Merge pull request #32 from gogetdata/cli_update

Cli update

Author: mikecormier

ggd/check_recipe.py

@@ -889,10 +889,10 @@ def check_files(
                 ":ggd:check-recipe: !!ERROR!!: with: %s(%s) must be sorted, bgzipped AND tabixed.\n"
                 % (P, n)
             )
-        elif n.endswith((".fasta", ".fa", ".fasta.gz", ".fa.gz")):
+        elif n.endswith((".fasta", ".fa", ".fasta.gz", ".fa.gz", ".fastq", ".fq", ".fastq.gz", ".fq.gz")):
             if (
                 not op.basename(n + ".fai") in fais
-                and not (re.sub("(.+).fa(?:sta)?$", "\\1", op.basename(n)) + ".fai")
+                and not (re.sub("(.+).f(?:sta)?$", "\\1", op.basename(n)) + ".fai")
                 in fais
             ):
                 not_faidxed.append(

ggd/make_bash.py

@@ -80,7 +80,9 @@ def add_make_bash(p):
     c2.add_argument(
         "-dv",
         "--data-version",
-        help="The version of the data (itself) being downloaded and processed (EX: dbsnp-127)",
+        help="The version of the data (itself) being downloaded and processed (EX: dbsnp-127)" +
+        " If there is no data version apparent we recommend you use the date associated with the files" +
+        " or something else that can uniquely identify the 'version' of the data",
         required=True,
     )
     c2.add_argument(
@@ -245,9 +247,9 @@ def make_bash(parser, args):
 
     ## Check coordinates
     assert (
-        args.coordinate_based in GENOMIC_COORDINATE_LIST
+        args.coordinate_base in GENOMIC_COORDINATE_LIST
     ), "{c} is not an acceptable genomic coordinate base".format(
-        c=args.coordinate_based
+        c=args.coordinate_base
     )
     # ("Please provide a genomic coordinate base from the follow list: {}".format(", ".join(GENOMIC_COORDINATE_LIST)))
 
@@ -286,7 +288,7 @@ def make_bash(parser, args):
             "keywords": args.keyword,
             "summary": args.summary,
             "tags": {
-                "genomic-coordinate-base": args.coordinate_based.strip(),
+                "genomic-coordinate-base": args.coordinate_base.strip(),
                 "data-version": args.data_version.strip(),
                 "data-provider": args.data_provider.strip(),
                 "file-type": [],

tests/test_internet_free.py

@@ -633,7 +633,7 @@ def test_make_bash_internet_free():
     args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
                         dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'], 
                         name='test-gaps', platform='noarch', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from UCSC',
-                        coordinate_based="0-based-inclusive", file_type= [],final_file=[])
+                        coordinate_base="0-based-inclusive", file_type= [],final_file=[])
 
     assert make_bash.make_bash((),args)