update docs

README.md

@@ -52,7 +52,7 @@ The output folder contains :
 
 (2) hit_table.tsv : results of the query. There are five columns in the file: query_name,gene_id,align_category,gene_dna,gene_protein.
 
-(3) genome_bin.tsv : results of times of a genome bin that genes hitting it.
+(3) genome_bin.tsv : times of a genome bin that input genes hitting it。
 
 (4) summary.txt : Summary of the query.
 

docs/index.md

@@ -22,7 +22,7 @@ The output folder contains :
 
 (2) hit_table.tsv : results of the query. There are five columns in the file: query_name,gene_id,align_category,gene_dna,gene_protein.
 
-(3) genome_bin.tsv : results of times of a genome bin that genes hitting it.
+(3) genome_bin.tsv : times of a genome bin that input genes hitting it
 
 (4) summary.txt : Summary of the query.
 

docs/output.md

@@ -0,0 +1,56 @@
+# Output
+
+Explaination of the files in the output
+
+
+
+## prodigal_out.faa , prodigal_out.fna , gene.coords.gbk
+These three files are the output of the prodigal.
+
+prodigal_out.faa is the protein sequence.
+
+prodigal_out.fna is the dna sequence.
+
+gene.coords.gbk is the gene information
+
+
+
+## hit_table.tsv :
+
+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 gene_id with the best hit_score in GMGC
+- align_category: there are four different classes of alignment
+- gene_dna : the dna sequence of the hitted gene in GMGC
+- gene_protein : the protein sequence of the hitted gene in GMGC
+
+#### Align_category
+
+- EXACT : above 95% nucleotide identity with at least 95% coverage
+
+- SIMILAR : above 80% nucleotide identity with at least 80% coverage
+
+- MATCH : above 50% nucleotide identity with at least 50% coverage
+
+- NO MATCH : no match in GMGC
+
+
+
+## genome_bin.tsv
+
+Times of a genome bin that input genes hitting it
+
+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 
+
+
+
+## summary.txt
+
+Summary of the query
+

mkdocs.yml

@@ -5,3 +5,4 @@ nav:
         - 'GMGC-Finder': index.md
         - 'Install': install.md
         - 'Usage': usage.md
+        - 'Output' : output.md