Minor adjustments

getzlab · Nov 2, 2024 · 0527487 · 0527487
1 parent 7ea6544
commit 0527487
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Showing 2 changed files with 15 additions and 32 deletions.
diff --git a/python/rnaseqc/legacy_exon_remap.py b/python/rnaseqc/legacy_exon_remap.py
@@ -1,5 +1,5 @@
 import argparse
-from agutil import status_bar
+from tqdm import tqdm
 import subprocess
 import csv
 import shutil
@@ -10,7 +10,7 @@ def run(args):
     print("Parsing GTF")
     gtf = Annotation(args.gtf.name)
     print("Parsing GCT")
-    numRows = int(subprocess.check_output("wc -l %s" % args.gct.name, shell=True).decode().strip().split()[0]) - 3
+    numRows = int(subprocess.check_output(f"wc -l {args.gct.name}", shell=True).decode().strip().split()[0]) - 3
     header = ''.join([next(args.gct), next(args.gct)])
     reader = csv.DictReader(args.gct, delimiter='\t')
     w = tempfile.NamedTemporaryFile('w')
@@ -19,7 +19,7 @@ def run(args):
     writer.writeheader()
     current = None
     features = []
-    for line in status_bar.iter(reader, maximum=numRows):
+    for line in tqdm(reader, total=numRows):
         gene = '_'.join(line['Name'].split('_')[:-1])
         if gene != current:
             if current is not None:
@@ -88,31 +88,14 @@ def run(args):
     print("Cleaning up")
     w.flush()
     args.gct.close()
-    shutil.copyfile(
-        args.gct.name,
-        args.gct.name+'.bak'
-    )
-    shutil.copyfile(
-        w.name,
-        args.gct.name
-    )
+    shutil.copyfile(args.gct.name, args.gct.name+'.bak')
+    shutil.copyfile(w.name, args.gct.name)
 
 
 def main():
     parser = argparse.ArgumentParser('flipper')
-
-    parser.add_argument(
-        'gct',
-        type=argparse.FileType('r'),
-        help="RNA-SeQC 2 Exon reads gct file"
-    )
-
-    parser.add_argument(
-        'gtf',
-        type=argparse.FileType('r'),
-        help="Reference GTF for the exons"
-    )
-
+    parser.add_argument('gct', type=argparse.FileType('r'), help="RNA-SeQC 2 Exon reads gct file")
+    parser.add_argument('gtf', type=argparse.FileType('r'), help="Reference GTF for the exons")
     args = parser.parse_args()
     run(args)
 

diff --git a/python/rnaseqc/run.py b/python/rnaseqc/run.py
@@ -39,25 +39,25 @@ def test_rnaseqc(path):
 
     print('['+datetime.now().strftime("%b %d %H:%M:%S")+'] Running RNA-SeQC', flush=True)
 
-    cmd = '{} {} {} {}'.format(locate_rnaseqc(), args.genes_gtf, args.bam_file, args.output_dir) \
-        + ' -s '+args.prefix \
+    cmd = f"{locate_rnaseqc()} {args.genes_gtf} {args.bam_file} {args.output_dir}" \
+        + f" -s {args.prefix}" \
         + ' -vv'
     if args.stranded is not None:
-        cmd += ' --stranded '+args.stranded
+        cmd += f" --stranded {args.stranded}"
     if args.bed is not None:
-        cmd += ' --bed '+args.bed
+        cmd += f" --bed {args.bed}"
     if args.mapping_quality is not None:
-        cmd += ' --mapping-quality {}'.format(args.mapping_quality)
+        cmd += f" --mapping-quality {args.mapping_quality}"
     if args.mismatch_threshold is not None:
-        cmd += ' --base-mismatch {}'.format(args.mismatch_threshold)
+        cmd += f" --base-mismatch {args.mismatch_threshold}"
     if args.coverage:
         cmd += ' --coverage'
-    print('  * command: "{}"'.format(cmd), flush=True)
+    print(f'  * command: "{cmd}"', flush=True)
     subprocess.check_call(cmd, shell=True)
 
     # gzip GCTs
     subprocess.check_call('gzip {0}.exon_reads.gct {0}.gene_tpm.gct {0}.gene_reads.gct {0}.gene_fragments.gct'.format(args.prefix), shell=True)
     if args.coverage:
-        subprocess.check_call('gzip {}.coverage.tsv'.format(args.prefix), shell=True)
+        subprocess.check_call(f'gzip {args.prefix}.coverage.tsv', shell=True)
 
     print('['+datetime.now().strftime("%b %d %H:%M:%S")+'] Finished RNA-SeQC', flush=True)