Merge pull request #5 from AmpliconSuite/develop

version 4.1, fixes issues with CLI use of Aggregator, improves logging

README.md

@@ -30,12 +30,13 @@ Aggregates the results from AmpliconSuite
 ## Installation
   - Option 1: Git Clone
     - Step 1: `git clone https://github.com/genepattern/AmpliconSuiteAggregator.git`
+    - Step 2: Install python package dependencies from list below.
     - **If running into dependency issues, please use the docker methods.** 
   - Option 2: Docker
     - Step 1: `docker pull genepattern/amplicon-suite-aggregator`
 
 ## Dependencies
-  - List of dependencies used: intervaltree, matplotlib, numpy, pandas, Pillow, requests, scipy, urllib3           
+  - List of python package dependencies used: intervaltree, matplotlib, numpy, pandas, Pillow, requests, scipy, urllib3           
 
 ## Options when running locally
 ### Amplicon Suite Aggregator related options

manifest

@@ -98,12 +98,12 @@ p7_TYPE=FILE
 p7_default_value=
 p7_description=A two column file providing current identifier for each sample (col 1), and a replacement name (col 2). 
 p7_fileFormat=
-p7_flag=--name_map
+p7_flag=--name_map 
 p7_name=name.map
 p7_numValues=0..1
 p7_optional=on
-p7_prefix=--name_map
-p7_prefix_when_specified=--name_map
+p7_prefix=--name_map 
+p7_prefix_when_specified=--name_map 
 p7_type=java.io.File
 p7_value=
 privacy=public

src/AmpliconSuiteAggregator.py

@@ -6,7 +6,7 @@
 from AmpliconSuiteAggregatorFunctions import *
 from ASA_POST import * 
 
-__version__ = "4.0"
+__version__ = "4.1"
 
 
 def get_zip_paths(filelist_fp):
@@ -33,11 +33,11 @@ def get_zip_paths(filelist_fp):
     group.add_argument("--files", nargs='+', type=str, help="List of files or directories to use")
     parser.add_argument("-o", "--output_name", type=str, help="Output Prefix and/or project name for site upload", default="output")
     parser.add_argument("-u", "--username", type=str, help = "Email address for Amplicon Repository. Setting this will "
-                        "trigger an attempt to upload the aggregated file to AmpliconRepository.org", required=False)
+                        "trigger an attempt to upload the aggregated file to AmpliconRepository.org", required=False, default="")
     # parser.add_argument('-t', '--testing', action = 'store_true', required = False)  # JL: This seems to be unused
     parser.add_argument("--upload_only", type=str, help="If 'Yes', then skip aggregation and classification and upload "
                         "the file as is. Note: the file must already be aggregated to successfully upload.",
-                        choices=['Yes', 'No'])
+                        choices=['Yes', 'No'], default="No")
     parser.add_argument("--name_map", type=str, help="A two column file providing the current identifier for each sample (col 1)"
                         " and a replacement name (col 2). Enables batch renaming of samples.")
     parser.add_argument("-c", "--run_classifier",type=str, help="If 'Yes', then run Amplicon Classifier on AA results. \

src/AmpliconSuiteAggregatorFunctions.py

@@ -53,7 +53,11 @@ def read_name_remap(name_remap_file):
                 fields = l.rstrip().rsplit()
                 name_remap[fields[0]] = fields[1]
 
-    print("Name remap has " + str(len(name_remap)) + " keys")
+        print("Name remap has " + str(len(name_remap)) + " keys")
+
+    else:
+        print("No name remap file provided. Sample names will detected from filenames.")
+
     return name_remap
 
 
@@ -419,7 +423,9 @@ def json_modifications(self):
                         feat_file = feat_file.replace('./results/', "")
                         sample_dct['Feature BED file'] = feat_file
                     else:
-                        print(f'Feature: "Feature BED file" {feat_file} doesnt exist for sample {sample_dct["Sample name"]}')
+                        if not feat_file.endswith("/NA"):
+                            print(f'Feature: "Feature BED file" {feat_file} doesnt exist for sample {sample_dct["Sample name"]}')
+
                         sample_dct['Feature BED file'] = "Not Provided"
 
                 else: