--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/process_input.py	Mon Oct 06 12:13:07 2025 +0000
@@ -0,0 +1,132 @@
+import json
+import os
+import sys
+
+import yaml
+
+
+def get_section_string(f, start_line, end_line, return_string=False):
+    # consume starting lines
+    start_string = iter(f.readline, start_line)
+    start_string = ''.join(line for line in start_string)
+    # read YAML lines
+    yaml_string = iter(f.readline, end_line)
+    if return_string:
+        return ''.join(x for x in yaml_string)
+    else:
+        return [x for x in yaml_string]
+
+
+def fill_from_yaml_data(yaml_only_dict, studies_samples_dict):
+    # fill experiment information (platform)
+    for index, exp in yaml_only_dict['ENA_experiment'].items():
+        study_alias = exp['study_alias']
+        sample_alias = exp['sample_alias']
+        if study_alias in studies_samples_dict.keys():
+            if sample_alias in studies_samples_dict[study_alias].keys():
+                studies_samples_dict[study_alias][sample_alias]['experiments'].append({'platform': exp['platform']})
+            else:
+                studies_samples_dict[study_alias][sample_alias] = {'experiments': [{'platform': exp['platform']}]}
+        else:
+            studies_samples_dict[study_alias] = {
+                sample_alias: {'experiments': [{'platform': exp['platform']}]}
+            }
+
+
+def load_receipt_data(input_file_path):
+    # should do some health check of the input file?
+    # load yaml section
+    loaded_data = {}
+    yaml_delimiter = 'YAML -------------\n'
+    with open(input_file_path) as input_file:
+        yaml_only_section = yaml.safe_load(
+            get_section_string(input_file, start_line=yaml_delimiter, end_line=yaml_delimiter, return_string=True)
+        )
+    fill_from_yaml_data(yaml_only_section, loaded_data)
+    # read study accessions
+    study_delimiter = 'Study accession details:\n'
+    end_line = '\n'
+    with open(input_file_path) as input_file:
+        studies_accession_lines = get_section_string(input_file, start_line=study_delimiter, end_line=end_line)
+
+    for study_line in studies_accession_lines:
+        if study_line != '\n':
+            alias, accession, *_ = study_line.split('\t')
+            try:
+                loaded_data[alias]['accession'] = accession
+            except KeyError:
+                print(f"Experiment {alias} has unknown study or sample")
+
+    samples_delimiter = 'Sample accession details:\n'
+    with open(input_file_path) as input_file:
+        samples_accession_lines = get_section_string(input_file, start_line=samples_delimiter, end_line=end_line)
+
+    for sample_line in samples_accession_lines:
+        if sample_line != '\n':
+            alias, accession, *_ = sample_line.split('\t')
+            for study in loaded_data.keys():
+                if alias in loaded_data[study].keys():
+                    loaded_data[study][alias]['accession'] = accession
+                    break
+
+    return loaded_data
+
+
+def main():
+    input_file_path = sys.argv[1]
+    fasta_names_list_path = sys.argv[2]
+    out_manifest_base = sys.argv[3]
+    manifest_template = sys.argv[4]
+
+    # load submitted data from receipt file
+    data_dict = load_receipt_data(input_file_path)
+
+    # iterate over the list of fasta files
+    with open(fasta_names_list_path, 'r') as fasta_files_json_file:
+        fasta_files_list = json.load(fasta_files_json_file)
+
+    with open('submit_list.tab', 'w') as written_manifests_out:
+        for fasta_file in fasta_files_list:
+            if fasta_file.endswith('.fasta.gz'):
+                sample_alias = fasta_file[:-9]
+            else:
+                sample_alias = fasta_file[:-6]
+
+            print(f'Processing {sample_alias}')
+            found_metadata = False
+
+            for study_alias in data_dict.keys():
+                if sample_alias in data_dict[study_alias].keys():
+                    sample_accession = data_dict[study_alias][sample_alias]['accession']
+                    study_accession = data_dict[study_alias]['accession']
+                    # TODO: get a string that concatenates platform information from multiple experiments
+                    platform = data_dict[study_alias][sample_alias]['experiments'][0]['platform']
+                    manifest_path = os.path.join(out_manifest_base, sample_alias + '.manifest.txt')
+
+                    with open(manifest_path, "w") as output_handle:
+                        # dump the contents of manifest template containing global vars
+                        with open(manifest_template) as m_template:
+                            output_handle.write(m_template.read())
+
+                        output_handle.write("ASSEMBLYNAME\tconsensus_" + sample_alias + "\n")
+                        output_handle.write("PLATFORM\t" + platform + "\n")
+                        output_handle.write("STUDY\t" + study_accession + "\n")
+                        output_handle.write("SAMPLE\t" + sample_accession + "\n")
+                        output_handle.write("FASTA\t" + sample_alias + '.fasta.gz' + "\n")
+                        agp_path = os.path.join("./fasta", sample_alias + ".agp")
+                        if os.path.exists(agp_path):
+                            output_handle.write("AGP\t" + sample_alias + ".agp\n")
+                        chr_list_path = os.path.join("./fasta", sample_alias + ".tsv.gz")
+                        if os.path.exists(chr_list_path):
+                            output_handle.write("CHROMOSOME_LIST\t" + sample_alias + ".tsv.gz\n")
+
+                    found_metadata = True
+                    written_manifests_out.write(manifest_path + '\n')
+                    break
+
+            if not found_metadata:
+                print(f'No metadata found for sample {sample_alias}')
+
+
+if __name__ == '__main__':
+    main()