Merge pull request #33 from snayfach/dev

Print full command and database path with parameters

scripts/build_midas_db.py

@@ -77,7 +77,6 @@ def check_args(args):
 
 
 if __name__ == "__main__":
-
 	args = fetch_arguments()
 	utility.add_executables(args)
 	check_args(args)

scripts/call_consensus.py

@@ -100,6 +100,7 @@ def print_args(args):
 	lines.append("  site_maf: %s" % args['site_maf'])
 	lines.append("  site_ratio: %s" % args['site_ratio'])
 	lines.append("  max_sites: %s" % args['max_sites'])
+	lines.append("================================")
 	sys.stdout.write('\n'.join(lines)+'\n')
 
 def check_args(args):

scripts/merge_midas.py

@@ -268,17 +268,22 @@ def print_arguments(program, args):
 
 def print_species_arguments(args):
 	print ("===========Parameters===========")
+	print ("Command: %s" % ' '.join(sys.argv))
 	print ("Script: merge_midas.py species")
+	print ("Database: %s" % args['db'])
 	print ("Input: %s" % args['input'])
 	print ("Input type: %s" % args['intype'])
 	print ("Output directory: %s" % args['outdir'])
 	print ("Minimum coverage for estimating prevalence: %s" % args['min_cov'])
 	if args['max_samples']: print ("Keep <= %s samples" % args['max_samples'])
+	print ("===============================")
 	print ("")
 
 def print_genes_arguments(args):
 	print ("===========Parameters===========")
+	print ("Command: %s" % ' '.join(sys.argv))
 	print ("Script: merge_midas.py genes")
+	print ("Database: %s" % args['db'])
 	print ("Input: %s" % args['input'])
 	print ("Input type: %s" % args['intype'])
 	print ("Output directory: %s" % args['outdir'])
@@ -292,11 +297,14 @@ def print_genes_arguments(args):
 	print ("Gene quantification criterea:")
 	print ("  present (1): genes with copy number >= %s" % args['min_copy'])
 	print ("  absent (0): genes with copy number < %s" % args['min_copy'])
+	print ("===============================")
 	print ("")
 
 def print_snps_arguments(args):
 	print ("===========Parameters===========")
+	print ("Command: %s" % ' '.join(sys.argv))
 	print ("Script: merge_midas.py snps")
+	print ("Database: %s" % args['db'])
 	print ("Input: %s" % args['input'])
 	print ("Input type: %s" % args['intype'])
 	print ("Output directory: %s" % args['outdir'])
@@ -312,6 +320,7 @@ def print_snps_arguments(args):
 	print ("  keep sites covered by >= %s reads across >= %s percent of samples" % (args['site_depth'], 100*args['site_prev']))
 	if args['max_sites'] != float('Inf'): print ("  keep <= %s sites" % (args['max_sites']))
 	print ("Number of CPUs to use: %s" % args['threads'])
+	print ("===============================")
 	print ("")
 
 def run_program(program, args):

scripts/run_midas.py

@@ -140,17 +140,20 @@ def species_arguments():
 def print_species_arguments(args):
 	lines = []
 	lines.append("===========Parameters===========")
+	lines.append("Command: %s" % ' '.join(sys.argv))
 	lines.append("Script: run_midas.py species")
+	lines.append("Database: %s" % args['db'])
 	lines.append("Output directory: %s" % args['outdir'])
 	lines.append("Input reads (1st mate): %s" % args['m1'])
 	lines.append("Input reads (2nd mate): %s" % args['m2'])
 	lines.append("Remove temporary files: %s" % args['remove_temp'])
 	lines.append("Word size for database search: %s" % args['word_size'])
 	if args['mapid']: lines.append("Minimum mapping identity: %s" % args['mapid'])
-	lines.append("Minimum alignment coverage: %s" % args['aln_cov'])
+	lines.append("Minimum mapping alignment coverage: %s" % args['aln_cov'])
 	lines.append("Number of reads to use from input: %s" % (args['max_reads'] if args['max_reads'] else 'use all'))
 	if args['read_length']: lines.append("Trim reads to %s-bp and discard reads with length < %s-bp" % (args['read_length'], args['read_length']))
 	lines.append("Number of threads for database search: %s" % args['threads'])
+	lines.append("================================")
 	args['log'].write('\n'.join(lines)+'\n')
 	sys.stdout.write('\n'.join(lines)+'\n')
 
@@ -267,7 +270,9 @@ def gene_arguments():
 def print_gene_arguments(args):
 	lines = []
 	lines.append("===========Parameters===========")
+	lines.append("Command: %s" % ' '.join(sys.argv))
 	lines.append("Script: run_midas.py genes")
+	lines.append("Database: %s" % args['db'])
 	lines.append("Output directory: %s" % args['outdir'])
 	lines.append("Remove temporary files: %s" % args['remove_temp'])
 	lines.append("Pipeline options:")
@@ -299,6 +304,7 @@ def print_gene_arguments(args):
 		lines.append("  minimum read quality score: %s" % args['readq'])
 		lines.append("  minimum mapping quality score: %s" % args['mapq'])
 		lines.append("  trim %s base-pairs from read-tails" % args['trim'])
+	lines.append("================================")
 	args['log'].write('\n'.join(lines)+'\n')
 	sys.stdout.write('\n'.join(lines)+'\n')
 
@@ -385,7 +391,9 @@ def snp_arguments():
 def print_snp_arguments(args):
 	lines = []
 	lines.append("===========Parameters===========")
+	lines.append("Command: %s" % ' '.join(sys.argv))
 	lines.append("Script: run_midas.py snps")
+	lines.append("Database: %s" % args['db'])
 	lines.append("Output directory: %s" % args['outdir'])
 	lines.append("Remove temporary files: %s" % args['remove_temp'])
 	lines.append("Pipeline options:")
@@ -420,6 +428,7 @@ def print_snp_arguments(args):
 		if args['discard']: lines.append("  discard discordant read-pairs")
 		if args['baq']: lines.append("  enable BAQ (per-base alignment quality)")
 		if args['adjust_mq']: lines.append("  adjust MAPQ")
+	lines.append("================================")
 	args['log'].write('\n'.join(lines)+'\n')
 	sys.stdout.write('\n'.join(lines)+'\n')
 

scripts/snp_diversity.py

@@ -110,6 +110,7 @@ def format_site_type(args):
 def print_args(args):
 	lines = []
 	lines.append("===========Parameters===========")
+	lines.append("Command: %s" % ' '.join(sys.argv))
 	lines.append("Script: snp_diversity.py")
 	lines.append("Input directory: %s" % args['indir'])
 	lines.append("Output file: %s" % args['out'])
@@ -135,6 +136,7 @@ def print_args(args):
 	lines.append("  site_ratio: %s" % args['site_ratio'])
 	lines.append("  site_freq: %s" % args['site_freq'])
 	lines.append("  max_sites: %s" % args['max_sites'])
+	print ("===============================")
 	sys.stdout.write('\n'.join(lines)+'\n')
 
 def check_args(args):