GitHub - brendane/miscellaneous_bioinfo_scripts

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 195 Commits
.gitignore		.gitignore
LICENSE		LICENSE
README		README
add_attr_splitstree_svg.py		add_attr_splitstree_svg.py
add_attr_splitstree_svg2.py		add_attr_splitstree_svg2.py
add_attr_splitstree_svg3.py		add_attr_splitstree_svg3.py
add_attr_splitstree_svg4.py		add_attr_splitstree_svg4.py
add_ld_groups_to_gemma_lmm_output.py		add_ld_groups_to_gemma_lmm_output.py
add_missing_to_maf.py		add_missing_to_maf.py
add_outgroup_vcf.py		add_outgroup_vcf.py
align_vcfs_from_genome_alignment.py		align_vcfs_from_genome_alignment.py
aligned_fasta_from_blat.py		aligned_fasta_from_blat.py
allele_freq_sync.py		allele_freq_sync.py
annotate_cdhit_from_ipscan.py		annotate_cdhit_from_ipscan.py
annotate_sibeliaz_blocks.py		annotate_sibeliaz_blocks.py
ath_go_terms_from_top_hits.py		ath_go_terms_from_top_hits.py
bamutils_rpkm2vcf.py		bamutils_rpkm2vcf.py
bamutils_rpkm2vcf2.py		bamutils_rpkm2vcf2.py
betweenness_centrality_plant_bacteria.py		betweenness_centrality_plant_bacteria.py
betweenness_centrality_plant_bacteria.r		betweenness_centrality_plant_bacteria.r
blast2graphs.py		blast2graphs.py
blast_best_hit_to_bed.py		blast_best_hit_to_bed.py
blast_fmt1_top_hits.py		blast_fmt1_top_hits.py
break_tree_into_chunks.py		break_tree_into_chunks.py
break_tree_into_chunks_approx.py		break_tree_into_chunks_approx.py
cdhit2orthotable.py		cdhit2orthotable.py
cdhit2tsv.py		cdhit2tsv.py
cdhit2vcf.py		cdhit2vcf.py
cdhit_seeds_fasta.py		cdhit_seeds_fasta.py
check_processed_fastq_by_raw.py		check_processed_fastq_by_raw.py
check_r2_groups_onevar.py		check_r2_groups_onevar.py
choose_top_bottom_strains.r		choose_top_bottom_strains.r
closest_downstream.py		closest_downstream.py
closest_downstream2.py		closest_downstream2.py
combine_depth_files.py		combine_depth_files.py
combine_ensembl_ncbi_gff.py		combine_ensembl_ncbi_gff.py
combine_gemma_annotation_ld_groups.py		combine_gemma_annotation_ld_groups.py
combine_mummer_extracted_snps.py		combine_mummer_extracted_snps.py
combine_orthofinder_dup_annotation_orthosets.py		combine_orthofinder_dup_annotation_orthosets.py
combine_orthofinder_duplication_batches.py		combine_orthofinder_duplication_batches.py
combine_orthotable_and_annotations.py		combine_orthotable_and_annotations.py
combine_random_mapit_runs.r		combine_random_mapit_runs.r
compare_aligned_reads.py		compare_aligned_reads.py
compare_divergence_orthosets.r		compare_divergence_orthosets.r
compare_mnp_real_coords.py		compare_mnp_real_coords.py
concatenate_reference_bam.py		concatenate_reference_bam.py
concatenate_reference_fasta.py		concatenate_reference_fasta.py
consensus_from_maf.py		consensus_from_maf.py
count_adjacent_snps_alignment_quality.py		count_adjacent_snps_alignment_quality.py
count_fastq_lines		count_fastq_lines
count_fastq_lines.cpp		count_fastq_lines.cpp
count_fastq_lines2.cpp		count_fastq_lines2.cpp
count_s_ns_sites.py		count_s_ns_sites.py
de_interleave.py		de_interleave.py
depth2cov.py		depth2cov.py
dnadiff_extract_simm.py		dnadiff_extract_simm.py
ensembl_to_gowinda.py		ensembl_to_gowinda.py
evaluate_mugsy_maf.py		evaluate_mugsy_maf.py
extract_and_align_mummer_coords.py		extract_and_align_mummer_coords.py
extract_bbh.py		extract_bbh.py
extract_blast_fmt7_bitscore.py		extract_blast_fmt7_bitscore.py
extract_blast_fmt7_lengths_bitscore.py		extract_blast_fmt7_lengths_bitscore.py
extract_bslmm_stats.r		extract_bslmm_stats.r
extract_from_fasta.py		extract_from_fasta.py
extract_gff_annot.py		extract_gff_annot.py
extract_orthogroups_seqs.py		extract_orthogroups_seqs.py
extract_orthosets_from_orthofinder.py		extract_orthosets_from_orthofinder.py
extract_orthosets_from_orthofinder_trees.py		extract_orthosets_from_orthofinder_trees.py
extract_orthosets_from_orthofinder_trees_dist.py		extract_orthosets_from_orthofinder_trees_dist.py
extract_orthosets_seqs.py		extract_orthosets_seqs.py
extract_orthosets_seqs2.py		extract_orthosets_seqs2.py
extract_random_bslmm_stats.r		extract_random_bslmm_stats.r
extract_ref_region_from_show_aligns.py		extract_ref_region_from_show_aligns.py
extract_replicons_random_gemma_runs.py		extract_replicons_random_gemma_runs.py
extract_simulated_reads.py		extract_simulated_reads.py
extract_simulated_reads_from_cram.py		extract_simulated_reads_from_cram.py
extract_worst_mutation.py		extract_worst_mutation.py
fasta2f84dist.sh		fasta2f84dist.sh
fasta2fastmephylip.py		fasta2fastmephylip.py
fasta2maf.py		fasta2maf.py
fasta_identity.py		fasta_identity.py
fasta_missingness_filter.py		fasta_missingness_filter.py
fetch_snps_vcf2tsv.py		fetch_snps_vcf2tsv.py
filter_dgrp.py		filter_dgrp.py
filter_fasta_length.py		filter_fasta_length.py
filter_fasta_names.py		filter_fasta_names.py
filter_maf_length.py		filter_maf_length.py
filter_plink_ld.py		filter_plink_ld.py
filter_vcf_genotype_allele_ratio.py		filter_vcf_genotype_allele_ratio.py
find_closest_gene_from_blast_hits.py		find_closest_gene_from_blast_hits.py
find_closest_gene_from_blast_hits2.py		find_closest_gene_from_blast_hits2.py
find_knockout_enzymes.py		find_knockout_enzymes.py
find_re_sites.py		find_re_sites.py
fishers_exact_pools.r		fishers_exact_pools.r
fishers_p_combiner_scans.r		fishers_p_combiner_scans.r
flatten_fasta.py		flatten_fasta.py
forward_r2_model_selection.r		forward_r2_model_selection.r
fpkm_from_htseq_count.py		fpkm_from_htseq_count.py
fq_counter		fq_counter
frqcount2popgen.py		frqcount2popgen.py

Repository files navigation

Various bioinformatic scripts I use at work. Some of them are one-off,
some of them are generally useful, and some of them don't work.

Uploaded to github as a backup.