Mercurial > repos > public-health-bioinformatics > change_fasta_deflines
changeset 0:6201f462adb7 draft
planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0-dirty
| author | public-health-bioinformatics |
|---|---|
| date | Wed, 09 Jan 2019 15:03:03 -0500 |
| parents | |
| children | ba7cee75eb68 |
| files | change_fasta_deflines.py change_fasta_deflines.xml test-data/csv_rename_file.csv test-data/fasta_2_rename.fasta test-data/tab_delim_rename_file.txt |
| diffstat | 5 files changed, 141 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/change_fasta_deflines.py Wed Jan 09 15:03:03 2019 -0500 @@ -0,0 +1,62 @@ +#!/usr/bin/env python +import sys, argparse +'''Accepts either csv (default) or tab-delimited files with old/new sequence names, creating a dictionary of +respective key:value pairs. Parses an input fasta file for 'old' names, replacing them with 'new' names, writing +renamed sequences to a fasta file. NOTE: use of tab-delim text file for renaming requires '-t' on cmd line.''' +#USAGE EXAMPLE 1: python change_fasta_def_lines.py csv_rename_file.csv fasta_2_rename.fasta renamedSequences.fasta +#USAGE EXAMPLE 2: python change_fasta_def_lines.py tab_delim_rename_file.txt -t fasta_2_rename.fasta renamedSequences.fasta + +'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory,Sept 2017''' + +#parse command line arguments +parser = argparse.ArgumentParser() +parser.add_argument ("-t", "--tab_delim", help = "name fasta definition lines from tab-delim file", action = "store_true") +parser.add_argument("inFileHandle") #csv file with current fasta file names in column 1 and desired names in col 2 +parser.add_argument("inFileHandle2") #fasta file containing sequences requiring name replacement +parser.add_argument("outFileHandle") #user-specified output filename +args = parser.parse_args() + +#open a writable output file that will be over-written if it already exists +outfile= open(args.outFileHandle,'w') +dict = {} #dictionary to hold old_name:new_name key:value pairs +splitter = ',' #default char to split lines at +#determine if input naming file is csv (default) or tab delim text +if args.tab_delim: + splitter = '\t' #change splitter to tab if comd line args contain '-t' + +#create dictionary using key/value pairs from csv file of old/new names +with open(args.inFileHandle,'r') as inputFile: +#read in each line and split at comma into key:value pairs + for line in inputFile: + #remove whitespace from end of lines, split at comma, assigning to key:value pairs + line2 = line.rstrip() + splitLine = line2.split(splitter) + old_name = splitLine[0] + new_name = splitLine[1] + dict[old_name] = new_name + +#parse fasta deflines for 'old' names and, if found, replace with new names +with open(args.inFileHandle2,'r') as inputFile2: + for line in inputFile2: + #find the definition lines, remove trailing whitespace & '>' + if ">" in line: + originalDefline = line.rstrip().replace(">","",1) + #check for a match to any of the dict key + if dict.has_key(originalDefline): + #find the index of that item in the list + newDefline= dict[originalDefline] + #print("the new name"), newDefline + # print each item to make sure the right name is being entered + outfile.write(">" + newDefline + "\n") + else: + #write out the original defline sequence name + print ("Defline not in dictionary: "), originalDefline + outfile.write(">" + originalDefline + "\n") + else: + #in lines without ">", write out sequence as it was + seq = line.rstrip() + outfile.write(seq+"\n") + +inputFile.close() +inputFile2.close() +outfile.close()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/change_fasta_deflines.xml Wed Jan 09 15:03:03 2019 -0500 @@ -0,0 +1,39 @@ +<tool id="change_fasta_deflines" name="Change Fasta Deflines" version="0.0.1"> + <requirements> + <requirement type="package" version="1.7.0">biopython</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + change_fasta_deflines.py + '$key_value_pairs' + '$input_fasta' + '$output_file' + #if $tab_delim + -t + #end if + ]]></command> + <inputs> + <param name="input_fasta" format="fasta" type="data" /> + <param name="tab_delim" type="boolean" label="Names file is tab-delimited." checked="false" /> + <param name="key_value_pairs" format="csv" type="data" /> + </inputs> + <outputs> + <data name="output_file" format="fasta"/> + </outputs> + <tests> + <test> + <param name="input_fasta" value="fasta_2_rename.fasta" /> + <param name="key_value_pairs" value="csv_rename_file.csv" /> + <output name="output_file" value="output.fasta" /> + </test> + <test> + <param name="input_fasta" value="fasta_2_rename.fasta" /> + <param name="key_value_pairs" value="tab_delim_rename_file.txt" /> + <param name="tab_delim" value="true" /> + <output name="output_file" value="output.fasta" /> + </test> + </tests> + <help><![CDATA[ + ]]></help> + <citations> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csv_rename_file.csv Wed Jan 09 15:03:03 2019 -0500 @@ -0,0 +1,10 @@ +s1,sample_1 +s2,sample_2 +s3,sample_3 +s4,sample_4 +s5,sample_5 +s6,sample_6 +s7,sample_7 +s8,sample_8 +s9,sample_9 +s10,sample_10
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