Fetch nucleotide chains

The fetch_nucleotide_chains module uses the yielded chaining results (tab-delimited table) to extract nucleotide chains in FASTA-format from the genomic sequence(s).

Input data:

The fetch_nucleotide_chains module requires the FASTA-file(s) to extract nucleotide chained sequences using the tab-delimited ouptut table of one of the chaining modules, for example, from SegMantX’s chain_self_alignments or chain_alignments module:

Click here to visit an example table

Examples:

I. Fetching chains from self-sequence alignment chaining:

SegMantX fetch_nucleotide_chains --input_file tests/NZ_AP022172.1.chains.tsv --fasta_file_query tests/NZ_AP022172.1.fasta --output_file tests/NZ_AP022172.1.chains.fasta

• -i or --input_file: Output file from chaining results as input.
• -fq or --fasta_file_query: Fasta file to extract from chains as nucleotide sequences.
• -o, --output_file: Output file: Fasta file containing nucleotide chains.

II. Fetching chains from sequence alignment chaining between two distinct sequences:

SegMantX fetch_nucleotide_chains --input_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.tsv --fasta_file_query tests/NZ_CP018634.1.fasta  --fasta_file_subject tests/NZ_CP022004.1.fasta --output_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.fasta

• -i or --input_file: Output file from chaining results as input.
• -fq or --fasta_file_query: Fasta file to extract from chains as nucleotide sequences.
• -fs or --fasta_file_subject: Fasta file to extract from chains as nucleotide sequences.
• -o, --output_file: Output file: Fasta file containing nucleotide chains.

Output:

Output of fetching nucleotide chains module:

For example:

>1_query NZ_AP022172.1:19940-79291 (+)
ATGCCGCATCAGCGGCATGGAAGGCGGCACTCTGTTGTTTCATATGATACAGGAGTAAAA
CCGCCGAAGCCCGGCGTAAGCCGGTACTGATTGATAGATTTCACCTTACCCATCCCCAGC
CCTGCCAGACCATACCCGCTTTCAGCCATGAGAGAGCTTCTGTGCGCGGTCGGAGTGGTC
CCGACGAGGGTTTACCCGAAGTCGGGGCGTATCTCCGCGTTAGCGGGCCGTGAGGGCCGC
TTACGAGCGTGTACTGAGAACTTCCAGCGAGAAGACTGACAGCGATGAAGATGTAGTTAC
...
>1_subject NZ_AP022172.1:89352-147930 (+)
ATGCCGCGCCAGCGGCATGGAAGGCGGCACGCTGTGGTTACATGTGATACCGGAGTAAAA
CCGCCGAAGCCCGGCGTCAGCCGGTACTGATTGATAGATTTCACCTTACCCATCCCTTGC
CCTGCCAGACCATACCTGTTTTCAGCCATGAGAGAGCTTCTGTGCGCGGTCGGAGTGGTC
CCGACGAGGGTTTACCCGAAGTCGGGGCGTATCTCCGCGTTAGCGGGCCGTCAGGGCCGC
TTACGAGCGTGTACTGAGGACTTCCAGCCAGAACACTGACAGCGATGACGGAGTATAGTT
...