Genomics scripts

Python scripts for manipulating various genomics-related file formats.
Some definitions are included in multiple scripts so they are as standalone as possible.

BED scripts

• bedIntersect2percentOverlap.py: output proportion of features participating in an overlap as found by bedtools bedIntersect -wa -wb
• gff2bed.py: convert a GFF3 file to a BED format file

BLAST scripts

• blast2gff: convert blastn, blastp, etc. tabular output to GFF3 format
• blastBestHit.py: output the highest-scoring hit from blastn, blastp, etc. tabular output (-outfmt 6 or 7)
• blastFilter.py: output lines from blastn, blastp, etc. tabular output (-outfmt 6 or 7) where the percent identity satisfies constraints

Circos scripts

• coverage2circosLine.py: calculate average depth of coverage form the output of bedtools genomecov -ibam -d and output a Circos line track
• fasta2GCcontentCircosHeatmap.py: calculate GC content for each window in each sequence in a FASTA file and output a Circos heatmap track
• fixTrackLabels.py: replace labels in Circos track file with the integer label from the associated Circos karyotype file
• gff2circosHeatmap.py: convert feature coordinates in a GFF3 file to Circos heatmap track format with specified bin size
• gff2circosTile.py: convert features in a GFF3 file to Circos tile track format
• vcfSNPrate2circosLine.py.untested: takes a VCF file with or without a GFF3 file whose features (genes) coordinates are represented in the VCF file and outputs SNPs rate per gene or a Circos heatmap track of SNP rate/bin size

FASTA scripts

• fasta2circosIdeograms: output sequence lengths as a Circos ideogram file
• fasta2GCcontentCircosHeatmap.py: calculate GC content for each window in each sequence in a FASTA file and output a Circos heatmap track
• fastaExtractSeqs.py: extract a subset of the sequences in a FASTA file
• fastaExtractNseqs.py: extract the first or second or third etc. n sequences from a FASTA file
• fastaRenameSeqs.py: rename FASTA sequence headers according to a mapping of old to new names
• fastaRenameSeqsByLength.py: sort FASTA sequences in descending order and rename sequences sequentially
• fastaSplitSeqs.py: write a new FASTA file for each sequence in a FASTA file
• gff2fasta.py: extract sequences from a FASTA file based on coordinates in a GFF3 file, using the value from a specified key in the GFF3 attributes column

GFF scripts

• blast2gff: convert blastn, blastp, etc. tabular output to GFF3 format
• gff2bed.py: convert a GFF3 file to a BED format file
• gff2circosHeatmap.py: convert feature coordinates in a GFF3 file to Circos heatmap track format with specified bin size
• gff2circosTile.py: convert features in a GFF3 file to Circos tile track format
• gff2fasta.py: extract sequences from a FASTA file based on coordinates in a GFF3 file using the value from a specified key in the GFF3 attributes column as the sequence name. Depends on BEDTools and BioPython
• gff2introns.py: create a GFF3 with intron features from a GFF3 with gene and exon features or output a list of intron lengths
• gff3line.py: contains the GFF3_class
• gffAddAttribute.py: add a key-value pair to the attributes column of a GFF3 file
• gffFilter.py: remove or retain GFF3 features on specified scaffolds or with specified values for the ID attribute
• gffMergeOverlaps.py: merge overlapping features in a GFF3 file
• gffRemoveScafPart.py: remove features in a GFF3 file whose coordinates
• gffRenameScafs.py: rename scaffolds in a GFF3 file per a two-column map
• gffSubset.py: extracts a subset of a GFF3 file based on values of a chosen attribute key
• gffSubsetLTRdigest.py: extracts feature blocks from a LTRharvest/LTRdigest GFF3
• gffv2Exonerate2gff3.py: convert an Exonerate-generated GFF2 file to GFF3 format

VCF scripts

• vcfSNPrate2circosLine.py.untested: takes a VCF file with or without a GFF3 file whose features (genes) coordinates are represented in the VCF file and outputs SNPs rate per gene or a Circos heatmap track of SNP rate/bin size

Other scripts

• meanMedianMinMax.py: takes input of a list of numbers and outputs the mean, median, minimum value, maximum value, and sum total
• repeatMaskerGFFsubset: takes input of RepeatMasker GFF and writes lines from several categories each into their own file
• repeatMaskerGFFsummarize: writes tables with summarized counts and lengths of features in a RepeatMasker-derived GFF3