coordinates_conversion

Conversion programs that use the output from fasta_diff to convert reference sequence IDs and coordinates in Gff3, bam, bed, or bedgraph file formats. Main contributors are Han Lin (original development) and interns of i5k workspace.

Prerequisite

• Python 2.7
• samtools (optional, only for SAM/BAM related scripts)

Installation

pip install git+https://github.com/NAL-i5K/coordinates_conversion.git

Features

Scripts to convert reference sequence IDs and coordinates in different file formats.

• fasta_diff
  • wiki page
• update_gff
  • wiki page
• update_bam
  • wiki page
• update_bed
  • wiki page
• update_bedgraph
  • wiki page
• update_vcf
  • wiki_page

Quick start

1. Run fasta_diff

• Compares two very similar FASTA files and outputs coordinate mappings using a multi stage algorithm:

• Stage 1: Find 100% matches

• Stage 2: Find 100% substrings, where the full length of a new sequence can be found as a substring of a oldsequence

• Stage 3: Find cases where part of the sequence was converted into Ns

• Stage 4: Find cases where a old sequence is split into two or more new sequences

• Outputs (match.tsv) the 6 columns as tab-separated values: old_id, old_start, old_end, new_id, new_start, new_end

  fasta_diff example_file/old.fa example_file/new.fa -o match.tsv -r report.txt

2. Select a conversion script that matches your file format

• Gff3 format: update_gff
• Bam format: bam_update
• Bed format: bed_update
• Bedgraph format: bedgraph_update

3. Run conversion script:

• update_gff

  update_gff -a match.tsv example_file/example1.gff3 example_file/example2.gff3

• update_bam

  • samtools needs to be installed before running this program:

  • If you have a bam file without a corresponding index file (.bai), you can generate one using:

    samtools index example_file/example.bam

  • Then use update_bam to convert your bam files

    update_bam -a match.tsv example_file/example.bam

  • update_bed

    update_bed -a match.tsv example_file/example.bed

  • update_bedgraph

    update_bedgraph -a match.tsv example_file/example.bedGraph

  • update_vcf

    update_vcf -a match.tsv example_file/example.vcf