Merge pull request #392 from smoe/adding_line_numbers_to_check_dev

check: Adding line number to error messages.

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#370](https://github.com/nf-core/chipseq/issues/370)] - Fix stack overflow exceptions in phantompeakqualtools ([see here](https://github.com/kundajelab/phantompeakqualtools/issues/3)).
 - [[#387](https://github.com/nf-core/chipseq/issues/387)] - Get rid of the `lib` folder and rearrange the pipeline accordingly.
 - [[#385](https://github.com/nf-core/chipseq/issues/385)] - Fix `--save_unaligned` description in schema.
+- [[PR #392](https://github.com/nf-core/chipseq/pull/392)] - Adding line numbers to warnings/errors messages in `bin/check_samplesheet.py`
 
 ### Software dependencies
 

bin/check_samplesheet.py

@@ -58,22 +58,22 @@ def check_samplesheet(file_in, file_out):
             sys.exit(1)
 
         ## Check sample entries
-        for line in fin:
+        for line_number, line in enumerate(fin, start=1):
             if line.strip():
                 lspl = [x.strip().strip('"') for x in line.strip().split(",")]
 
                 # Check valid number of columns per row
                 if len(lspl) < len(HEADER):
                     print_error(
-                        "Invalid number of columns (minimum = {})!".format(len(HEADER)),
-                        "Line",
+                        "Invalid number of columns (found = {}, minimum = {})!".format(len(lspl),len(HEADER)),
+                        "Line {}".format(line_number),
                         line,
                     )
                 num_cols = len([x for x in lspl[: len(HEADER)] if x])
                 if num_cols < MIN_COLS:
                     print_error(
-                        "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
-                        "Line",
+                        "Invalid number of populated columns (found = {}, minimum = {})!".format(num_cols,MIN_COLS),
+                        "Line {}".format(line_number),
                         line,
                     )
 
@@ -83,23 +83,23 @@ def check_samplesheet(file_in, file_out):
                     print(f"WARNING: Spaces have been replaced by underscores for sample: {sample}")
                     sample = sample.replace(" ", "_")
                 if not sample:
-                    print_error("Sample entry has not been specified!", "Line", line)
+                    print_error("Sample entry has not been specified!", "Line {}".format(line_number), line)
 
                 ## Check FastQ file extension
                 for fastq in [fastq_1, fastq_2]:
                     if fastq:
                         if fastq.find(" ") != -1:
-                            print_error("FastQ file contains spaces!", "Line", line)
+                            print_error("FastQ file contains spaces!", "Line {}".format(lineNo), line)
                         if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
                             print_error(
                                 "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
-                                "Line",
+                                "Line {}".format(lineNo),
                                 line,
                             )
 
                 ## Check replicate column is integer
                 if not replicate.isdecimal():
-                    print_error("Replicate id not an integer!", "Line", line)
+                    print_error("Replicate id not an integer!", "Line {}".format(lineNo), line)
                     sys.exit(1)
 
                 ## Check antibody and control columns have valid values
@@ -110,7 +110,7 @@ def check_samplesheet(file_in, file_out):
                     if not control:
                         print_error(
                             "Both antibody and control columns must be specified!",
-                            "Line",
+                            "Line {}".format(line_number),
                             line,
                         )
 
@@ -119,13 +119,13 @@ def check_samplesheet(file_in, file_out):
                         print(f"WARNING: Spaces have been replaced by underscores for control: {control}")
                         control = control.replace(" ", "_")
                     if not control_replicate.isdecimal():
-                        print_error("Control replicate id not an integer!", "Line", line)
+                        print_error("Control replicate id not an integer!", "Line {}".format(line_number), line)
                         sys.exit(1)
                     control = "{}_REP{}".format(control, control_replicate)
                     if not antibody:
                         print_error(
                             "Both antibody and control columns must be specified!",
-                            "Line",
+                            "Line {}".format(line_number),
                             line,
                         )
 
@@ -138,7 +138,7 @@ def check_samplesheet(file_in, file_out):
                 elif sample and fastq_1 and not fastq_2:
                     sample_info = ["1", fastq_1, fastq_2, replicate, antibody, control]
                 else:
-                    print_error("Invalid combination of columns provided!", "Line", line)
+                    print_error("Invalid combination of columns provided!", "Line {}".format(line_number), line)
 
                 ## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, replicate, antibody, control ]]}
                 replicate = int(replicate)
@@ -149,7 +149,7 @@ def check_samplesheet(file_in, file_out):
                     sample_mapping_dict[sample][replicate] = [sample_info]
                 else:
                     if sample_info in sample_mapping_dict[sample][replicate]:
-                        print_error("Samplesheet contains duplicate rows!", "Line", line)
+                        print_error("Samplesheet contains duplicate rows!", "Line {}".format(line_number), line)
                     else:
                         sample_mapping_dict[sample][replicate].append(sample_info)