get bin list

ohmeta · Jun 5, 2022 · dc9535e · dc9535e
1 parent fdad1f3
commit dc9535e
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/metapi/rules/binning_report.smk b/metapi/rules/binning_report.smk
@@ -19,7 +19,7 @@ if len(BINNERS_CHECKM) != 0:
             shell('''rm -rf {output.report_dir}''')
             shell('''mkdir -p {output.report_dir}''')
 
-            bin_list =  glob.glob(os.path.dirname(input[0]) + "/*bin*fa")
+            bin_list =  glob.glob(os.path.dirname(input[0]) + "/*.fa")
             header_list = ["assembly_group", "bin_id", "bin_file", "assembler", "binner",
                            "chr", "length", "#A", "#C", "#G", "#T",
                            "#2", "#3", "#4", "#CpG", "#tv", "#ts", "#CpG-ts"]

diff --git a/metapi/rules/predict_bins.smk b/metapi/rules/predict_bins.smk
@@ -78,7 +78,7 @@ if config["params"]["predict"]["bins_to_gene"]["prokka"]["do"]:
             import time
             import subprocess
 
-            bin_list = glob.glob(input.bins_dir + "/*bin*fa")
+            bin_list = glob.glob(input.bins_dir + "/*.fa")
             gff_count = 0
 
             for bin_fa in bin_list:

diff --git a/metapi/sampler.py b/metapi/sampler.py
@@ -88,7 +88,7 @@ def parse_samples(
 
 def parse_bins(bins_dir):
     bin_list = []
-    for bin_ in glob.glob(bins_dir + "/*/*bin*fa"):
+    for bin_ in glob.glob(bins_dir + "/*/*.fa"):
         bin_dict = dict()
         bin_dict["path"] = bin_.strip()
         bin_dict["id"] = os.path.basename(bin_).rstrip(".fa")

diff --git a/scripts/batch_prokka.py b/scripts/batch_prokka.py
@@ -12,7 +12,7 @@ def run(dir_list, outdir, logdir):
     with open(dir_list) as f:
         for dir in f:
             count += 1
-            bin_list = glob.glob(dir.strip() + "/*bin*fa")
+            bin_list = glob.glob(dir.strip() + "/*.fa")
             for bin in bin_list:
                 bin_id = os.path.basename(bin).rstrip(".fa")
                 prokka_dir = os.path.join(outdir,

diff --git a/scripts/get_bins_id.py b/scripts/get_bins_id.py
@@ -9,7 +9,7 @@
 
 def parse_bins(bins_dir):
     bin_list = []
-    pattern = bins_dir + "/*/*bin*fa"
+    pattern = bins_dir + "/*/*.fa"
     for bin in glob.glob(pattern):
         bin_dict = {}
         bin_fa = os.path.basename(bin)