DOC Better output.md

Fix some grammar mistakes. More explicit information

docs/output.md

@@ -1,10 +1,11 @@
-# Output
+# Output of GMGC-finder
 
-Explanation of the files in the output
+Explanation of the files in the output directory
 
 ## Prodigal output
 
-These three files are the output prodigal.
+These three files are the output of prodigal (if GMGC-finder was called in
+genome mode)
 
 - `prodigal_out.faa` protein sequence
 - `prodigal_out.fna` DNA sequence
@@ -17,8 +18,8 @@ The results of the queries to the GMGC.
 
 There are five columns in the file.
 
-- `query_name`: the name/id of the input genome contig
-- `gene_id`: the Unigene with the best score in GMGC
+- `query_name`: the name/id of the input gene
+- `gene_id`: the Unigene with the best score in the GMGC
 - `align_category: there are four different classes of alignment (see below)
 - `gene_dna`: the DNA sequence of the best hit in GMGC
 - `gene_protein`: the protein sequence of the best hit in GMGC
@@ -36,28 +37,26 @@ There are five columns in the file.
 
 ## Genome bins (`genome_bin.tsv`)
 
-Genome bins (MAGs) found in the results (and a count of how often many genes
-are contained in them).
+Genome bins (MAGs) found in the results (and a count of how many genes are
+contained in them).
 
 There are two columns in the file.
 
 - `genome_bin`: the name of genome bins in GMGC
 - `times_gene_hit`: the times of input genes hitting it 
 
-Note that GMGC unigenes can while not all GMGC unigenes are contained in a
-genome bin, some are contained in many. Thus, the total counts will not (except
-by coincidence) correspond to the number of genes queried.
+Note while not all GMGC unigenes are contained in a genome bin, some are
+contained in many. Thus, the total counts will not (except by coincidence)
+correspond to the number of genes queried.
 
 ## Summary (`summary.txt` and `runlog.yaml`)
 
 The file `summary.txt` provides a human-readable summary of the results, while
-`runlog.yaml` is a summary of run (as a YaML file, it is both machine and
-human-readable).
-
+`runlog.yaml` is a summary of run metadata (as a YaML file, it is both machine
+and human-readable).
 
 The file `summary.txt` should be reproducible and running GMGC-finder twice on
 the same input should produce the same results. By design, though,
-`runglog.yaml` includes information on timing and, thus, is not reproducible.
-
-
+`runglog.yaml` includes information such as the time when the analysis was run
+which is not reproducible.