Clarify log output. Note GENCODE annotation requirement.

README.md

@@ -12,7 +12,7 @@
 
 ## Usage
 
-`rosewater` is fairly simple to use. It requires an annotation GTF file, a TSV file of TPMs with the gene name column named 'gene' (these should match the 'gene_name' attributes in the annotation GTF), the name of the sample column in the TPM file, and an output file from [ROSE](https://bitbucket.org/young_computation/rose/src/master/). Optionally, users can set a TPM threshold (set to 5 by default) for filtering out lowly/non-expressed genes prior to assignment.
+`rosewater` is fairly simple to use. It requires a GENCODE annotation GTF file, a TSV file of TPMs with the gene name column named 'gene' (these should match the 'gene_name' attributes in the annotation GTF), the name of the sample column in the TPM file, and an output file from [ROSE](https://bitbucket.org/young_computation/rose/src/master/). Optionally, users can set a TPM threshold (set to 5 by default) for filtering out lowly/non-expressed genes prior to assignment.
 
 ```
 Usage: rosewater [OPTIONS]

rosewater.py

@@ -237,11 +237,11 @@ def assign_genes(enh_bedtools, tpms, transcript_dict, genetype_dict, out_file, l
                                          enh_bedtools.count()), file=log_file)
     print("Enhancers overlapping no TSS: " + str(no_tss) + ", " +
           str(100 * (no_tss / total_enh)) + "% of total enhancers", file=log_file)
-    print("Enhancers overlapping one TSS: " + str(one_tss) + ", " +
+    print("Enhancers overlapping TSSes from one gene: " + str(one_tss) + ", " +
           str(100 * (one_tss / total_enh)) + "% of total enhancers", file=log_file)
-    print("Enhancers overlapping two TSSes: " + str(two_tss) + ", " +
+    print("Enhancers overlapping TSSes from two genes: " + str(two_tss) + ", " +
           str(100 * (two_tss / total_enh)) + "% of total enhancers", file=log_file)
-    print("Enhancers overlapping three or more TSSes: " + str(three_or_more_tss) + ", " + str(100 * (three_or_more_tss / total_enh)) + "% of total enhancers",
+    print("Enhancers overlapping TSSes from three or more genes: " + str(three_or_more_tss) + ", " + str(100 * (three_or_more_tss / total_enh)) + "% of total enhancers",
           file=log_file)
     print("Enhancers using all TSSes where assignment differed from ROSE: " + str(all_diff_from_rose) + ", " +
           str(100 * (all_diff_from_rose / total_enh)) + "% of total enhancers", file=log_file)

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='rosewater',
-    version='0.1.0',
+    version='0.1.1',
     description='Expression-aware gene assignment of ROSE output.',
     long_description=long_description,
     long_description_content_type="text/markdown",