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