fix(sra): improve layout extraction from NCBI db (#168)

workflow/rules/sra_download.smk

@@ -42,12 +42,15 @@ checkpoint get_layout:
         ),
     shell:
         """
-        (mkdir -p {output.outdir} && \
+        (mkdir -p {output.outdir}; \
         layout=$(efetch -db sra \
         -id {wildcards.sample} \
-        -format runinfo | \
-        awk -F, 'BEGIN {{ exitval = 1 }} NR>1 && $1 == "{wildcards.sample}" {{ print $16; exitval=0 }} END {{ exit exitval }}') && \
-        touch {output.outdir}/$layout.info; \
+        -format runinfo \
+        -mode xml | \
+        xtract -pattern Row \
+        -if Run -equals {wildcards.sample} \
+        -element LibraryLayout); \
+        touch {output.outdir}/$layout.info ; \
         ) 1> {log.stdout} 2> {log.stderr}
         """
 
@@ -80,44 +83,27 @@ rule prefetch:
 
 
 def get_layouts(wildcards):
-    """Get the layout of each sample."""
-
-    # populate layout dictionary
-    layouts = {}
-    for sample in samples[
-        samples.index.str.contains("^.RR", regex=True, case=True)
-    ].index.tolist():
-        layouts[sample] = []
+    layouts = []
+    for each_sample in samples.index.tolist():
         checkpoint_output = checkpoints.get_layout.get(
-            sample=sample, **wildcards
+            sample=each_sample, **wildcards
         ).output.outdir
-        _files = [
-            os.path.join(checkpoint_output, _file)
-            for _file in os.listdir(checkpoint_output)
-            if _file.endswith(".info")
-        ]
-        assert len(_files) == 1
-        layouts[sample] = os.path.splitext(os.path.basename(_files[0]))[0]
-
-    # convert layouts to short form
-    layouts_short = {}
-    for key, val in layouts.items():
-        if val == "PAIRED":
-            layouts_short[key] = "pe"
-        elif val == "SINGLE":
-            layouts_short[key] = "se"
+        layout = glob_wildcards(os.path.join(checkpoint_output, "{layout}.info")).layout
+        if "PAIRED" in layout:
+            layouts.append(
+                os.path.join(
+                    config["outdir"], "compress", each_sample, each_sample + ".pe.tsv"
+                )
+            )
+        elif "SINGLE" in layout:
+            layouts.append(
+                os.path.join(
+                    config["outdir"], "compress", each_sample, each_sample + ".se.tsv"
+                )
+            )
         else:
-            raise ValueError(f"Layout {val} for sample {key} not recognized.")
-
-    # return layouts
-    layouts = expand(
-        os.path.join(
-            config["outdir"], "compress", "{sample}", "{sample}.{seqmode}.tsv"
-        ),
-        zip,
-        sample=layouts_short.keys(),
-        seqmode=layouts_short.values(),
-    )
+            pass
+        print(layouts)
     return layouts