[MRG] add sig cat --from-file (#1657)

* add sig cat --from-file

* improve output a bit

* add test for sig cat --from-file

src/sourmash/cli/sig/cat.py

@@ -6,7 +6,11 @@
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('cat')
-    subparser.add_argument('signatures', nargs='+')
+    subparser.add_argument('signatures', nargs='*')
+    subparser.add_argument(
+        '--from-file',
+        help='a text file containing a list of files to load signatures from'
+    )
     subparser.add_argument(
         '-q', '--quiet', action='store_true',
         help='suppress non-error output'

src/sourmash/sig/__main__.py

@@ -74,6 +74,11 @@ def cat(args):
     save_sigs = sourmash_args.SaveSignaturesToLocation(args.output)
     save_sigs.open()
 
+    if args.from_file:
+        more_files = sourmash_args.load_pathlist_from_file(args.from_file)
+        args.signatures = list(args.signatures)
+        args.signatures.extend(more_files)
+
     for sigfile in args.signatures:
         try:
             loader = sourmash_args.load_file_as_signatures(sigfile,

src/sourmash/sourmash_args.py

@@ -558,7 +558,7 @@ def short_notify(self, msg_template, *args, **kwargs):
         notify(msg, end=end)
 
     def notify(self, location):
-        self.short_notify(f"...reading from file '{location}'", end='\r')
+        self.short_notify(f"...{self.n_sig} sigs so far. Now reading from file '{location}'", end='\r')
 
     def start_file(self, location, loader):
         n_this = 0
@@ -581,7 +581,8 @@ def start_file(self, location, loader):
         finally:
             self.n_sig += n_this
 
-        self.short_notify(f"loaded {n_this} sigs from '{location}'")
+        self.short_notify(f"Loaded {n_this} sigs from '{location}'",
+                          end='\r')
 
 
 #

tests/test_cmd_signature.py

@@ -763,31 +763,13 @@ def test_sig_cat_2_out_inplace(c):
 
 
 @utils.in_tempdir
-def test_sig_cat_filelist(c):
+def test_sig_cat_3_filelist(c):
     # cat using a file list as input
     sig47 = utils.get_test_data('47.fa.sig')
-    # sig47list = list(load_signatures(sig47))
-    # print("sig47: ",sig47)
-    # print(type(sig47))
-    # print("length sig47: ",len(sig47list))
-    # print("\n")
-
     sig47abund = utils.get_test_data('track_abund/47.fa.sig')
-    # sig47abundlist = list(load_signatures(sig47abund))
-    # print("sig47abund: ",sig47abund)
-    # print(type(sig47abund))
-    # print("length sig47abund: ",len(sig47abundlist))
-    # print("\n")
-
     multisig = utils.get_test_data('47+63-multisig.sig')
-    # multisiglist = list(load_signatures(multisig))
-    # print("multisig: ",multisig)
-    # print(type(multisig))
-    # print("length multisig: ",len(multisiglist))
-    # print("\n")
 
     filelist = c.output("filelist")
-
     with open(filelist, 'w') as f:
         f.write("\n".join((sig47, sig47abund, multisig)))
 
@@ -814,16 +796,48 @@ def test_sig_cat_filelist(c):
     # sort the signatures by something deterministic and unique
     siglist.sort(key = lambda x: x.md5sum())
 
-    # print(len(siglist))
+    assert repr(siglist) == """[SourmashSignature('NC_009665.1 Shewanella baltica OS185, complete genome', 09a08691), SourmashSignature('NC_009665.1 Shewanella baltica OS185, complete genome', 09a08691), SourmashSignature('NC_011665.1 Shewanella baltica OS223 plasmid pS22303, complete sequence', 485c3377), SourmashSignature('NC_009665.1 Shewanella baltica OS185, complete genome', 57e2b22f), SourmashSignature('NC_011668.1 Shewanella baltica OS223 plasmid pS22302, complete sequence', 837bf2a7), SourmashSignature('NC_011664.1 Shewanella baltica OS223 plasmid pS22301, complete sequence', 87a9aec4), SourmashSignature('NC_009661.1 Shewanella baltica OS185 plasmid pS18501, complete sequence', bde81a41), SourmashSignature('NC_011663.1 Shewanella baltica OS223, complete genome', f033bbd8)]"""
+
+
+@utils.in_tempdir
+def test_sig_cat_4_filelist_with_dbs(c):
+    # cat using a file list as input
+    sig47 = utils.get_test_data('47.fa.sig')
+    sig47abund = utils.get_test_data('track_abund/47.fa.sig')
+    sbt = utils.get_test_data('v6.sbt.zip')
+
+    filelist = c.output("filelist")
+    with open(filelist, 'w') as f:
+        f.write("\n".join((sig47, sig47abund, sbt)))
+
+    c.run_sourmash('sig', 'cat', filelist,
+                   '-o', 'out.sig')
+
+    # stdout should be same signatures
+    out = c.output('out.sig')
+
+    siglist = list(load_signatures(out))
+    print(len(siglist))
     # print("siglist: ",siglist)
     # print("\n")
-    # print("\n")
 
-    assert repr(siglist) == """[SourmashSignature('NC_009665.1 Shewanella baltica OS185, complete genome', 09a08691), SourmashSignature('NC_009665.1 Shewanella baltica OS185, complete genome', 09a08691), SourmashSignature('NC_011665.1 Shewanella baltica OS223 plasmid pS22303, complete sequence', 485c3377), SourmashSignature('NC_009665.1 Shewanella baltica OS185, complete genome', 57e2b22f), SourmashSignature('NC_011668.1 Shewanella baltica OS223 plasmid pS22302, complete sequence', 837bf2a7), SourmashSignature('NC_011664.1 Shewanella baltica OS223 plasmid pS22301, complete sequence', 87a9aec4), SourmashSignature('NC_009661.1 Shewanella baltica OS185 plasmid pS18501, complete sequence', bde81a41), SourmashSignature('NC_011663.1 Shewanella baltica OS223, complete genome', f033bbd8)]"""
+    # verify the number of signatures matches what we expect to see based
+    # on the input files
+    all_sigs = []
+    all_sigs += list(load_signatures(sig47))
+    all_sigs += list(load_signatures(sig47abund))
+    all_sigs += list(sourmash.load_file_as_signatures(sbt))
+
+    assert len(all_sigs) == len(siglist)
+
+    # sort the signatures by something deterministic and unique
+    siglist.sort(key = lambda x: x.md5sum())
+
+    assert repr(siglist) == """[SourmashSignature('', 0107d767), SourmashSignature('NC_009665.1 Shewanella baltica OS185, complete genome', 09a08691), SourmashSignature('NC_009665.1 Shewanella baltica OS185, complete genome', 09a08691), SourmashSignature('', 4e94e602), SourmashSignature('', 60f7e23c), SourmashSignature('', 6d6e87e1), SourmashSignature('', b59473c9), SourmashSignature('', f0c834bc), SourmashSignature('', f71e7817)]"""
 
 
 @utils.in_tempdir
-def test_sig_cat_filelist_with_dbs(c):
+def test_sig_cat_5_from_file(c):
     # cat using a file list as input
     sig47 = utils.get_test_data('47.fa.sig')
     sig47abund = utils.get_test_data('track_abund/47.fa.sig')
@@ -833,7 +847,7 @@ def test_sig_cat_filelist_with_dbs(c):
     with open(filelist, 'w') as f:
         f.write("\n".join((sig47, sig47abund, sbt)))
 
-    c.run_sourmash('sig', 'cat', filelist,
+    c.run_sourmash('sig', 'cat', '--from-file', filelist,
                    '-o', 'out.sig')
 
     # stdout should be same signatures