Erick Cardenas Scripts

A collection of scripts for bioinformatics analysis

I work mostly with metagenomic data so my scripts handle tasks like quality control, general statistics (on contigs, bams, etc), and parsing of blast and hmmer results

Feel free to use and modify.

EC

Name		Name	Last commit message	Last commit date
Barcode_Preparation_Toolbox		Barcode_Preparation_Toolbox
dist		dist
.gitignore		.gitignore
GET_LINEAGES_NCBI.EC.py		GET_LINEAGES_NCBI.EC.py
GET_LINEAGES_NCBI.py		GET_LINEAGES_NCBI.py
HMM_search_and_parse_and_extract.py		HMM_search_and_parse_and_extract.py
HMM_search_and_parse_and_extract_2.py		HMM_search_and_parse_and_extract_2.py
Nonpareil.R		Nonpareil.R
add_coverage_to_fasta_contigs.py		add_coverage_to_fasta_contigs.py
add_coverage_to_fasta_contigs_2.py		add_coverage_to_fasta_contigs_2.py
add_lineage_to_dictionary.py		add_lineage_to_dictionary.py
add_lineage_to_dictionary_2.py		add_lineage_to_dictionary_2.py
all_hmm_ps.len		all_hmm_ps.len
all_hmm_ps_2.len		all_hmm_ps_2.len
annotate_blast.py		annotate_blast.py
annotate_blast_part2.py		annotate_blast_part2.py
bam_to_fastq.sh		bam_to_fastq.sh
bowtie2sam.pl		bowtie2sam.pl
calculate_coverage_from_bed_coverage.R		calculate_coverage_from_bed_coverage.R
calculate_sequence_conservation.py		calculate_sequence_conservation.py
clean_blast_result.py		clean_blast_result.py
compare_lists.py		compare_lists.py
concatenate_cazy_results.R		concatenate_cazy_results.R
convert_fasta_to_list.py		convert_fasta_to_list.py
correct_cazy_dictionary.py		correct_cazy_dictionary.py
count_hmmer_hits.py		count_hmmer_hits.py
create_detailed_bed_graph.R		create_detailed_bed_graph.R
create_foly_dictionary.py		create_foly_dictionary.py
create_max_bits_dictionary.py		create_max_bits_dictionary.py
create_multiple_hmm.sh		create_multiple_hmm.sh
create_newcazy_dictionary.py		create_newcazy_dictionary.py
create_newcazy_dictionary_with_subfamilies.py		create_newcazy_dictionary_with_subfamilies.py
create_sample_by_OTU_table.R		create_sample_by_OTU_table.R
dbCAN_HMM_Genomes.py		dbCAN_HMM_Genomes.py
dereplicate_fasta.py		dereplicate_fasta.py
estimate_gene_coverage_from_simulated_fasta.py		estimate_gene_coverage_from_simulated_fasta.py
estimate_gene_coverage_from_simulated_fasta_v_cryptococcus.py		estimate_gene_coverage_from_simulated_fasta_v_cryptococcus.py
estimate_gene_coverage_from_simulated_fasta_v_neurospora.py		estimate_gene_coverage_from_simulated_fasta_v_neurospora.py
estimate_richness_by_family.R		estimate_richness_by_family.R
extract_sam_columns.py		extract_sam_columns.py
fasta2stockholm.pl		fasta2stockholm.pl
fasta_removal.py		fasta_removal.py
fasta_to_stockholm.py		fasta_to_stockholm.py
fastaselection_nucleotide.py		fastaselection_nucleotide.py
fastaselection_protein.py		fastaselection_protein.py
fastaselection_protein_v2.py		fastaselection_protein_v2.py
fastq-to-fasta.py		fastq-to-fasta.py
fastq_to_fasta.py		fastq_to_fasta.py
fastqcing.sh		fastqcing.sh
fetch_genome_xml.py		fetch_genome_xml.py
filter_blast_by_query_coverage.py		filter_blast_by_query_coverage.py
filter_by_size.py		filter_by_size.py
filter_fasta.py		filter_fasta.py
filter_fasta_by_completeness.py		filter_fasta_by_completeness.py
filter_mothur_biome.py		filter_mothur_biome.py
find_linear_correlation.R		find_linear_correlation.R
find_unique_contigs.hit.py		find_unique_contigs.hit.py
fq_gz-fa.py		fq_gz-fa.py
fq_gz-first_100000.fa.py		fq_gz-first_100000.fa.py
gbk2faa.txt		gbk2faa.txt
gbk2fna.txt		gbk2fna.txt
genbank_to_fasta.py		genbank_to_fasta.py
genbank_to_table.py		genbank_to_table.py
genome_len_dict3.pkl		genome_len_dict3.pkl
get_full_name.py		get_full_name.py
get_gi_number_from_cazy_blast.py		get_gi_number_from_cazy_blast.py
get_gi_number_from_cazy_fasta.py		get_gi_number_from_cazy_fasta.py
get_hmm_len.py		get_hmm_len.py
get_name_and_description.py		get_name_and_description.py
get_protein_from_nucleotide_accession.py		get_protein_from_nucleotide_accession.py
get_protein_from_nucleotide_accession_v2.py		get_protein_from_nucleotide_accession_v2.py
get_protein_with_gi_number.py		get_protein_with_gi_number.py
heatmap_3.R		heatmap_3.R
heatmap_colors_in.cols.R		heatmap_colors_in.cols.R
hmmscan-parser.sh		hmmscan-parser.sh
len_stats_from.fasta.py		len_stats_from.fasta.py
modify_dereplicated.py		modify_dereplicated.py
multi_selection.py		multi_selection.py
multi_selection_for7.py		multi_selection_for7.py
multiline_fasta_to_fasta.py		multiline_fasta_to_fasta.py
nmds.R		nmds.R
normalize_kegg.py		normalize_kegg.py
parse_hmm_tabular_output.sh		parse_hmm_tabular_output.sh
parse_taxonomic_distribution_and_activities_from_cazy_htmls.py		parse_taxonomic_distribution_and_activities_from_cazy_htmls.py
parse_taxonomic_distribution_from_cazy_htmls.py		parse_taxonomic_distribution_from_cazy_htmls.py
parse_taxonomy.py		parse_taxonomy.py
parse_xml_result.py		parse_xml_result.py
pheatmap.R		pheatmap.R
pkl_to_csv.py		pkl_to_csv.py
plot_gene_expression.R		plot_gene_expression.R
print_checkm_output.py		print_checkm_output.py
process_Dave_data.sh		process_Dave_data.sh
progress_bar.py		progress_bar.py
progress_bar.pyc		progress_bar.pyc
quality-trim.py		quality-trim.py
quality-trim_to_gz.py		quality-trim_to_gz.py
readme.md		readme.md
remoteblastp.py		remoteblastp.py
remoteblastp_vs_refsq.py		remoteblastp_vs_refsq.py
rename_fasta-to-fasta.py		rename_fasta-to-fasta.py

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