Merge branch 'simon-reformatted-python' into simon-add-black-check

bioprojects/PRJEB13833/metadata/prepare-metadata.py

@@ -3,12 +3,15 @@
     with open("metadata.tsv", "w") as outf:
         for line in inf:
             line = line.strip()
-            if line.startswith("run"): continue
+            if line.startswith("run"):
+                continue
 
-            run_accession, sample_accession, sample_alias, sample_title = \
-                line.split("\t")
+            run_accession, sample_accession, sample_alias, sample_title = line.split(
+                "\t"
+            )
 
             _, yyyy, mm, dd, site = sample_title.split("_")
 
-            outf.write("%s\t%s-%s-%s\tCluster %s\n" % (
-                run_accession, yyyy, mm, dd, site))
+            outf.write(
+                "%s\t%s-%s-%s\tCluster %s\n" % (run_accession, yyyy, mm, dd, site)
+            )

bioprojects/PRJEB14051/metadata/prepare_meatadata.py

@@ -6,18 +6,24 @@
 with open("table-s4.tsv") as inf:
     for line in inf:
         bits = line.strip().split("\t")
-        if not bits[0].isdigit(): continue
+        if not bits[0].isdigit():
+            continue
 
         sample_info[bits[0]] = bits[1], bits[2]
 
 with open("raw_metadata.tsv") as inf:
     with open("metadata.tsv", "w") as outf:
         for line in inf:
-            if line.startswith("run_accession"): continue
+            if line.startswith("run_accession"):
+                continue
 
             run_accession, library_name = line.strip().split("\t")
 
-            outf.write("%s\t%s\t%s\n" % (
-                run_accession,
-                sample_info[library_name][0],
-                sample_info[library_name][1]))
+            outf.write(
+                "%s\t%s\t%s\n"
+                % (
+                    run_accession,
+                    sample_info[library_name][0],
+                    sample_info[library_name][1],
+                )
+            )

bioprojects/PRJEB28033/metadata/parse_metadata.py

@@ -4,6 +4,7 @@
 
 import sys
 
+
 def start(raw_metadata_in, common_metadata_out):
     data = []
     with open(raw_metadata_in) as inf:
@@ -13,15 +14,16 @@ def start(raw_metadata_in, common_metadata_out):
             accession, fastq_ftps, sampleid = line.split("\t")
 
             if fastq_ftps == "fastq_ftp":
-                continue # skip header line
+                continue  # skip header line
 
-            sampleid = "NYC-%s"%(sampleid.split("-")[-1].zfill(2))
+            sampleid = "NYC-%s" % (sampleid.split("-")[-1].zfill(2))
 
             data.append([accession, sampleid])
 
     with open(common_metadata_out, "w") as outf:
         for accession, sampleid in data:
             outf.write("\t".join([accession, sampleid]) + "\n")
 
+
 if __name__ == "__main__":
     start(*sys.argv[1:])

bioprojects/PRJEB49260/metadata/prepare_metadata.py

@@ -3,9 +3,14 @@
 with open("raw_metadata.tsv") as inf:
     with open("metadata.tsv", "w") as outf:
         for line in inf:
-            run_accession, sample_accession, read_counts, sample_alias = \
-                line.strip().split("\t")
-            if run_accession == "run_accession": continue
+            (
+                run_accession,
+                sample_accession,
+                read_counts,
+                sample_alias,
+            ) = line.strip().split("\t")
+            if run_accession == "run_accession":
+                continue
 
             location_id, date = sample_alias.rsplit("_", 1)
 
@@ -20,7 +25,5 @@
             mm = date[0:2]
             dd = date[2:4]
             yy = date[4:6]
-
-            outf.write("%s\t20%s-%s-%s\t%s\n" % (
-                run_accession, yy, mm, dd, location
-            ))
+
+            outf.write("%s\t20%s-%s-%s\t%s\n" % (run_accession, yy, mm, dd, location))

bioprojects/PRJNA438174/metadata/process-metadata.py

@@ -5,7 +5,8 @@
 with open("table-s1.tsv") as inf:
     for line in inf:
         line = line.strip()
-        if line.startswith("Sample type"): continue
+        if line.startswith("Sample type"):
+            continue
 
         bits = line.split("\t")
         sample_type, date_sampled, _, _, _, _, sra_experiment_accession = bits
@@ -22,13 +23,14 @@
         }[month]
 
         date_sampled = "%s-%s" % (year, month)
-        
+
         sample_metadata[sra_experiment_accession] = sample_type, date_sampled
 
 with open("raw_metadata.tsv") as inf:
     with open("metadata.tsv", "w") as outf:
         for line in inf:
             run_accession, sra_experiment_accession = line.strip().split("\t")
-            outf.write("%s\t%s\t%s\n" % (
-                run_accession, *sample_metadata[sra_experiment_accession]))
-
+            outf.write(
+                "%s\t%s\t%s\n"
+                % (run_accession, *sample_metadata[sra_experiment_accession])
+            )

bioprojects/PRJNA645711/metadata/prepare-metadata.py

@@ -3,14 +3,15 @@
 with open("raw_metadata.tsv") as inf:
     with open("metadata.tsv", "w") as outf:
         for line in inf:
-            (run_accession,
-             sample_accession,
-             run_alias,
-             sample_alias,
-             sample_title) = line.strip().split("\t")
+            (
+                run_accession,
+                sample_accession,
+                run_alias,
+                sample_alias,
+                sample_title,
+            ) = line.strip().split("\t")
 
-            if run_accession == "run_accession": continue
+            if run_accession == "run_accession":
+                continue
 
-            outf.write("%s\t%s\n" % (
-                run_accession,
-                sample_title.split()[-1]))
+            outf.write("%s\t%s\n" % (run_accession, sample_title.split()[-1]))

bioprojects/PRJNA661613/metadata/process-metadata.py

@@ -3,8 +3,10 @@
 accession_to_sample_id = {}
 with open("raw-metadata.tsv") as inf:
     for line in inf:
-        if not line.strip(): continue
-        if line.startswith("run_accession"): continue
+        if not line.strip():
+            continue
+        if line.startswith("run_accession"):
+            continue
         line = line[:-1]  # drop final newline
         accession, sample_id, upload_date = line.split("\t")
         accession_to_sample_id[accession] = sample_id
@@ -13,12 +15,22 @@
 sample_info = {}
 with open("sample_metadata.tsv") as inf:
     for line in inf:
-        if not line.strip(): continue
-        if line.startswith("sample"): continue  # header row
+        if not line.strip():
+            continue
+        if line.startswith("sample"):
+            continue  # header row
         line = line[:-1]  # drop final newline
 
-        sample, core, location, method, date, mean_ct, ct_from_replicate, \
-            sequencing = line.split("\t")
+        (
+            sample,
+            core,
+            location,
+            method,
+            date,
+            mean_ct,
+            ct_from_replicate,
+            sequencing,
+        ) = line.split("\t")
 
         sample = sample.strip()
         if sample == "9_09_S1":
@@ -40,11 +52,14 @@
         }
 
 with open("metadata.tsv", "w") as outf:
-    for accession, sample_id in sorted(
-            accession_to_sample_id.items()):
-        outf.write("%s\t%s\t%s\t%s\t%s\n" % (
-            accession,
-            sample_info[sample_id]["location"],
-            sample_info[sample_id]["date"],
-            sample_info[sample_id]["method"],
-            sample_info[sample_id]["sequencing"]))
+    for accession, sample_id in sorted(accession_to_sample_id.items()):
+        outf.write(
+            "%s\t%s\t%s\t%s\t%s\n"
+            % (
+                accession,
+                sample_info[sample_id]["location"],
+                sample_info[sample_id]["date"],
+                sample_info[sample_id]["method"],
+                sample_info[sample_id]["sequencing"],
+            )
+        )

bioprojects/PRJNA729801/metadata/parse_metadata.py

@@ -4,6 +4,7 @@
 
 import sys
 
+
 def start(raw_metadata_in, parsed_metadata_out):
     data = []
     with open(raw_metadata_in) as inf:
@@ -13,7 +14,7 @@ def start(raw_metadata_in, parsed_metadata_out):
             _, _, fastq_ftps, alias = line.split("\t")
 
             if fastq_ftps == "fastq_ftp":
-                continue # skip header line
+                continue  # skip header line
 
             enriched = not alias.endswith("_unenriched")
             alias = alias.removesuffix("_unenriched")
@@ -23,12 +24,13 @@ def start(raw_metadata_in, parsed_metadata_out):
             plant, month, day, year = alias.split("_")
 
             if len(year) == 2:
-                year = '20%s' % year
+                year = "20%s" % year
 
             date = "%s-%s-%s" % (year, month.zfill(2), day.zfill(2))
 
             for fastq_ftp in fastq_ftps.split(";"):
-                if not fastq_ftp: continue
+                if not fastq_ftp:
+                    continue
 
                 filename = fastq_ftp.split("/")[-1]
 
@@ -41,5 +43,6 @@ def start(raw_metadata_in, parsed_metadata_out):
         for plant, date, filename, is_enriched in data:
             outf.write("\t".join([filename, date, plant, is_enriched]) + "\n")
 
+
 if __name__ == "__main__":
     start(*sys.argv[1:])

bioprojects/PRJNA812772/metadata/prepare_metadata.py

@@ -4,7 +4,8 @@
 
 with open("dataset-s4.tsv") as inf:
     for line in inf:
-        if line.startswith("SI no."): continue # header
+        if line.startswith("SI no."):
+            continue  # header
 
         bits = line.strip().split("\t")
         sample_accession = bits[2]
@@ -15,13 +16,11 @@
 with open("raw_metadata.tsv") as inf:
     with open("metadata.tsv", "w") as outf:
         for line in inf:
-            sample_accession, run_accession, sample_alias = \
-                line.strip().split("\t")
+            sample_accession, run_accession, sample_alias = line.strip().split("\t")
 
             _, strategy = sample_alias.split("_")
-            if strategy == "sarscov2": continue
+            if strategy == "sarscov2":
+                continue
 
-            collection_date = sample_accession_to_collection_date[
-                sample_accession]
-            outf.write("%s\t%s\t%s\n" % (
-                run_accession, strategy, collection_date))
+            collection_date = sample_accession_to_collection_date[sample_accession]
+            outf.write("%s\t%s\t%s\n" % (run_accession, strategy, collection_date))

bioprojects/PRJNA924011/metadata/prepare_metadata.py

@@ -2,20 +2,23 @@
 with open("metadata.tsv", "w") as outf:
     with open("raw_metadata.tsv") as inf:
         for line in inf:
-            (run_accession,
-             sample_accession,
-             instrument_model,
-             fastq_ftp,
-             sample_alias,
-             first_created) = line.strip().split("\t")
+            (
+                run_accession,
+                sample_accession,
+                instrument_model,
+                fastq_ftp,
+                sample_alias,
+                first_created,
+            ) = line.strip().split("\t")
+
+            if run_accession == "run_accession":
+                continue
 
-            if run_accession == "run_accession": continue
-
             if instrument_model == "MinION":
                 continue  # Pipeline can't handle long-read yet
 
             location, raw_date = sample_alias.split("_")
-            
+
             if len(raw_date) == 5:
                 mm = "0" + raw_date[0]
                 dd = raw_date[1:3]
@@ -24,7 +27,7 @@
                 mm = raw_date[0:2]
                 dd = raw_date[2:4]
                 yy = raw_date[4:6]
-                
+
             date = "20%s-%s-%s" % (yy, mm, dd)
-            
+
             outf.write("%s\t%s\t%s\n" % (run_accession, location, date))

bioprojects/PRJNA966185/metadata/prepare-metadata.py

@@ -17,8 +17,10 @@
                 continue
             run_accession, run_alias, _, sample_id = line.split("\t")
 
-            record = [run_accession,
-                      sample_id,
-                      "0" if "unenriched" in run_alias else "1"]
+            record = [
+                run_accession,
+                sample_id,
+                "0" if "unenriched" in run_alias else "1",
+            ]
             record.extend(sample_info[sample_id])
             outf.write("\t".join(record) + "\n")