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Summarize Gene Cts Specifications

Process Details

  • Name: summarize_gene_cts
  • Process UUID: f9318pdpptgn3xywu6ynad04uck9c0
  • Process Group: MAG-qc

Overview

This process summarizes gene counts from multiple annotation files, generating consolidated reports for quality control analysis of metagenome-assembled genomes (MAGs). The process iterates through text files containing gene annotations and combines them with corresponding TSV files to produce individual CSV summaries, culminating in a comprehensive report file.

This process is implemented in Bash, which invokes a Python script for gene count summarization.

Key Functionality

  • Batch Processing: Processes multiple gene annotation files simultaneously
  • Data Integration: Combines information from TXT and TSV file pairs for comprehensive analysis
  • Report Generation: Creates individual CSV summaries and a consolidated report
  • Quality Control: Provides standardized output format for downstream MAG quality assessment

Input/Output Specification

Inputs

Required Inputs

  • Input File Set (TXT)

    • Description: Set of text files containing gene annotation data
    • Format: TXT

  • Input File (TSV)

    • Description: Tab-separated values file with corresponding annotation information
    • Format: TSV

Outputs

  • CSV Output
    • Description: Consolidated CSV report containing summarized gene count statistics for all processed files
    • Format: CSV

References & Resources

  • Tool Documentation: Contact the team for details on summarize_gene_cts.py