producing sorted vcf output, by default to stdout

surpyvor/parse_arguments.py

@@ -13,8 +13,10 @@ def get_args():
                         version='surpyvor: {}, SURVIVOR {}'.format(
                             __version__, get_survivor_version()),
                         help="Print version and quit.")
+
     subparsers = parser.add_subparsers(dest='command',
                                        title='[sub-commands]')
+
     merge = subparsers.add_parser("merge",
                                   help="merging vcf files of SVs",
                                   formatter_class=ArgumentDefaultsHelpFormatter)
@@ -23,10 +25,10 @@ def get_args():
                            nargs='+',
                            required=True,
                            help="vcf files to merge")
-    merge_req.add_argument("-o", "--output",
-                           help="output file",
-                           required=True)
     merge_opt = merge.add_argument_group('optional arguments')
+    merge_opt.add_argument("-o", "--output",
+                           help="output file",
+                           default="stdout")
     merge_opt.add_argument("-d", "--distance",
                            type=int,
                            default=500,
@@ -51,6 +53,7 @@ def get_args():
                            action="store_true",
                            default=False,
                            help="Estimate distance between calls")
+
     highsens = subparsers.add_parser("highsens",
                                      help="get union of SV vcfs",
                                      formatter_class=ArgumentDefaultsHelpFormatter)
@@ -59,9 +62,11 @@ def get_args():
                               nargs='+',
                               required=True,
                               help="vcf files to merge")
-    highsens_req.add_argument("-o", "--output",
+    highsens_opt = highsens.add_argument_group('optional arguments')
+    highsens_opt.add_argument("-o", "--output",
                               help="output file",
-                              required=True)
+                              default="stdout")
+
     highconf = subparsers.add_parser("highconf",
                                      help="get intersection of SV vcfs",
                                      formatter_class=ArgumentDefaultsHelpFormatter)
@@ -70,9 +75,11 @@ def get_args():
                               nargs='+',
                               required=True,
                               help="vcf files to merge")
-    highconf_req.add_argument("-o", "--output",
+    highconf_opt = highconf.add_argument_group('optional arguments')
+    highconf_opt.add_argument("-o", "--output",
                               help="output file",
-                              required=True)
+                              default="stdout")
+
     prf = subparsers.add_parser('prf',
                                 help="calculate precision, recall and F-measure",
                                 formatter_class=ArgumentDefaultsHelpFormatter)
@@ -107,6 +114,7 @@ def get_args():
     prf_opt.add_argument("--matrix",
                          help="Make a confusion matrix.",
                          action="store_true")
+
     venn = subparsers.add_parser('venn',
                                  help="Make venn diagram for 2 or 3 SV vcf files",
                                  formatter_class=ArgumentDefaultsHelpFormatter)
@@ -134,6 +142,7 @@ def get_args():
     venn_opt.add_argument("--plotout",
                           help="Name of output plot",
                           default="venn.png")
+
     upset = subparsers.add_parser('upset',
                                   help="Make upset plot for multiple SV vcf files",
                                   formatter_class=ArgumentDefaultsHelpFormatter)

surpyvor/surpyvor.py

@@ -57,6 +57,7 @@ def sv_merge(samples, distance, callers, require_type, require_strand,
     -specify minimal size of SV event (minlength, int)
     """
     fhf, fofn_f = tempfile.mkstemp()
+    fhs, interm_out = tempfile.mkstemp(suffix=".vcf")
     with open(fofn_f, 'w') as fofn:
         for s in [utils.decompress(s) for s in samples]:
             fofn.write(s + "\n")
@@ -68,11 +69,13 @@ def sv_merge(samples, distance, callers, require_type, require_strand,
         str=1 if require_strand else -1,
         estm=1 if estimate_distance else -1,
         ml=minlength,
-        out=output)
+        out=interm_out)
     print("Executing SURVIVOR...", end="", flush=True, file=sys.stderr)
     subprocess.call(shlex.split(survivor_cmd), stdout=subprocess.DEVNULL)
     print("DONE", file=sys.stderr)
+    utils.vcf_sort(interm_out, output)
     os.close(fhf)
+    os.close(fhs)
 
 
 def default_merge(args, variants):
@@ -101,7 +104,7 @@ def precision_recall_fmeasure(args):
     print(f"Precision: {round(precision, ndigits=4)}")
     recall = tp / len(truth_set)
     print(f"Recall: {round(recall, ndigits=4)}")
-    fmeasure = 2*(precision*recall)/(precision + recall)
+    fmeasure = 2 * (precision * recall) / (precision + recall)
     print(f"F-measure: {round(fmeasure, ndigits=4)}")
     if args.bar:
         plots.bar_chart(vcf_out)

surpyvor/utils.py

@@ -1,6 +1,6 @@
 import os
 import sys
-import shutil
+from shutil import which
 import tempfile
 from cyvcf2 import VCF
 import subprocess
@@ -127,14 +127,19 @@ def decompress(vcf):
 
 
 def test_dependencies():
-    def which(exec):
-        return shutil.which(exec)
     for dependency in ['bcftools', 'bgzip', 'tabix', 'SURVIVOR']:
         if not which(dependency):
             sys.exit("ERROR: Could not find required executable '{}'.\n"
                      "Make sure it is installed and in $PATH".format(dependency))
 
 
+def vcf_sort(input, output):
+    if output in ["stdout", "-"]:
+        subprocess.call(shlex.split('bcftools sort {}'.format(input)))
+    else:
+        subprocess.call(shlex.split('bcftools sort {} -o {}'.format(input, output)))
+
+
 def confusion_matrix(vcff, names):
     """
     First level of the dict is the "first" call, second level is the "second" sample

surpyvor/version.py

@@ -1 +1 @@
-__version__ = "0.4.1"
+__version__ = "0.5.0"