Template tests

changelog.md

@@ -39,7 +39,9 @@ resolution
 - Added seed parameter to `downsample_fastq` component.
 - Added bacmet database to `abricate` component.
 - Added default docker option to avoid docker permission errors.
-- Changed the default URL generated by inspect and report commands.
+- Added tests for `mash_screen`, `mash_dist`, `mapping_patlas` python 
+templates
+- Changed the default URL generated by inspect and report commands. 
 - Added directives to `-L` parameter of build module.
 
 ### Bug fixes

docs/dev/create_template.rst

@@ -85,13 +85,16 @@ Versioning and logging
 FlowCraft has a specific ``logger``
 (:func:`~flowcraft.templates.flowcraft_utils.flowcraft_base.get_logger`) and
 versioning system that can be imported from
-:mod:`flowcraft.templates.flowcraft_utils`: ::
+:mod:`flowcraft.templates.flowcraft_utils` as follows: ::
 
     # the module that imports the logger and the decorator class for versioning
     # of the script itself and other software used in the script
-    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
-
+    try:
+        from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+    except ImportError:
+        from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, MainWrapper
 
+The ``try/except`` is used for test purposes.
 
 Logger
 ^^^^^^

flowcraft/templates/assembly_report.py

@@ -43,7 +43,11 @@
 from collections import OrderedDict
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/downsample_fastq.py

@@ -47,7 +47,11 @@
 
 from os.path import basename
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/fastqc.py

@@ -42,7 +42,11 @@
 from subprocess import PIPE
 from os.path import exists, join
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/fastqc_report.py

@@ -58,7 +58,11 @@
 
 from collections import OrderedDict
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/integrity_coverage.py

@@ -86,7 +86,11 @@
 
 from itertools import chain
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/mapping2json.py

@@ -37,7 +37,11 @@
 import sys
 from pympler.asizeof import asizeof
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
@@ -46,18 +50,21 @@
     JSON_LENGTH = '$lengthJson'
     CUTOFF = '$cov_cutoff'
     SAMPLE_ID = '$sample_id'
-else:
-    DEPTH_TXT = sys.argv[1]
-    JSON_LENGTH = sys.argv[2]
-    CUTOFF = sys.argv[3]
-    SAMPLE_ID = sys.argv[4]
-
-logger.debug("List of arguments given: {}".format([
-    DEPTH_TXT,
-    JSON_LENGTH,
-    CUTOFF,
-    SAMPLE_ID
-]))
+
+try:
+    logger.debug("List of arguments given: {}".format([
+        DEPTH_TXT,
+        JSON_LENGTH,
+        CUTOFF,
+        SAMPLE_ID
+    ]))
+except NameError:
+    # this is used for unit tests where this variables are not required to
+    # test some of the functions within this script
+    DEPTH_TXT, JSON_LENGTH, CUTOFF, SAMPLE_ID = None, None, None, None
+    logger.debug("Input variables 'DEPTH_TXT, JSON_LENGTH, CUTOFF and "
+                 "SAMPLE_ID' are not defined. Are you using this for "
+                 "unit tests?")
 
 # check if all variables are assigned
 if DEPTH_TXT and JSON_LENGTH and SAMPLE_ID and CUTOFF:
@@ -119,6 +126,12 @@ def generate_jsons(depth_dic_coverage, plasmid_length, cutoff):
     ----------
     depth_dic_coverage: dict
          dictionary with the coverage per position for each plasmid
+    plasmid_length: dict
+        dictionary with the correspondence between each reference plasmid and
+        its length
+    cutoff: float
+        the value of percentage identity that is used to discard entries in
+        the txt file generated by mash screen.
 
     Returns
     -------
@@ -161,14 +174,16 @@ def generate_jsons(depth_dic_coverage, plasmid_length, cutoff):
             # array to store the values of coverage for each interval
             array_of_cov = []
             # the counter that is used to output the values per interval
-            reset_counter = 0
+            reset_counter = 1
             # loop to generate dict_cov
             logger.info("Generating plot data for plasmid: {}".format(ref))
             for i in range(int(plasmid_length[ref])):
                 # checks if key for a given position is in dict and if so
                 # adds it to array of cov, otherwise it will add a 0
                 try:
-                    array_of_cov.append(int(depth_dic_coverage[ref][str(i)]))
+                    array_of_cov.append(int(
+                        depth_dic_coverage[ref][str(i + 1)]
+                    ))
                 except KeyError:
                     array_of_cov.append(0)
 
@@ -178,7 +193,8 @@ def generate_jsons(depth_dic_coverage, plasmid_length, cutoff):
                         int(sum(array_of_cov)/len(array_of_cov))
                     )
                     # reset counter
-                    reset_counter = 0
+                    reset_counter = 1
+                    array_of_cov = []
                 else:
                     # if counter is less than interval then sums 1
                     reset_counter += 1

flowcraft/templates/mashdist2json.py

@@ -29,7 +29,11 @@
 import json
 import os
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
@@ -56,10 +60,8 @@ def send_to_output(master_dict, mash_output, sample_id, assembly_file):
     master_dict: dict
         dictionary that stores all entries for a specific query sequence
         in multi-fasta given to mash dist as input against patlas database
-    last_seq: str
-        string that stores the last sequence that was parsed before writing to
-        file and therefore after the change of query sequence between different
-        rows on the input file
+    assembly_file: str
+        the string with the assembly file name
     mash_output: str
         the name/path of input file to main function, i.e., the name/path of
         the mash dist output txt file.
@@ -129,6 +131,8 @@ def main(mash_output, hash_cutoff, sample_id, assembly_file):
         to the results outputs
     sample_id: str
         The name of the sample.
+    assembly_file: str
+        The name of the assembly file
     """
 
     input_f = open(mash_output, "r")

flowcraft/templates/mashscreen2json.py

@@ -30,7 +30,11 @@
 import os
 import json
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 
@@ -42,9 +46,10 @@
     logger.debug("MASH_TXT: {}".format(MASH_TXT))
     logger.debug("SAMPLE_ID: {}".format(MASH_TXT))
 
+
 @MainWrapper
 def main(mash_output, sample_id):
-    '''
+    """
     converts top results from mash screen txt output to json format
 
     Parameters
@@ -55,7 +60,7 @@ def main(mash_output, sample_id):
     sample_id: str
         sample name
 
-    '''
+    """
     logger.info("Reading file : {}".format(mash_output))
     read_mash_output = open(mash_output)
 
@@ -94,7 +99,7 @@ def main(mash_output, sample_id):
             # estimated copy number
             copy_number = int(float(v[1]) / median_cutoff)
             # assure that plasmid as at least twice the median coverage depth
-            if float(v[1]) > median_cutoff:
+            if float(v[1]) >= median_cutoff:
                 filtered_dic["_".join(k.split("_")[0:3])] = [
                     round(float(v[0]),2),
                     copy_number
@@ -103,7 +108,8 @@ def main(mash_output, sample_id):
             "Exported dictionary has {} entries".format(len(filtered_dic)))
     else:
         # if no entries were found raise an error
-        logger.error("No matches were found using mash screen for the queried reads")
+        logger.error("No matches were found using mash screen for the queried "
+                     "reads")
 
     output_json.write(json.dumps(filtered_dic))
     output_json.close()

flowcraft/templates/megahit.py

@@ -47,7 +47,11 @@
 
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/metaspades.py

@@ -45,7 +45,11 @@
 
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/pATLAS_consensus_json.py

@@ -33,7 +33,10 @@
 import os
 import json
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, MainWrapper
 
 logger = get_logger(__file__)
 
@@ -80,12 +83,11 @@ def main(list_of_jsons):
 
     json_dic = {
         "patlas_mashscreen": json_dict
-        # TODO add information for report webapp
     }
 
     with open(".report.json", "w") as json_report:
         json_report.write(json.dumps(json_dic, separators=(",", ":")))
 
 
 if __name__ == "__main__":
-    main(LIST_OF_FILES)
+    main(LIST_OF_FILES)

flowcraft/templates/pipeline_status.py

@@ -29,7 +29,11 @@
 
 from os.path import join
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/process_abricate.py

@@ -39,7 +39,11 @@
 
 from subprocess import PIPE
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/process_assembly.py

@@ -53,7 +53,11 @@
 import json
 import operator
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)
 

flowcraft/templates/process_assembly_mapping.py

@@ -59,7 +59,11 @@
 from subprocess import PIPE
 from collections import OrderedDict
 
-from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+try:
+    from flowcraft_utils.flowcraft_base import get_logger, MainWrapper
+except ImportError:
+    from flowcraft.templates.flowcraft_utils.flowcraft_base import get_logger, \
+        MainWrapper
 
 logger = get_logger(__file__)