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.
- Python 2.7
- samtools (optional, only for SAM/BAM related scripts)
pip install git+https://github.com/NAL-i5K/coordinates_conversion.git
Scripts to convert reference sequence IDs and coordinates in different file formats.
- fasta_diff
- update_gff
- update_bam
- update_bed
- update_bedgraph
- update_vcf
- Run
fasta_diff
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Compares two very similar FASTA files and outputs coordinate mappings using a multi stage algorithm:
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Stage 1: Find 100% matches
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Stage 2: Find 100% substrings, where the full length of a new sequence can be found as a substring of a oldsequence
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Stage 3: Find cases where part of the sequence was converted into Ns
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Stage 4: Find cases where a old sequence is split into two or more new sequences
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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
- 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
- Run conversion script:
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update_gff
update_gff -a match.tsv example_file/example1.gff3 example_file/example2.gff3 -
update_bam
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samtools needs to be installed before running this program:
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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
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