Scripts

This document contains all the scripts for/by CGAT. Scripts are written to be called from the command line.

Genomics

• bam2geneprofile.py - build meta-gene profile for a set of transcripts/genes
• bed2bed - manipulate bed files
• bed2gff.py - convert bed to gff/gtf
• gff2bed.py - convert from gff/gtf to bed
• diff_gtf.py - compute overlap between multiple gtf files
• gff2psl.py - convert from gff to psl
• gff2coverage.py - compute genomic coverage of gff intervals
• gff2fasta.py - output sequences from genomic features
• gff2gff.py - manipulate gff files
• gff2histogram.py - compute histograms from intervals in gff or bed format
• gff2stats.py - count features, etc. in gff file
• gtf2gff.py - convert a transcript set to genomic features
• gtf2gtf.py - manipulate transcript models
• gtf2fasta.py - annotate genomic bases from a gene set
• bam2wiggle.py - convert bam to wig/bigwig file
• bed2annotator.py - convert bed to annotator format
• bed2graph.py - compute the overlap graph between two bed files
• chain2psl.py - convert a chain file to a psl file
• diff_bed.py - count differences between several bed files
• fasta2bed.py - segment sequences
• gff2table.py - compute features for intersection of two gff files

Visualization

Sequences and rates

• index_fasta.py - Index fasta formatted files
• diff_fasta.py - compare contents of two fasta files

Matrices and Tables

• csvs2csv.py - join tables
• csv2csv.py - operate on tables
• csv2db.py - upload table to database
• csv_cut.py - select columns from a table
• csv_intersection.py - intersect two tables
• csv_rename.py - rename columns in a table
• csv_set.py - set operations on a table
• cat_tables.py - concatenate tables
• table2table.py - operate on tables

Stats

• data2histogram.py - histogram data in a table

Tools

Cluster and jobs

• split_file.py - split a file into parts

Other

• cgat_script_template.py - template for cgat scripts

Unsorted

• bam2UniquePairs.py - filter/report uniquely mapped read pairs from a (bwa!) bam-file
• bam2bam.py - modify bam files
• bam2bed.py - convert bam formatted file to bed formatted file
• bam2fastq.py - output fastq files from a bam-file
• bam2peakshape.py - compute peak shape features from a bam-file
• Purpose
• Usage
• Documentation
• Command line options
• beds2counts - compute overlap stats between multiple bed files
• bed2fasta.py - get sequences from bed file
• bed2stats.py - summary of bed file contents
• beds2beds.py - decompose bed files
• combine_tables.py - join tables
• diff_chains.py - compare to chain formatted files
• fasta2variants.py - create sequence variants from a set of sequences
• fastq2fastq.py - manipulate fastq files
• fastq2table.py - compute stats on reads in fastq files
• genome_bed.py - Create a bed file tiling a genome from a fai file
• index2bed.py - convert indexed fasta file to bed file
• medip_merge_intervals.py - merge differentially methylated regions
• cgat_rebuild_extensions.py - rebuild all cython extensions
• vcf2vcf.py - manipulate vcf files
• vcfstats_sqlite.py - reformat output of vcf-stats for database loading
• bam_vs_bam.py - compute coverage correlation between bam files
• bam_vs_bed.py - count context that reads map to
• bam_vs_gtf.py - compare bam file against gene set
• diff_bam.py - compare multiple bam files against each other
• fasta2fasta.py - operate on sequences
• fasta2kmercontent.py
• fastas2fasta.py - concatenate sequences from multiple fasta files
• fastqs2fasta.py - interleave two fastq files
• fastqs2fastqs.py - manipulate (merge/reconcile) fastq files
• gtf2tsv.py - convert gtf file to a tab-separated table
• gtfs2tsv.py - compare two genesets
• rnaseq_junction_bams2bam.py - convert mappings against junctions to genomic coordinates
• split_gff - split a gff file into chunks
• bams2bam.py - merge genomic and transcriptome mapped bamfiles
• bed.plot.py - create genomic snapshots using the IGV Viewer
• cgat2dot.py - create a graph between cgat scripts
• cgat_get_options.py - build a sorted list of all options used in scripts
• cgat_pep8_check_code_quality.py - check PEP8 conformance of cgat Code
• csv_select.py - select rows from a table
• fastq2summary.py - compute summary stats for a fastq file
• fastqs2fastq.py - merge reads in fastq files
• gff32gtf.py - various methods for converting gff3 files to gtf
• script_template.py
• split_fasta.py
• transfac2transfac.py - filter transfac motif files
• wig2bed.py - convert densities to intervals