📦 mipe

22 pages

C

  • csv2mipe(1)Generates MIPE file based on 3 tab-delimited files based on MIPE version v1.1 arguments: * tab-delimited file with PCR-level data * tab-delimited file with SNP-level data * tab-delimited file with…✨

G

  • genotype2mipe(1)Inserts SNP data into MIPE file based on MIPE version v0.9 Make sure SNPs are already defined in the USE part of the PCR record. arguments: * mipe_file * STDIN: tab-delimited list of data, in the…✨

M

  • mipe06to07(1)Reads a MIPE file version 0.6 and prints it in version 0.7✨
  • mipe08to09(1)Reads a MIPE file version 0.8 and prints it in version 0.9✨
  • mipe0_9to1_0(1)Reads a MIPE file version 0.9 and prints it in version 1.0✨
  • mipe2dbSTS(1)Generates input file for submission to dbSTS included in output: STS section of dbSTS submission based on MIPE version v1.1 arguments: * mipe_file * config file * (optional) list of PCR IDs The…✨
  • mipe2fas(1)Generates FASTA file included in output: FASTA formatted seq based on MIPE version v1.1 arguments: * [design|use] * mipe_file * (optional) list of PCR IDs✨
  • mipe2genotypes(1)Generates list of genotypes from a MIPE file included in output: PCR ID, list of SNP IDs, genotypes for each sample based on MIPE version v1.1 arguments: * mipe_file * (optional) list of PCR IDs✨
  • mipe2html(1)Generates HTML page based on MIPE file based on MIPE version v1.1 arguments: * mipe_file * (optional) list of PCR IDs✨
  • mipe2pcroverview(1)Generates overview of PCRs from a MIPE file included in output: PCR ID, projects, researchers, number of SNPs, length of PCR fragment, remarks based on MIPE version v1.1 arguments: * mipe_file *…✨
  • mipe2pcrprimers(1)Generates list of pcrprimers from a MIPE file based on MIPE version v1.1 arguments: * mipe_file * (optional) list of PCR IDs✨
  • mipe2putativesbeprimers(1)Generates list of putative SBE primers from a MIPE file included in output: PCR ID, SNP ID, putative forward SBE primer, putative reverse SBE primer based on MIPE version v1.1 arguments: * mipe_file…✨
  • mipe2sbeprimers(1)Generates list of SBE primers from a MIPE file included in output: PCR ID, SNP ID, SBE ID, SBE oligo, SBE strand, SBE tail, SBE specific, SBE remark based on MIPE version v1.1 arguments: * mipe_file…✨
  • mipe2snps(1)Generates list of SNPs from a MIPE file included in output: PCR ID, SNP ID, SNP pos, SNP amb, allele freqs, number of animals genotyped, SNP rank, flanking seqs, SNP remarks based on MIPE version…✨
  • mipeCheckSanity(1)Check sanity of MIPE file, focussing on contents (vs 'form', that can be checked using xmllint) based on MIPE version v0.9 arguments: * mipe_file * (optional) list of PCR IDs✨

R

  • removePcrFromMipe(1)Removes PCR data from MIPE file based on MIPE version v0.7 arguments: * mipe_file * STDIN: PCR ID✨
  • removeSbeFromMipe(1)Removes SBE data from MIPE file based on MIPE version v0.9 arguments: * mipe_file * STDIN: tab-delimited list of data, in the following order: PCR ID, SNP ID, SBE ID✨
  • removeSnpFromMipe(1)Removes SNP data from MIPE file based on MIPE version v0.9 arguments: * mipe_file * STDIN: tab-delimited list of data, in the following order: PCR ID, SNP ID✨

S

  • sbe2mipe(1)Inserts SBE data into MIPE file CAUTION: DOES NOT WORK AT THE MOMENT!! based on MIPE version v1.1 arguments: * mipe_file * STDIN: tab-delimited list of data, in the following order: PCR ID, SNP ID…✨
  • snp2mipe(1)Inserts SNP data into MIPE file CAUTION: DOES NOT WORK WITH MIPEv1.0 YET!! based on MIPE version v0.9 arguments: * mipe_file * STDIN: tab-delimited list of data, in the following order: PCR ID, SNP…✨
  • snpPosOnDesign(1)Adds pos_design to SNP based on MIPE version v1.1 arguments: * mipe_file * STDIN: tab-delimited list of data, in the following order: PCR ID, SNP ID✨
  • snpPosOnSource(1)Adds pos_source to SNP based on MIPE version v1.1 arguments: * mipe_file * STDIN: tab-delimited list of data, in the following order: PCR ID, SNP ID✨