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1 parent db5217b commit 6af210eCopy full SHA for 6af210e
build/utils/tpmFromCounts.py
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'''
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python script to read in counts matrix and gene lengths to calculate tpm
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-Input: expects patient Id's on column names
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-
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-Args:
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-genome_link : str
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- Link to human genome build. Defualts to "https://ftp.ensembl.org/pub/grch37/release-113/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz"
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-cols_to_exclude : list
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- List of column names to exclude. Script assumes that patient Id's are in column names. Put columns to exclude (that don't have patient info in them).
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import argparse
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