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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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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

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