Crm/brca

README.md

@@ -19,11 +19,9 @@ source activate vcf_parse
 
 
 ```
-usage: vcf_parse.py [-h] [-v] [-O OUTPUT] [-t TRANSCRIPTS]
-                    [-T TRANSCRIPT_STRICTNESS] [-b BED | -B BED_FOLDER]
-                    [-k KNOWN_VARIANTS] [-c CONFIG] [-l]
-                    input
-
+usage: vcf_parse.py [-h] [-v] [-i INPUT VCF] [-O OUTPUT]
+                    [-t TRANSCRIPTS] [-n NTC]
+
 summary:
 Takes a VCF file and parses the variants to produce a tab delimited
 variant report.
@@ -34,109 +32,17 @@ positional arguments:
 optional arguments:
   -h, --help            show this help message and exit
   -v, --version         show program's version number and exit
-  -O OUTPUT, --output OUTPUT
 
+  -i INPUT VCF --inp INPUT VCF
+                        VCF file and filepath
+
+ -o OUTPUT, --outfile OUTPUT
                         Filepath to folder where output reports will be saved.
                         If missing, defaults to current directory.
 
-  -t TRANSCRIPTS, --transcripts TRANSCRIPTS
-
-                        Filepath to preferred transcripts file.
-
-                        Must be a tab seperated file with preferred transcripts in the second
-                        column. If missing, all entries in the preferred transcript column
-                        will be labelled as 'Unknown'.
-
-  -T TRANSCRIPT_STRICTNESS, --transcript_strictness TRANSCRIPT_STRICTNESS
-
-                        Strictness of matching while annotating preferred transcripts.
-                        Default setting is low.
-
-                        Options:
-
-                        high - Transcripts must be an exact match.
-                               e.g. NM_001007553.2 and NM_001007553.1 won't match,
-                                    NM_001007553.1 and NM_001007553.1 will.
-
-                        low  - Transcripts will match regardless of the version number. The
-                               version number is after the . at the end of a transcript
-                               e.g. NM_001007553.2 and NM_001007553.1 will match.
-
-  -b BED, --bed BED
-                        Filepath to a single BED file.
-
-                        The BED file will be applied to the variant report and a seperate
-                        report saved with the BED file applied. This report will be saved in
-                        the same output folder as the original variant report, with the BED
-                        file name added to it.
-                        Cannot be used together with -B flag.
-
-  -B BED_FOLDER, --bed_folder BED_FOLDER
-
-                        Filepath to folder containing BED files.
-
-                        Each BED file will be applied to the variant report and a seperate
-                        report saved with the BED file applied. These reports will be saved in
-                        a new folder within the output folder, named the same as the input BED
-                        folder.
-                        The file names will be the same as the original variant report, with
-                        the BED file name added to them.
-                        Cannot be used together with -b flag.
-
-  -k KNOWN_VARIANTS, --known_variants KNOWN_VARIANTS
-
-                        Filepath to known variants file.
-
-                        This is a VCF file containing any known variants and an associated
-                        classification. The classification will be added to the variant
-                        report. The VCF must have an annotation named 'Classification' within
-                        the INFO field for each variant.
-
-                        Key:
-                        0 - Artifact
-                        1 - Benign
-                        2 - Likely benign
-                        3 - VUS
-                        4 - Likely pathogenic
-                        5 - Pathogenic
-
-  -c CONFIG, --config CONFIG
-
-                        Filepath to config file.
-
-                        This is a tab seperated text file containing a number of rows, where
-                        each row specifies an annotation to be included in the variant report.
-                        Only annotations included in the config file will be included in the
-                        variant report.
-                        The columns in the variant report will be in the same order as the
-                        order in which the annotations appear in the config file.
-
-                        Each row contains:
-
-                        Column 1 - Required. Annotation headers, these must match up with how
-                                   they appear in the VCF (case sensitive).
-
-                        Column 2 - Required. Location where to find the data within the VCF,
-                                   used to select the correct parsing function.
-                                   options: info, format, vep, filter or pref.
-
-                        Column 3 - Optional. Alternative name for column header.
-
-                        To make a config file with all available options from a VCF, run:
-                            vcf_parse -l path_to_input_vcf > config.txt
-
-  -l, --config_list
-                        Return a list of all availabile config to the screen, then exit.
-                        See CONFIG section for usage.
+-t PREFERRED TRANSCRIPT --pref_trans PREFERRED TRANSCRIPT
+                        Preferred transcript file and filepath   
 ```
 
-### Special formatting for report fields:  
-- % Allele frequency has been calculated from the AD
-- Genotypes are reformatted from 0/0, 0/1 and 1/1 to HOM_REF, HET and HOM_ALT, respectively, to prevent them from appearing as dates in Excel
-- dbSNP, COSMIC and HGMD are parsed from the 'Existing_variation' VEP field
-- All population frequencies from ExAC and 1KG are re-formatted to a percentage
-- Intron and exon numberings are renamed from x/y to x|y (where x and y are numbers), to prevent them appearing as dates in Excel
-- HGVS coding (HGVSc) and protein (HGVSp) sequences have had the transcript name trimmed off
-
 ### Testing
 To run unit tests run `python -m unittest test`

env/vcf_parse.yaml

@@ -1,8 +1,9 @@
-name: vcf_parse
+name: vcf_parse_somamp
 channels:
 - bioconda
 dependencies:
-- python=2.7
+- python=3.9.16
 - bedtools=2.27.1
 - pip:
-  - pyvcf==0.6.8
+  - pyvariantfilter==1.6.2
+  - pysam==0.20.0