diff --git a/README.md b/README.md index e93b5da..7c4f800 100644 --- a/README.md +++ b/README.md @@ -2,12 +2,13 @@ Custom script for processing a list of ids (HGNC, transcript) or coordinates with associated annotation, into a comprehensive bed file for the corresponding refseq transcripts for each ID entry. -## What are typical use cases for this app? +## What are typical use cases for this script? - Converting a list of HGNC ids + associated gene level annotation information into a comprehensive bed file for annotation with Ensemble's VEP. -- Other use cases include providing different inputs such a list of transcripts/exact coordinates. +- Other use cases include providing different inputs such a list of transcripts. + Or using exact coordinates to flag a regions such as TERT promoter. -## What data are required for this app to run? +## What data are required for this script to run? - List of ids and annotation information in TSV format. - Human Genome Reference (i.e. hs37d5) @@ -33,10 +34,10 @@ and bed file aligned with the respecive annotation. to determine the corresponding chromosome for each transcript. ## Requirements + - pysam - pandas - igv-reports (v) - argparse - numpy - re diff --git a/gene_annotation2bed.py b/gene_annotation2bed.py index 5bcbd77..71b8af9 100644 --- a/gene_annotation2bed.py +++ b/gene_annotation2bed.py @@ -9,15 +9,13 @@ -o "test6" """ - -import pandas as pd -import numpy as np -import re - import argparse + import argcomplete import igv_report as igv - +import numpy as np +import pandas as pd +import re import gff2pandas as gffpd diff --git a/gff2pandas.py b/gff2pandas.py index 1a77b2e..cd5f61c 100644 --- a/gff2pandas.py +++ b/gff2pandas.py @@ -23,6 +23,7 @@ """ import itertools + import pandas as pd import numpy as np