Update README.md

Author: TCLamnidis

README.md

@@ -11,73 +11,68 @@ A tool to check two different EingenStrat databses for shared individuals, and e
 ```
 usage: eigenstrat_database_tools.py (-i <Input file prefix>) (-c <input ind file> | -R | -E) [-L <SAMPLE LIST> | -S Ind [-S Ind2]] [-o <OUTPUT FILE PREFIX>]
 
-A tool to check two different EingenStrat databses for shared individuals, and
-extract or remove individuals from an EigenStrat database.
+A tool to check two different EingenStrat databses for shared individuals, and extract or remove individuals from an EigenStrat database.
 
 Available options:
   -h, --help            show this help message and exit
-  -i <INPUT FILES PREFIX>, --Input <INPUT FILES PREFIX>
-                        The desired input file prefix. Input files are assumed
-                        to be <INPUT PREFIX>.geno, <INPUT PREFIX>.snp and
-                        <INPUT PREFIX>.ind .
+  -g <GENO FILE NAME>, --genoFn <GENO FILE NAME>
+                        The path to the input geno file.
+  -s <SNP FILE NAME>, --snpFn <SNP FILE NAME>
+                        The path to the input snp file.
+  -i <IND FILE NAME>, --indFn <IND FILE NAME>
+                        The path to the input ind file.
   -o <OUTPUT FILES PREFIX>, --Output <OUTPUT FILES PREFIX>
-                        The desired output file prefix. Three output files are
-                        created, <OUTPUT FILES PREFIX>.geno , <OUTPUT FILES
-                        PREFIX>.snp and <OUTPUT FILES PREFIX>.ind .
-  -s <INPUT FILE SUFFIX>, --Suffix <INPUT FILE SUFFIX>
-                        The suffix (if any) that follows .geno/.snp/.ind in
-                        the input files. For example, specifying '-s .txt'
-                        will treat <INPUT PREFIX>.{geno,snp,ind}.txt as the
-                        desired input files.
+                        The desired output file prefix. Three output files are created, <OUTPUT FILES PREFIX>.geno , <OUTPUT FILES PREFIX>.snp and <OUTPUT FILES PREFIX>.ind .
   -C <INPUT FILE>, --Check <INPUT FILE>
-                        Check the -i .ind file and the second .ind file for
-                        duplicate individuals. Population assignment and/or
-                        individual sex are not checked, only individual names.
-                        Names are case sensitive.
-  -E, --Extract         Extract the selected individuals from the EigenStrat
-                        database, creating a new set of EigenStrat files with
-                        the selected individuals only.
-  -R, --Remove          Remove the selected individuals from the EigenStrat
-                        database, creating a new set of EigenStrat files
-                        without the selected individuals.
+                        Check the -i .ind file and the second .ind file for duplicate individuals. Population assignment and/or individual sex are not checked, only individual names. Names are case
+                        sensitive.
+  -E, --Extract         Extract the selected individuals from the EigenStrat database, creating a new set of EigenStrat files with the selected individuals only.
+  -R, --Remove          Remove the selected individuals from the EigenStrat database, creating a new set of EigenStrat files without the selected individuals.
   -L <INDIVIDUAL LIST FILE>, --SampleList <INDIVIDUAL LIST FILE>
-                        A list of samples to be Extracted (-E) or Removed (-R)
-                        from the database. Can be a list of individual names
-                        (1 per line), or the output of duplicate check (-C).
-                        Required with -E or -R. Mutually exclusive with -S.
+                        A list of samples to be Extracted (-E) or Removed (-R) from the database. Can be a list of individual names (1 per line), or the output of duplicate check (-C). Required with -E
+                        or -R. Mutually exclusive with -S.
   -S <INDIVIDUAL>, --Sample <INDIVIDUAL>
-                        A samples to be Extracted (-E) or Removed (-R) from
-                        the database. Can be called multiple times. Required
-                        with -E or -R. Mutually exclusive with -L.
+                        A samples to be Extracted (-E) or Removed (-R) from the database. Can be called multiple times. Required with -E or -R. Mutually exclusive with -L.
   -v, --version         Print the version and exit.
-
 ```
 ---
 # Eigenstrat SNP Coverage
-A tool to calculate the numbered of covered and total reads for each individual in an EigenStrat dataset. 
+A tool to calculate the numbered of covered and total reads for each individual in an EigenStrat dataset.
 
 ```
 usage: eigenstrat_snp_coverage.py (-i <Input file prefix>) [-s <Input file suffix>] [-o <Output filepath>] [-j | --json]
 
-A tool to check two different EingenStrat databses for shared individuals, and
-extract or remove individuals from an EigenStrat database.
+A tool to check two different EingenStrat databses for shared individuals, and extract or remove individuals from an EigenStrat database.
 
 Available options:
   -h, --help            show this help message and exit
-  -i <INPUT FILES PREFIX>, --Input <INPUT FILES PREFIX>
-                        The desired input file prefix. Input files are assumed
-                        to be <INPUT PREFIX>.geno, <INPUT PREFIX>.snp and
-                        <INPUT PREFIX>.ind .
-  -s <INPUT FILE SUFFIX>, --Suffix <INPUT FILE SUFFIX>
-                        The suffix (if any) that follows .geno/.snp/.ind in
-                        the input files. For example, specifying '-s .txt'
-                        will treat <INPUT PREFIX>.{geno,snp,ind}.txt as the
-                        desired input files.
+  -g <GENO FILE NAME>, --genoFn <GENO FILE NAME>
+                        The path to the input geno file.
+  -s <SNP FILE NAME>, --snpFn <SNP FILE NAME>
+                        The path to the input snp file.
+  -i <IND FILE NAME>, --indFn <IND FILE NAME>
+                        The path to the input ind file.
   -o <OUTPUT FILEPATH>, --Output <OUTPUT FILEPATH>
-                        The filepath where the output table should be saved.
-                        Omit to print to stdout.
-  -j, --json            Create additional json formatted output file named
-                        <OUTPUT FILE>.json . [Default: '<INPUT FILES
-                        PREFIX>_eigenstrat_coverage_mqc.json']
+                        The filepath where the output table should be saved. Omit to print to stdout.
+  -j <JSON OUTPUT FILEPATH>, --json <JSON OUTPUT FILEPATH>
+                        Create additional json formatted output file named <JSON OUTPUT FILEPATH> .
   -v, --version         Print the version and exit.
 ```
+# Rename Snps
+A tool to rename the SNPs in an EigenStrat snp file based on a reference EigenStrat or plink snp file. Uses the genetic coordinate of SNPs to determine identity.
+
+```
+usage: rename_snps.py (-i <INPUT .SNP FILE>) (-n <NAMED SNP FILE>) [-f <NAMED FILE FORMAT>]
+
+Rename the SNPs in an eigenstrat snp file based on a reference eigenstrat or plink snp file. Uses the genetic coordinate of SNPs to determine identity.
+
+Available options:
+  -h, --help            show this help message and exit
+  -i <INPUT .SNP FILE>, --Input <INPUT .SNP FILE>
+                        The input snp file.
+  -n <NAMED SNP FILE>, --Name_file <NAMED SNP FILE>
+                        An Eigenstrat or plink formatted snp file with the desired SNP names.
+  -f <NAMED FILE FORMAT>, --Format <NAMED FILE FORMAT>
+                        The format of the desired snp name file. Can be either 'EIGENSTRAT' or 'PLINK' [default: EIGENSTRAT]
+  -v, --version         Print the version and exit.
+```