Rule 'collect_abundance' for single-read data was ommited.

snakemake/Snakefile.single

@@ -39,6 +39,36 @@ rule run_salmon_gz:
         SALMON_PATH + " quant -i {input.idx} -l A -r {input.r} -o {output} -p " + NUM_THREADS + " 2>/dev/null"
 
 
+rule collect_abundance:
+    input:
+        expand(join(OUTPUT_DIR,"{sample_fq}"), sample_fq = SAMPLES_FQ) +
+        expand(join(OUTPUT_DIR,"{sample_gz}"), sample_gz = SAMPLES_GZ) 
+    output:
+        join(OUTPUT_DIR,"EXPR.csv")
+    run:
+        def get_abundance(fname):
+            from collections import defaultdict
+            abundance = defaultdict( float )
+            with open(fname, "r") as inp:
+                line = inp.readline()
+                for line in inp:
+                    line = line.strip().split()
+                    name = line[0]
+                    abundance[name] += float(line[3]) if EXPR_TYPE is "TPM" else float(line[-1])
+
+            return abundance
+
+        tb = dict()
+        for file in input:
+            file = join(file, "quant.sf")
+            sid = file.split("/")[-2]
+            tb[sid] = get_abundance(file) 
+
+        import pandas as pd
+        with open(str(output), "w") as oup:
+            oup.write(pd.DataFrame(tb).to_csv(sep=",", index_label="TE"))
+
+
 rule collect_mappability:
     input:
         expand(join(OUTPUT_DIR,"{sample_fq}"), sample_fq = SAMPLES_FQ) +