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Updating header in 7b_SummaryStats.py

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Auden Cote-L'Heureux 2024-01-26 11:05:28 -05:00 committed by GitHub
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PTL1/Transcriptomes/Scripts/7b_SummaryStats.py
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@ -1,3 +1,15 @@
# Last updated Sept 2023
# Author: Auden Cote-L'Heureux
# This script produces both taxon- and sequence-level statistics to describe the ReadyToGo files
# output by PhyloToL Part 1, as well as some OG-level information from the Hook (OG reference)
# database and the original input assembled transcripts. It relies on the utility script CUB.py
# to calculate composition statistics (GC content, Effective Number of Codons, etc.). Both sequence
# level and taxon-level stats are summarized in tab-separated outputs written to the Output folder.
# This script requires that the OG reference database is available as an amino acid fasta file
# in the Databases/db_OG folder with the same file name as the .dmnd file used in script 3. This script
# is intended to be run as part of the PhyloToL 6 Part 1 pipeline using the script wrapper.py.
import os, sys
import argparse
from Bio import SeqIO