pyAlignment2Tab
pyAlignment2Tab is part of the pyCRAC package. Converts pyReadAligner fasta output to a tabular alignment output.
Example:
The tool expects a standard pyReadAligner fasta-formatted output file: >GeneX ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAACAGCAGCAGCGAGAGTAGTAGTAACAAAAACAATATCAATGTCGGCGTCGGTGACGATAGCGGTAA >257930-10 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT---------------------------------------------------------------------------------------------------------------- >3664964-1 ---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT---------------------------------------------------------------------------------------------------------------- >4033560-1 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT---------------------------------------------------------------------------------------------------------------- >8571880-1 ---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT---------------------------------------------------------------------------------------------------------------- >9617396-1 ---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT---------------------------------------------------------------------------------------------------------------- >843368-5 ------------AACAcGGATACAAGACACGCACATTCTG------------------------------------------------------------------------------------------------------------------- >854553-5 ------------AACATGGATACAAGACACGCAC--TCTG------------------------------------------------------------------------------------------------------------------- >1522401-2 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA----------------------------------------------------------------------------------------------------- >5981234-1 --------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA----------------------------------------------------------------------------------------------------- >997684-4 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA----------------------------------------------------------------------------------------------------- >1046653-4 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC---------------------------------------------------------------------------------------------------- >1103730-4 ---------------ATGGATACAAGACACGCACAcTCTG------------------------------------------------------------------------------------------------------------------- >1603913-2 ---------------ATGGATACAAGAaACGCACAcTCTG------------------------------------------------------------------------------------------------------------------- >180349-12 ---------------ATGGATACAAGACACGCACATTCcGCTTTACTG----------------------------------------------------------------------------------------------------------- >1985106-1 ---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC---------------------------------------------------------------------------------------------------- >1987775-1 ---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC---------------------------------------------------------------------------------------------------- >2258725-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC---------------------------------------------------------------------------------------------------- >2631987-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC---------------------------------------------------------------------------------------------------- This will be converted into: 1 .........|.........|.........|.........|.........|.........|.........|.........|.........| 90 >GeneX ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAAC >257930-10 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT----------------------------------------------- >3664964-1 ---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT----------------------------------------------- >4033560-1 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT----------------------------------------------- >8571880-1 ---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT----------------------------------------------- >9617396-1 ---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT----------------------------------------------- >843368-5 ------------AACAcGGATACAAGACACGCACATTCTG-------------------------------------------------- >854553-5 ------------AACATGGATACAAGACACGCAC--TCTG-------------------------------------------------- >1522401-2 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA------------------------------------ >5981234-1 --------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA------------------------------------ >997684-4 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA------------------------------------ >1046653-4 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC----------------------------------- >1103730-4 ---------------ATGGATACAAGACACGCACAcTCTG-------------------------------------------------- >1603913-2 ---------------ATGGATACAAGAaACGCACAcTCTG-------------------------------------------------- >180349-12 ---------------ATGGATACAAGACACGCACATTCcGCTTTACTG------------------------------------------ >1985106-1 ---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC----------------------------------- >1987775-1 ---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC----------------------------------- >2258725-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC----------------------------------- >2631987-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC----------------------------------- >337206-9 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCAC----------------------------------- >4616761-1 ---------------ATGGATAgAAGACACGCACATTCTGCTTTACTGGtAGCAC----------------------------------- >4756312-1 ---------------ATGGATACAAcACACGCACAcTCTG-------------------------------------------------- >4763682-1 ---------------ATGGATACAAGACACGCACATTCcGCTTTcCTG------------------------------------------ >5971268-1 ---------------ATGGATACAAGACACGCACATTCcGCTcTACTc------------------------------------------ >6644790-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTcGCAGCAC----------------------------------- >7112423-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGtCAGCAC----------------------------------- >7559990-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCcGgAC----------------------------------- >8007281-1 ---------------ATGGATAtAAGACACGCACAcTCTG-------------------------------------------------- >9150255-1 ---------------ATGGATACAcGACACGCACATTCcGCTTTcCTG------------------------------------------ >9180814-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgcC----------------------------------- >963117-4 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGCAC----------------------------------- >9672073-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCcC----------------------------------- >971218-4 ---------------ATGGATACAAGACACGCACATcCTGCTTTACTGG-AGCACC---------------------------------- >10040274-1 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGgACCACA------------------------------- >1063072-4 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCACCACA------------------------------- >1430188-2 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACA------------------------------- >5196741-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCcGCACCACA------------------------------- >6017337-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGtCAGaACCcCA------------------------------- >7159053-1 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCcaA------------------------------- >7528336-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCAaCACA------------------------------- >735584-6 --------------------------------------------------------ACAGAGTGCTACTGCAAAcAGCAGGAGCAGCAAC >8551047-1 --------------------------------------------------------ACAGAGTGCTAtTGCAAAcAGCAGGAGtAGtAAC >3000121-1 ------------------------------------------------------------AGTcCTACcGCAAATAGCAGcAGCAGCAAC >928481-5 ------------------------------------------------------------AGTGCTACcGCAAATAGCAGGAGCAGCAAC >126987-15 ----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC >3122797-1 ----------------------------------------------------------------------CAAATAGCAGGcGCAGCAAC >6684686-1 ----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC Note that the column width here was set to 90 characters
Parameter list
Options:
-f data.fasta Type the path to the fasta file that you want to use. --limit=90 Allows the user to set the column width of the alignment. Default=90 characters -o output.fasta Provide the name of your output file