aseSnvs.pl -- To get the ASE and Powerful SNVs from the input SNV file (in config_file) along with their Chi-Squared Goodness of Fit Test p-values. It is an introductory application script to get familiar with the ASARP pipeline (asarp).
perl aseSnvs.pl output_file config_file [optional: parameter_file]
The config_file (same in the ASARP pipeline) is used to obtain the input SNV file path. Other files/paths are read through and ignored.
The criteria (powerful and ASE, i.e. p-value, cutoffs) are contained in the parameter_file (same in the ASARP pipelien). Other parameters are read through and ignored.
The application counts the powerful SNVs and ASE SNVs. It accepts the same configuration and parameter file formats as the full ASARP pipeline. See below and asarp for more details.
config_file is the input configuration file which contains all the input file keys and their paths. The format is <key>tab<path>. Line starting with # are comments. Example: default.config
parameter_file is the parameter configuration file which contains all the thresholds and cutoffs, e.g. p-value cuttoffs and bounds for absolute allelic ratio difference. The format of each line is <parameter>tab<value>. Lines starting with # are comments. It is optional and the default is: default.param
See the format descriptions in snpParser for more details about the input SNV list content.
There will be two result files: "output_file.ase" with the ASE SNVs (a subset of the powerful SNVs), and "output_file.pwr" with the powerful SNVs
Format (space dilimited): chromosome position ref>alt dbSNP_ID ref#:alt#:0 [strand_info] p-value allelic_ratio ref indicates the reference allele, and alt the alternative allele. ref# and alt# are their respective counts (wrong nucleotides are not used so 0 is output in ref#:alt#:0). allelic_ratio = ref#/(ref#+alt#). p-value is the Chi-Squared Test p-value. Examples:
chr1 68591173 A>G rs1046835 103:55:0 [+] 0.651898734177215 0.0001341704 chr5 96111371 G>A rs13160562 73:41:0 [+] 0.640350877192982 0.00272584 chr5 96215303 C>T na 96:3:0 [+] 0.9696969696969 79.029544e-21
The strand_info shown in [ ] will only be output if the input file config has the strand-specific flag set. If it is unset, the [ ] will not be output
asarp, snp_distri, fileParser, snpParser, MyConstants
This pipeline is free software; you can redistribute it and/or modify it given that the related works and authors are cited and acknowledged.
This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.
Cyrus Tak-Ming CHAN
Xiao Lab, Department of Integrative Biology & Physiology, UCLA