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Typographical and Syntactical Errors #2

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dab850a
Changed the options "help" to improve comprehension.
harish0201 Jul 27, 2018
12d0e5f
Update VCF-Simplify.py
harish0201 Jul 27, 2018
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31 changes: 13 additions & 18 deletions README.md
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -17,15 +17,10 @@ and comprehensive scripts.

<br>

**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.


<br>

## Prerequisites :
Expand Down Expand Up @@ -95,12 +90,12 @@ optional arguments:

Additional flags for &quot;VCF To Haplotype&quot;:
-PG PG FORMAT tag containing the phased genotype of the
SAMPLE. Only applicable on &apos;haplotype file output&apos;.
SAMPLE. Only applicable for &apos;haplotype file output&apos;.
-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
&apos;haplotype file output&apos;. Note: &apos;CHROM&apos; 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 &quot;VCF To Table&quot;:
Expand Down Expand Up @@ -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 &apos;VCF-Simplify&apos;; only long format table is
supported for now.
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8 changes: 4 additions & 4 deletions VCF-Simplify.py
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Expand Up @@ -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,
Expand Down