_failed=True)
     # parse results
     with open(output, 'w') as out:
         with open(blast_tmp, 'r') as results:
@@ -64,7 +64,7 @@ def SwissProtBlast(input, cpus, evalue, tmpdir, GeneDict, diamond=True):
                '-num_threads', str(cpus), '-max_target_seqs', '1',
                '-evalue', str(evalue), '-query', input]
     if not lib.checkannotations(blast_tmp):
-        lib.runSubprocess4(cmd, '.', lib.log)
+        lib.runSubprocess(cmd, '.', lib.log, only_failed=True)
     # parse results
     counter = 0
     total = 0
@@ -1443,7 +1443,7 @@ def __init__(self, prog):
                '--db', mibig_db, '--max-hsps', '1',
                '--evalue', '0.001', '--max-target-seqs', '1',
                '--outfmt', '6']
-        lib.runSubprocess4(cmd, '.', lib.log)
+        lib.runSubprocess(cmd, '.', lib.log, only_failed=True)
         # now parse blast results to get {qseqid: hit}
         MIBiGBlast = {}
         with open(mibig_blast, 'r') as input:

funannotate/aux_scripts/augustus_parallel.py

@@ -97,7 +97,7 @@ def runAugustus(Input):
         core_cmd.insert(2, '--predictionStart='+str(start))
         core_cmd.insert(3, '--predictionEnd='+str(end))
     # try using library module
-    lib.runSubprocess2(core_cmd, '.', lib.log, aug_out)
+    lib.runSubprocess(core_cmd, '.', lib.log, capture_output=aug_out)
 
 
 log_name = args.logfile

funannotate/aux_scripts/funannotate-p2g.py

@@ -109,13 +109,13 @@ def runDiamond(input, query, cpus, output, premade_db=None):
     if premade_db is None:
         db_cmd = ['diamond', 'makedb', '--threads',
                   str(cpus), '--in', query, '--db', 'diamond']
-        lib.runSubprocess4(db_cmd, output, lib.log)
+        lib.runSubprocess(db_cmd, output, lib.log, only_failed=True)
     else:
         lib.log.debug('Using premade Diamond database: {}'.format(premade_db))
         os.symlink(os.path.abspath(premade_db),
                    os.path.join(output, 'diamond.dmnd'))
     # now run search
-    lib.runSubprocess4(cmd, output, lib.log)
+    lib.runSubprocess(cmd, output, lib.log, only_failed=True)
 
 
 def runtblastn(input, query, cpus, output, maxhits):

funannotate/aux_scripts/phobius-multiproc.py

@@ -51,7 +51,7 @@ def runPhobiusLocal(Input):
     base = base.split('.fa')[0]
     OUTPATH = os.path.join(TMPDIR, base+'.phobius')
     cmd = ['phobius.pl', '-short', Input]
-    lib.runSubprocess2(cmd, TMPDIR, lib.log, OUTPATH)
+    lib.runSubprocess(cmd, TMPDIR, lib.log, capture_output=OUTPATH)
 
 
 global parentdir

funannotate/aux_scripts/trinity.py

@@ -46,7 +46,7 @@ def runTrinityGG(genome, readTuple, longReads, shortBAM, output, args=False):
         lib.log.info("Building Hisat2 genome index")
         cmd = ['hisat2-build', '-p',
                str(args.cpus), genome, os.path.join(tmpdir, 'hisat2.genome')]
-        lib.runSubprocess4(cmd, '.', lib.log)
+        lib.runSubprocess(cmd, '.', lib.log, only_failed=True)
         # align reads using hisat2
         lib.log.info("Aligning reads to genome using Hisat2")
         # use bash wrapper for samtools piping for SAM -> BAM -> sortedBAM
@@ -96,7 +96,7 @@ def runTrinityGG(genome, readTuple, longReads, shortBAM, output, args=False):
     cmd = cmd + jaccard_clip
     if longReads and lib.checkannotations(longReads):
         cmd = cmd + ['--long_reads', os.path.realpath(longReads)]
-    lib.runSubprocess2(cmd, '.', lib.log, TrinityLog)
+    lib.runSubprocess(cmd, '.', lib.log, capture_output=TrinityLog)
     commands = os.path.join(tmpdir, 'trinity_gg', 'trinity_GG.cmds')
 
     # this will create all the Trinity commands, will now run these in parallel using multiprocessing
@@ -122,7 +122,7 @@ def runTrinityGG(genome, readTuple, longReads, shortBAM, output, args=False):
     # now grab them all using Trinity script
     cmd = ['perl', os.path.abspath(os.path.join(
         TRINITY, 'util', 'support_scripts', 'GG_partitioned_trinity_aggregator.pl')), 'Trinity_GG']
-    lib.runSubprocess5(cmd, '.', lib.log, outputfiles, output)
+    lib.runSubprocess(cmd, '.', lib.log, in_file=outputfiles, capture_output=output)
     lib.log.info('{:,} transcripts derived from Trinity'.format(
         lib.countfasta(output)))