Open loic-couderc opened 7 years ago
The read_fasta_file_handle function is duplicated in many locations:
scripts/compute_assembly_stats.py scripts/compute_lca_from_tab.py scripts/compute_pairwise_distance_matrix.py scripts/compute_ref_coverage_histogram.py scripts/exonerate_to_sam.py scripts/extract_taxo_from_fasta.py scripts/fasta_clean_name.py scripts/fasta_get_lengths.py scripts/fasta_length_filter.py scripts/fasta_name_filter.py scripts/filter_sam_by_coverage.py scripts/filter_sam_by_pid.py scripts/get_HMP_OTU_psn.py scripts/matam_assembly.py scripts/remove_redundant_sequences.py scripts/replace_Ns_by_As.py scripts/replace_Ns_by_rand_nu.py scripts/sort_fasta_by_length.py
The issue #8 introduce a new module (scripts/fasta_utils.py). Use this to deduplicate the code.
The scripts/compute_abundance.py and scripts/krona.py use the one from fasta_clean_name. Replace the import.
Some other function may be to replace as well ( read_fastq_file_handle, format_seq...).
The read_fasta_file_handle function is duplicated in many locations:
The issue #8 introduce a new module (scripts/fasta_utils.py). Use this to deduplicate the code.
The scripts/compute_abundance.py and scripts/krona.py use the one from fasta_clean_name. Replace the import.
Some other function may be to replace as well ( read_fastq_file_handle, format_seq...).