Merge pull request #108 from jonasscheid/dsl2

Update check_samplesheet.py script for new format #102

bin/check_samplesheet.py

@@ -1,12 +1,10 @@
 #!/usr/bin/env python
 
-# TODO nf-core: Update the script to check the samplesheet
-# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
 
 import os
 import sys
-import errno
 import argparse
+import re
 
 
 def parse_args(args=None):
@@ -15,19 +13,10 @@ def parse_args(args=None):
 
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
     parser.add_argument("FILE_IN", help="Input samplesheet file.")
-    parser.add_argument("FILE_OUT", help="Output file.")
+    parser.add_argument("FILE_OUT", help="Output samplesheet file.")
     return parser.parse_args(args)
 
 
-def make_dir(path):
-    if len(path) > 0:
-        try:
-            os.makedirs(path)
-        except OSError as exception:
-            if exception.errno != errno.EEXIST:
-                raise exception
-
-
 def print_error(error, context="Line", context_str=""):
     error_str = "ERROR: Please check samplesheet -> {}".format(error)
     if context != "" and context_str != "":
@@ -38,103 +27,121 @@ def print_error(error, context="Line", context_str=""):
     sys.exit(1)
 
 
-# TODO nf-core: Update the check_samplesheet function
+def check_allele_nomenclature(allele):
+    pattern = re.compile("(^[A-Z][\*][0-9][0-9][:][0-9][0-9])$")
+    return pattern.match(allele) is not None
+
+
+def make_dir(path):
+    if len(path) > 0:
+        try:
+            os.makedirs(path)
+        except OSError as exception:
+            if exception.errno != errno.EEXIST:
+                raise exception
+
+
 def check_samplesheet(file_in, file_out):
     """
     This function checks that the samplesheet follows the following structure:
 
-    sample,fastq_1,fastq_2
-    SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
-    SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
-    SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
+    sample,alleles,filename
+    GBM_1,A*01:01;A*02:01;B*07:02;B*24:02;C*03:01;C*04:01,gbm_1_anno.vcf|gbm_1_peps.tsv|gbm_1_prot.fasta
+    GBM_2,A*02:01;A*24:01;B*07:02;B*08:01;C*04:01;C*07:01,gbm_2_anno.vcf|gbm_2_peps.tsv|gbm_2_prot.fasta
+
+    or
+
+    sample,alleles,filename
+    GBM_1,gbm_1_alleles.txt,gbm_1_anno.vcf|gbm_1_peps.tsv|gbm_1_prot.fasta
+    GBM_2,gbm_2_alleles.txt,gbm_2_anno.vcf|gbm_2_peps.tsv|gbm_2_prot.fasta
+
+
+    where the FileName column contains EIHTER a vcf file, a tsv file (peptides), or a fasta file (proteins)
+    and the Alleles column contains EITHER a string of alleles separated by semicolon or the path to a text file
+    containing one allele per line (no header)
+
+    Furhter Examples:
+    - Class2 allele format => https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/alleles/alleles.DRB1_01_01.txt
+    - Mouse allele format => https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/alleles/alleles.H2.txt 
+    - pep.tsv => https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/peptides/peptides.tsv
+    - annotated_variants.tsv => https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/variants/variants.tsv
+    - annotated_variants.vcf => https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/variants/variants.vcf
 
-    For an example see:
-    https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
     """
 
-    sample_mapping_dict = {}
+    sample_run_dict = {}
     with open(file_in, "r") as fin:
 
         ## Check header
-        MIN_COLS = 2
-        # TODO nf-core: Update the column names for the input samplesheet
-        HEADER = ["sample", "fastq_1", "fastq_2"]
+        COL_NUM = 3
+        HEADER = ["sample", "alleles", "filename"]
         header = [x.strip('"') for x in fin.readline().strip().split(",")]
         if header[: len(HEADER)] != HEADER:
-            print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER)))
+            print("ERROR: Please check samplesheet header -> {} != {}".format("\t".join(header), "\t".join(HEADER)))
             sys.exit(1)
 
         ## Check sample entries
         for line in fin:
-            lspl = [x.strip().strip('"') for x in line.strip().split(",")]
-
-            # Check valid number of columns per row
-            if len(lspl) < len(HEADER):
+            lspl = [x.strip('"').replace(" ","") 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)),
+                    "Invalid number of columns (valid = {})!".format(len(HEADER)),
                     "Line",
                     line,
                 )
             num_cols = len([x for x in lspl if x])
-            if num_cols < MIN_COLS:
+            if num_cols != COL_NUM:
                 print_error(
-                    "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
+                    "Invalid number of populated columns (valid = {})!".format(COL_NUM),
                     "Line",
                     line,
                 )
-
-            ## Check sample name entries
-            sample, fastq_1, fastq_2 = lspl[: len(HEADER)]
-            sample = sample.replace(" ", "_")
-            if not sample:
-                print_error("Sample entry has not been specified!", "Line", 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)
-                    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,
-                        )
-
-            ## Auto-detect paired-end/single-end
-            sample_info = []  ## [single_end, fastq_1, fastq_2]
-            if sample and fastq_1 and fastq_2:  ## Paired-end short reads
-                sample_info = ["0", fastq_1, fastq_2]
-            elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
-                sample_info = ["1", fastq_1, fastq_2]
+
+            sample, alleles, filename = lspl[: len(HEADER)]
+
+
+            ## Check if the alleles given in the text file are in the right format
+            if alleles.endswith(".txt"):
+                with open(alleles, "r") as af:
+                    alleles = ';'.join([al.strip('\n') if check_allele_nomenclature(al) else \
+                    print_error("Allele format is not matching the nomenclature", "Line", line) for al in af.readlines()])
+
+
+            ## Get annotation of filename column
+            if filename.endswith(".vcf"):
+                anno = "variant"
+            elif filename.endswith(".tsv"):
+                ## Check if it is a variant annotation file or a peptide file
+                with open(filename, "r") as tsv:
+                    first_header_col = [col.lower() for col in tsv.readlines()[0].split('\t')][0]
+                    if first_header_col == "id":
+                        anno = "pep"
+                    elif first_header_col == "#chr": 
+                        anno = "variant"   
             else:
-                print_error("Invalid combination of columns provided!", "Line", line)
+                anno = "prot"
 
-            ## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 ] }
-            if sample not in sample_mapping_dict:
-                sample_mapping_dict[sample] = [sample_info]
+            sample_info = [sample, alleles, filename, anno]
+            ## Create sample mapping dictionary 
+            if sample not in sample_run_dict:
+                sample_run_dict[sample] = [sample_info]
             else:
-                if sample_info in sample_mapping_dict[sample]:
+                if sample_info in sample_run_dict[sample]:
                     print_error("Samplesheet contains duplicate rows!", "Line", line)
                 else:
-                    sample_mapping_dict[sample].append(sample_info)
+                    sample_run_dict[sample].append(sample_info)
 
     ## Write validated samplesheet with appropriate columns
-    if len(sample_mapping_dict) > 0:
+    if len(sample_run_dict) > 0:
         out_dir = os.path.dirname(file_out)
         make_dir(out_dir)
         with open(file_out, "w") as fout:
-            fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n")
-            for sample in sorted(sample_mapping_dict.keys()):
-
-                ## Check that multiple runs of the same sample are of the same datatype
-                if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]):
-                    print_error("Multiple runs of a sample must be of the same datatype!", "Sample: {}".format(sample))
+            fout.write(",".join(["sample", "alleles", "filename", "anno"]) + "\n")
 
-                for idx, val in enumerate(sample_mapping_dict[sample]):
-                    fout.write(",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n")
-    else:
-        print_error("No entries to process!", "Samplesheet: {}".format(file_in))
+            for sample in sorted(sample_run_dict.keys()):
+                for idx, val in enumerate(sample_run_dict[sample]):
+                    fout.write(",".join(val) + "\n")
 
 
 def main(args=None):
@@ -143,4 +150,4 @@ def main(args=None):
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    sys.exit(main())