Make and making executable

Makefile

@@ -3,6 +3,10 @@
 # Even if you never use these commands here, they provide a good example of ways to use the python
 #  scripts included in this project.
 
+# --- put test first, so `make` runs this and exits
+test:
+	python bin/test_requirements.py
+
 #---------------Bio 496, Project ---------------
 
 prot_and_dna: diamond_db bowtie2_index
@@ -119,9 +123,6 @@ protein_hits:
 
 
 
-test:
-	python bin/test_requirements.py
-
 demo: clean
 	#Download 100 sample reads
 	fastq-dump --outdir Input/SRA_datasets/ -X 100000 --skip-technical --readids  --dumpbase --clip SRR3403834

bin/bam_stats.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import argparse
 import pysam
 import os

bin/conserved_regions_csv.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3'
+
 import os
 import sys
 import argparse

bin/coverage_depth_csv.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import argparse
 import os
@@ -92,4 +94,4 @@ def condense_list(big_list, condense_size=100):
             outfile.write(','.join(x) + '\n')
         with open(args.output + '.row_labels.txt', 'a') as outfile:
             outfile.write(args.output + '\n')
-    sys.exit(0)
+    sys.exit(0)

bin/csv_to_heatmap.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import numpy as np
 from numpy import vstack  # VSTACK((a,b)) stacks B on TOP of A
 import seaborn as sns; sns.set()

bin/genome_coverage.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import pysam
 import argparse

bin/hits_by_organism.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import os
 import argparse
 import sys
@@ -30,4 +32,4 @@
             organisms[line[1]] = organisms.get(line[1], 0) + int(line[2])
     with open(args.output, 'w') as outfile:
         for k in sorted(organisms, key=organisms.get, reverse=True):
-            outfile.write(delim.join([str(k),str(organisms[k])]) + '\n')
+            outfile.write(delim.join([str(k),str(organisms[k])]) + '\n')

bin/m8_hits.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import os
 import argparse

bin/m8_reader.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 """
 M8_Reader! This package is designed to read .m8 files produced by diamond blastx, specifically with a command
 to include the actual DNA sequence matched to the protein. This information is not provided by default when using

bin/m8_stats.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import os
 import argparse
@@ -37,4 +39,4 @@
             line = [str(x) for x in line]
             outfile.write('\t'.join(line))
             outfile.write('\n')
-        outfile.close()
+        outfile.close()

bin/pbs_aggregator.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import os
 import argparse

bin/rapsearch_fastq_fixer.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import os
 import sys
 import argparse
@@ -45,4 +47,4 @@
         ret_code = subprocess.call(mv_command)
         if ret_code != 0:
             sys.stderr.write("Error running command \"{}\"\n".format(' '.join(mv_command)))
-            sys.exit(1)
+            sys.exit(1)

bin/remove_short_reads.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import os
 import argparse

bin/sam_hits.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import os
 import argparse
@@ -16,4 +18,4 @@
         sys.exit(1)
 
     samfiles = Sam_Reader(args.input)
-    samfiles.hits(write_file=args.output)
+    samfiles.hits(write_file=args.output)

bin/sam_stats.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import os
 import argparse

bin/single_pbs.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import os
 import argparse
@@ -17,4 +19,4 @@
         sys.exit(1)
 
     data = Sam_Reader(args.input)
-    data.per_base_stats(write_file=args.output)
+    data.per_base_stats(write_file=args.output)

bin/split_bam.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import argparse
 import pysam
@@ -87,4 +89,4 @@ def split_sam(infile, minimum_match_length, out_directory):
     if not args.length:
         args.length = 0
 
-    split_sam(args.input, args.length, args.output)
+    split_sam(args.input, args.length, args.output)

bin/target_sites.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import argparse
 import sys
 import operator

bin/test_requirements.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import sys
 import subprocess
 

bin/xml_scrape.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import os
 import sys
 import argparse