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#Usage
usage: pancake create [-h] [--sequences SEQUENCES [SEQUENCES ...]] [--ids IDS [IDS ...]] [--email EMAIL] [--pan_file PAN_FILE] [--ali [ALI [ALI ...]]] [--min_len MIN_LEN] [--no_self_alignments] [--no_refinement] [--max_ref_len MAX_REF_LEN] [--min_entries MIN_ENTRIES] optional arguments: -h, --help show this help message and exit --sequences SEQUENCES [SEQUENCES ...], -s SEQUENCES [SEQUENCES ...] fasta or multiple fasta file providing input chromosome sequences --ids IDS [IDS ...], -i IDS [IDS ...] gi ids of sequences to download from NCBI --email EMAIL, -e EMAIL if downloading your sequences via gi ids, please specify your email address; in case of excessive usage, NCBI will attempt to contact a user at the e-mail address provided prior to blocking access to the E-utilities --pan_file PAN_FILE, -p PAN_FILE File name of new PanCake Object (DEFAULT=pancake.pan) --ali [ALI [ALI ...]], -a [ALI [ALI ...]] pairwise alignments (BLAST or nucmer output) to include in PanCake Object --min_len MIN_LEN, -l MIN_LEN minimum length of pairwise alignments to include (DEFUALT=25) --no_self_alignments, -nsa if set, skip pairwise alignments between regions on identical chromosomes as input (DEFAULT=False) --no_refinement, -nr if set, no post-processing refinements will be done after inclusion of pairwise alignments (DEFAULT=False) --max_ref_len MAX_REF_LEN post processing parameter: maximum length of SF's reference sequence to be treated (DEFAULT=3) --min_entries MIN_ENTRIES post processing parameter: minimum count of entries in an SF to be treated (DEFUALT=10)
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