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278 Commits
alignment
alignment
 
 
api_web_scraping
api_web_scraping
 
 
automation
automation
 
 
cdhit_clustering
cdhit_clustering
 
 
edirect_related
edirect_related
 
 
genbank-fan
genbank-fan
 
 
get_aa_by_org_names
get_aa_by_org_names
 
 
parsers
parsers
 
 
quick_shell
quick_shell
 
 
seq_util
seq_util
 
 
tiedje-scripts
tiedje-scripts
 
 
tools
tools
 
 
uclust_py
uclust_py
 
 
16s_seq_process.sh
16s_seq_process.sh
 
 
LICENSE
LICENSE
 
 
MiSeq_rdptool_map_parser.py
MiSeq_rdptool_map_parser.py
 
 
Pull_seq_from_uniprot.py
Pull_seq_from_uniprot.py
 
 
README.md
README.md
 
 
add_file_name_to_reads.py
add_file_name_to_reads.py
 
 
add_file_name_to_txt.py
add_file_name_to_txt.py
 
 
bin_reads.py
bin_reads.py
 
 
blast_parser.py
blast_parser.py
 
 
blast_parser_grep_high_evalues.py
blast_parser_grep_high_evalues.py
 
 
cdhit_clst_parser.py
cdhit_clst_parser.py
 
 
cdhit_parser_copy.py
cdhit_parser_copy.py
 
 
check_chimera_numbers.py
check_chimera_numbers.py
 
 
check_derep_seq_abundance.py
check_derep_seq_abundance.py
 
 
clst_abundance.py
clst_abundance.py
 
 
clustal_to_fasta.py
clustal_to_fasta.py
 
 
combine_clstr_blast_wrap.sh
combine_clstr_blast_wrap.sh
 
 
combine_desc_clstr.py
combine_desc_clstr.py
 
 
combine_nwk_id_w_organisms.py
combine_nwk_id_w_organisms.py
 
 
combine_taxa.py
combine_taxa.py
 
 
count_clst_abundance.py
count_clst_abundance.py
 
 
counter.py
counter.py
 
 
counter.pyc
counter.pyc
 
 
fastq_to_fasta.py
fastq_to_fasta.py
 
 
file_line_stats.py
file_line_stats.py
 
 
fix_index_fastqgz_names.py
fix_index_fastqgz_names.py
 
 
get_taxa_uniprot_txt.py
get_taxa_uniprot_txt.py
 
 
grep_seq_header_add_index.py
grep_seq_header_add_index.py
 
 
grep_seq_header_add_sample_name.py
grep_seq_header_add_sample_name.py
 
 
hmmalign_wrap.sh
hmmalign_wrap.sh
 
 
id_tax_split.py
id_tax_split.py
 
 
insert_desc_blast+.py
insert_desc_blast+.py
 
 
length_summary.py
length_summary.py
 
 
mac2unix.pl
mac2unix.pl
 
 
make_wrapper.sh
make_wrapper.sh
 
 
map_rdp_classifer_to_otus.py
map_rdp_classifer_to_otus.py
 
 
rdp_assem_stat_parser.py
rdp_assem_stat_parser.py
 
 
revcomp_rdp_format.py
revcomp_rdp_format.py
 
 
seq_process_summary_parser.py
seq_process_summary_parser.py
 
 
strip_id.py
strip_id.py
 
 
subset_I_for_pandaseq.py
subset_I_for_pandaseq.py
 
 
test_bio.py
test_bio.py
 
 
uniprot_dat.py
uniprot_dat.py
 
 
uniprot_euk_fungi.py
uniprot_euk_fungi.py
 
 
uniprot_id_all.py
uniprot_id_all.py
 
 
uniprot_id_microbes.py
uniprot_id_microbes.py
 
 
uniprot_id_prok.py
uniprot_id_prok.py
 
 
uniprot_ref_taxa.py
uniprot_ref_taxa.py
 
 
usearch_denovo_chim_remover.py
usearch_denovo_chim_remover.py
 
 
usearch_map_uc_parser.py
usearch_map_uc_parser.py
 
 
xander_start_quality_check.py
xander_start_quality_check.py
 
 

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code

This directory contains some useful scripts (solely python at the moment) for some basic file parsing.

    1. blast table output
    1. addition of blast descriptions
    1. uniprot .dat parser
    1. cdhit clstr parser
    1. bash automation scripts

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useful scripts

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