ENH use --dbdir to run outsite the main dir

Author: cocodyq

README.md

@@ -51,6 +51,10 @@ If you want to check if the installation works well, you can test with mock data
 
 Please make `GMSC-mapper` as your work directory.
 
+```bash
+cd GMSC-mapper
+```
+
 - Create GMSC database index
 
 Default alignment tool is Diamond.
@@ -68,87 +72,108 @@ gmsc-mapper createdb -i ./examples/target.faa -o ./examples/ -m mmseqs
 - Input is genome contig sequences.
 
 ```bash
-gmsc-mapper -i ./examples/example.fa -o ./examples_output/ --db ./examples/targetdb.dmnd --habitat ./examples/ref_habitat.npy --habitat-index ./examples/ref_habitat_index.tsv --quality ./examples/ref_quality.txt --taxonomy ./examples/ref_taxonomy.npy --taxonomy-index ./examples/ref_taxonomy_index.tsv --domain ./examples/ref_domain.txt
+gmsc-mapper -i ./examples/example.fa -o ./examples_output/ --dbdir ./examples/ 
 ```
 
 - Input is amino acid sequences.
 
 ```bash
-gmsc-mapper --aa-genes ./examples/example.faa -o ./examples_output/ --db ./examples/targetdb.dmnd --habitat ./examples/ref_habitat.npy --habitat-index ./examples/ref_habitat_index.tsv --quality ./examples/ref_quality.txt --taxonomy ./examples/ref_taxonomy.npy --taxonomy-index ./examples/ref_taxonomy_index.tsv --domain ./examples/ref_domain.txt
+gmsc-mapper --aa-genes ./examples/example.faa -o ./examples_output/ --dbdir ./examples/
 ```
 
 - Input is nucleotide gene sequences.
 
 ```bash
-gmsc-mapper --nt-genes ./examples/example.fna -o ./examples_output/ --db ./examples/targetdb.dmnd --habitat ./examples/ref_habitat.npy --habitat-index ./examples/ref_habitat_index.tsv --quality ./examples/ref_quality.txt --taxonomy ./examples/ref_taxonomy.npy --taxonomy-index ./examples/ref_taxonomy_index.tsv --domain ./examples/ref_domain.txt
+gmsc-mapper --nt-genes ./examples/example.fna -o ./examples_output/ --dbdir ./examples/
 ```
 
 - Check another alignment tool: MMseqs2
 
 ```bash
-gmsc-mapper -i ./examples/example.fa -o ./examples_output/ --db ./examples/targetdb --habitat ./examples/ref_habitat.npy --habitat-index ./examples/ref_habitat_index.tsv --quality ./examples/ref_quality.txt --taxonomy ./examples/ref_taxonomy.npy --taxonomy-index ./examples/ref_taxonomy_index.tsv --domain ./examples/ref_domain.txt --tool mmseqs
+gmsc-mapper -i ./examples/example.fa -o ./examples_output/ --dbdir ./examples/ --tool mmseqs
 ```
 
 ## Usage
-Please make `GMSC-mapper` as your work directory.
 
 ### Download GMSC database
-`--dbdir`: Path to database output directory.(default: `GMSC-mapper/db`)
 
-`--all`: Download all database
+We recommend to use `GMSC-mapper` as your current work directory. You can derectly follow the commonds below.
 
-`-f`: Force download even if the files exist
+`--dbdir`: Path to GMSC database annotation index files. (default: `./db`. If `GMSC-mapper` is your current work directory, the database files will be downloaded at `GMSC-mapper/db`)
 
+```bash
+cd GMSC-mapper
 ```
-gmsc-mapper downloaddb
+
+```bash
+gmsc-mapper downloaddb --dbdir ./db
 ```
 
+Otherwise if you want to use custom `--dbdir` directory, it should be consistent with `-o` (Path to database index output of Diamond and MMseqs2) in the creating index step
+
 ### Create GMSC database index of Diamond/MMseqs2
-`-o`: Path to database output directory.(default: `GMSC-mapper/db`)
+
+We also recommend to use `GMSC-mapper` as your current work directory. You can derectly follow the commonds below.
+
+The input (`i`) is the fasta file (`GMSC10.90AA.faa.gz`) downloaded to the dbdir (default: `./db`. If `GMSC-mapper` is your current work directory, the dbdir is `GMSC-mapper/db`) in the downloading step.
+
+`-o`: Path to database index output of Diamond and MMseqs2. (default: `./db`. If `GMSC-mapper` is your current work directory, the database files will be created at `GMSC-mapper/db`)
 
 `-m`: Alignment tool (Diamond / MMseqs2).
 
+```bash
+cd GMSC-mapper
 ```
-gmsc-mapper createdb -i ./db/GMSC10.90AA.faa.gz -m diamond
+
+```bash
+gmsc-mapper createdb -i ./db/GMSC10.90AA.faa.gz -o ./db -m diamond
 ```
 or
-```
-gmsc-mapper createdb -i ./db/GMSC10.90AA.faa.gz -m mmseqs
+```bash
+gmsc-mapper createdb -i ./db/GMSC10.90AA.faa.gz -o ./db -m mmseqs
 ```
 
+Otherwise if you want to use custom `-o` directory, it should be consistent with `--dbdir` (Path to GMSC database annotation index files) in the download step.
+
 ### Default
-GMSC database / habitat / taxonomy / quality / domain file path and output directory path can be assigned on your own.Default is `GMSC-mapper/db` and `GMSC-mapper/output`.
+GMSC Database directory (`--dbdir`) and output directory (`-o`) can be assigned on your own. Default is `./db` and `./output`. If `GMSC-mapper` is your current work directory, they will be `GMSC-mapper/db` and `GMSC-mapper/output`. 
+
+If you use `GMSC-mapper` as your current work directory. You can derectly follow the commonds below. Otherwise, you need to assign your custom `--dbdir` which contains database files.
+
+```bash
+cd GMSC-mapper
+```
 
 1. Input is genome contig sequences.
 
 ```bash
-gmsc-mapper -i ./examples/example.fa
+gmsc-mapper -i ./examples/example.fa --dbdir ./db
 ```
 
 2. Input is amino acid sequences.
 
 ```bash
-gmsc-mapper --aa-genes ./examples/example.faa 
+gmsc-mapper --aa-genes ./examples/example.faa --dbdir ./db
 ```
 
 3. Input is nucleotide gene sequences.
 
 ```bash
-gmsc-mapper --nt-genes ./examples/example.fna
+gmsc-mapper --nt-genes ./examples/example.fna --dbdir ./db
 ```
 
 ### Alignment tool: Diamond / MMseqs2 is optional
 If you want to change alignment tool (Diamond / MMseqs2), you can use `--tool`.
 
 ```bash
-gmsc-mapper -i ./examples/example.fa --tool mmseqs
+gmsc-mapper -i ./examples/example.fa --dbdir ./db --tool mmseqs
 ```
 
 ### Habitat / taxonomy / quality / domain annotation is optional
 If you don't want to annotate habitat / taxonomy / quality / domain you can use `--no-habitat`/`--no-taxonomy`/`--no-quality`/`--no-domain`.
 
 ```bash
-gmsc-mapper -i ./examples/example.fa --no-habitat --no-taxonomy --no-quality --no-domain
+gmsc-mapper -i ./examples/example.fa --dbdir ./db --no-habitat --no-taxonomy --no-quality --no-domain
 ```
 
 ## Output files
@@ -247,7 +272,9 @@ The output folder will contain
 
 * `--nt-genes`: Path to the input nucleotide gene sequence FASTA file (possibly .gz compressed).
 
-* `-o/--output`: Output directory (will be created if non-existent). (default: ../output)
+* `--dbdir`: Path to the GMSC database directory. (default: `./db`)
+
+* `-o/--output`: Output directory (will be created if non-existent). (default: `./output`)
 
 * `--tool`: Sequence alignment tool (Diamond / MMseqs). (default: diamond)
 
@@ -274,11 +301,21 @@ The output folder will contain
 * `--quiet`: Disable alignment console output. (default:False)
 
 ### Subcommands and Parameters 
+#### Download GMSC database annotation index files
+Subcommands: `gmsc-mapper downloaddb`
+
+* `--dbdir`: Path to GMSC database annotation index files. (default: `./db`. If `GMSC-mapper` is your current work directory, the database files will be downloaded at `GMSC-mapper/db`)
+
+* `--all`: Download all database
+
+* `-f`: Force download even if the files exist
+
+#### Create database index of Diamond and mmseqs
 Subcommands: `gmsc-mapper createdb`
 
 * `-i`: Path to the GMSC FASTA file.
 
-* `-o/--output`: Path to database output directory. (default: ../db)
+* `-o/--output`: Path to database index output of Diamond and MMseqs2. (default: `./db`. If `GMSC-mapper` is your current work directory, the database files will be created at `GMSC-mapper/db`)
 
 * `-m/--mode`: Alignment tool (Diamond / MMseqs2).
 

examples/GMSC10.90AA.cdd.tsv.xz

@@ -0,0 +1,24 @@
+0	air
+1	annelidae associated
+2	anthropogenic
+3	built environment
+4	built environment,human skin
+5	chicken gut
+6	coral associated,marine
+7	human gut
+8	human gut,isolate
+9	human skin
+10	isolate
+11	lake associated
+12	lake associated,river associated
+13	lake associated,water associated
+14	marine
+15	marine,isolate
+16	marine,wastewater,water associated
+17	marine,water associated
+18	plant associated
+19	river associated
+20	soil
+21	termite gut
+22	wastewater
+23	water associated

examples/GMSC10.90AA.habitat.index.tsv

@@ -0,0 +1,19 @@
+0	Unknown
+1	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrososphaeraceae;g__Nitrososphaera;s__Nitrososphaera sp002494895
+2	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrososphaeraceae;g__UBA10452;s__UBA10452 sp003176995
+3	d__Bacteria
+4	d__Bacteria;p__Actinobacteriota;c__Actinomycetia
+5	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium;s__Microbacterium sp003476465
+6	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae
+7	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__UBA9676;s__UBA9676 sp003541285
+8	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter
+9	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia
+10	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales
+11	d__Bacteria;p__Firmicutes_A
+12	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster;s__Enterocloster sp900551225
+13	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales
+14	d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1242;g__UBA6345;s__UBA6345 sp002437945
+15	d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1242;g__UMGS687;s__UMGS687 sp900545735
+16	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01;s__SYFN01 sp005800405
+17	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7;s__Arctic96AD-7 sp002685535
+18	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Pedosphaeraceae;g__UBA11358