From dab850a3dcdc4a00cff4cfc61960a3060271f8be Mon Sep 17 00:00:00 2001 From: Harish Date: Fri, 27 Jul 2018 15:47:25 +0530 Subject: [PATCH 1/2] Changed the options "help" to improve comprehension. --- README.md | 31 +++++++++++++------------------ 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 53108f9..0f27200 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ # VCF-Simplify     v2.1 -A python parser to simplify the vcf file into table like format. -There are several tools available to mainpulate and alter VCF file. -But, a simple and comprehensive tool that can produce a most simple -output required by emperical biologist is still amiss. +A python parser to simplify the vcf file into a (pseudo-)tabular format. +There are several tools available to mainpulate and alter VCF files. +But, a simple but expansive tool that can produce most simple +output is required by empirical biologist is still amiss. - **Convert VCF to TABLE**\ - This tool takes in sorted vcf file and reports a simplified table output + This tool takes in a sorted vcf file and reports a simplified tabular output for `INFO` and `FORMAT` field for each `SAMPLE` of interest. With default state (minimal code) all the `INFO`, `FORMAT` for all the `SAMPLE` are simplified. Fields can be further narrowed down using very convenient @@ -17,15 +17,10 @@ and comprehensive scripts.
-**Exclusively for [phase-Stitcher](https://github.com/everestial/pHASE-Stitcher) and [phase-Extender](https://github.com/everestial/phase-Extender).** +**Exclusively for [phase-Stitcher](https://github.com/everestial/pHASE-Stitcher) and [phase-Extender](https://github.com/everestial/phase-Extender).** Controlled workflows are included. - **Convert VCF to Haplotype**\ - It is also possible to convert the TABLE file into VCF. Controlled, - workflows are included. - - **Convert Haplotype to VCF**\ - It is also possible to convert the TABLE file into VCF. Controlled, - workflows are included. - +
## Prerequisites : @@ -95,12 +90,12 @@ optional arguments: Additional flags for "VCF To Haplotype": -PG PG FORMAT tag containing the phased genotype of the - SAMPLE. Only applicable on 'haplotype file output'. + SAMPLE. Only applicable for 'haplotype file output'. -PI PI FORMAT tag representing the unique index of RBphased - haplotype block in the SAMPLE. Only applicable on + haplotype block in the SAMPLE. Only applicable for 'haplotype file output'. Note: 'CHROM' can also be used as PI if VCF is phased chromosome-wide. - -unphased UNPHASED include unphased variants in the output. Aavailable + -unphased UNPHASED include unphased variants in the output. Available options: yes, no Additional flags for "VCF To Table": @@ -264,10 +259,10 @@ usage: VCF-Simplify BuildVCF [-h] -fromType FROMTYPE -inFile INFILE -outVCF optional arguments: -h, --help show this help message and exit - -fromType FROMTYPE Type of the input file the VCF is being prepared from. + -fromType FROMTYPE Type of the input file to prepare the VCF from. Options: haplotype, table - -inFile INFILE Sorted table or haplotype file.This haplotype file - should be obtained from phase-Stitcher, phase- + -inFile INFILE Sorted table or haplotype file. This haplotype file + can be obtained from phase-Stitcher or phase- Extender. The table file should be in the format output by 'VCF-Simplify'; only long format table is supported for now. From 12d0e5f8fe45cb60c9c29d8f48a226703de9eae5 Mon Sep 17 00:00:00 2001 From: Harish Date: Fri, 27 Jul 2018 15:50:39 +0530 Subject: [PATCH 2/2] Update VCF-Simplify.py --- VCF-Simplify.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/VCF-Simplify.py b/VCF-Simplify.py index 583d27b..9d2b8f9 100644 --- a/VCF-Simplify.py +++ b/VCF-Simplify.py @@ -81,20 +81,20 @@ def main(): "Options: no(0), yes(1). Default: 0 .", required=False, default=0) - '''Task-B: Sub parser for "BuildVCF". To create VCF from simple Table like format. ''' + '''Task-B: Sub parser for "BuildVCF". To create VCF from a tabular format. ''' parser_b = subparsers.add_parser('BuildVCF', help='Create VCF : from a haplotype or a table file. ') # upper level parser within BuildVCF ''' Task - B(01) : From Haplotype To VCF - only require these arguments. ''' parser_b.add_argument("-fromType", required=True, - help="Type of the input file the VCF is being prepared from. " + help="Type of the input file to prepare the VCF. " "Options: haplotype, table ") parser_b.add_argument("-inFile", required=True, help="Sorted table or haplotype file." - "This haplotype file should be obtained from phase-Stitcher, " + "This haplotype file can be obtained from phase-Stitcher or " "phase-Extender. The table file should be in the format " - "output by 'VCF-Simplify'; only long format table is supported for now.") + "output by 'VCF-Simplify'; only long format table is currently supported.") parser_b.add_argument("-outVCF", help="Name of the output VCF file.", required=True) parser_b.add_argument("-vcfHeader", required=True,