| Previous changeset 0:951cb6b3979b (2015-06-21) Next changeset 2:330dd8a8c31a (2016-03-25) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f |
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modified:
fasta_tabular_converter.py fasta_tabular_converter.xml |
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| diff -r 951cb6b3979b -r 2f7278120be9 fasta_tabular_converter.py --- a/fasta_tabular_converter.py Sun Jun 21 14:28:49 2015 -0400 +++ b/fasta_tabular_converter.py Tue Mar 22 18:54:00 2016 -0400 |
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| @@ -1,19 +1,37 @@ #!/usr/bin/python # import sys +import string +import argparse from collections import defaultdict -def readfasta_writetabular(fasta, tabular): - F = open(fasta, "r") - for line in F: - if line[0] == ">": continue - else: - seqdic[line[:-1]] += 1 - F.close() - F = open(tabular, "w") - for seq in sorted(seqdic, key=seqdic.get, reverse=True): - print >> F, "%s\t%s" % (seq, seqdic[seq]) - F.close() +def Parser(): + the_parser = argparse.ArgumentParser() + the_parser.add_argument( + '--input', action="store", type=str, help="input file") + the_parser.add_argument( + '--output', action="store", type=str, help="output converted file") + the_parser.add_argument( + '--type', action="store", type=str, help="type of convertion") + args = the_parser.parse_args() + return args + +def readfasta_writetabular(fasta, tabular, mode="oneline"): + F = open(fasta, "r") + for line in F: + if line[0] == ">": + try: + seqdic["".join(stringlist)] += 1 # to dump the sequence of the previous item - try because of first missing stringlist variable + except: pass + stringlist=[] + else: + stringlist.append(line[:-1]) + seqdic["".join(stringlist)] += 1 # for the last sequence + F.close() + F = open(tabular, "w") + for seq in sorted(seqdic, key=seqdic.get, reverse=True): + print >> F, "%s\t%s" % (seq, seqdic[seq]) + F.close() def readtabular_writefasta(tabular, fasta): @@ -72,17 +90,19 @@ F.close() Fw.close() - -seqdic = defaultdict(int) -option = sys.argv[3] +def main(input, output, type): + if type == "fasta2tabular": + readfasta_writetabular(input, output) + elif type == "tabular2fasta": + readtabular_writefasta(input, output) + elif type == "tabular2fastaweight": + readtabular_writefastaweighted (input, output) + elif type == "fastaweight2fastaweight": + readfastaeighted_writefastaweighted(input, output) + elif type == "fastaweight2fasta": + readfastaeighted_writefasta(input, output) -if option == "fasta2tabular": - readfasta_writetabular(sys.argv[1], sys.argv[2]) -elif option == "tabular2fasta": - readtabular_writefasta(sys.argv[1], sys.argv[2]) -elif option == "tabular2fastaweight": - readtabular_writefastaweighted (sys.argv[1], sys.argv[2]) -elif option == "fastaweight2fastaweight": - readfastaeighted_writefastaweighted(sys.argv[1], sys.argv[2]) -elif option == "fastaweight2fasta": - readfastaeighted_writefasta(sys.argv[1], sys.argv[2]) +if __name__ == "__main__": + seqdic = defaultdict(int) + args = Parser() + main (args.input, args.output, args.type) \ No newline at end of file |
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| diff -r 951cb6b3979b -r 2f7278120be9 fasta_tabular_converter.xml --- a/fasta_tabular_converter.xml Sun Jun 21 14:28:49 2015 -0400 +++ b/fasta_tabular_converter.xml Tue Mar 22 18:54:00 2016 -0400 |
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| @@ -1,6 +1,10 @@ -<tool id="fasta_tabular_converter" name="fasta - tabular" version="1.0.2"> +<tool id="fasta_tabular_converter" name="fasta - tabular" version="1.1.0"> <description>conversions</description> - <command interpreter="python">fasta_tabular_converter.py $input $output $switch.conversionType</command> + <command interpreter="python">fasta_tabular_converter.py + --input $input + --output $output + --type $switch.conversionType + </command> <inputs> <conditional name="switch"> <param name="conversionType" type="select" label="conversion option"> @@ -10,23 +14,22 @@ <option value="fastaweight2fastaweight">recompile weighted fasta to catenated fasta weighted</option> <option value="fastaweight2fasta">fasta weighted to fasta</option> </param> - <when value="fasta2tabular"> - <param name="input" type="data" format="fasta" label="fasta file to convert to tabular"/> - </when> - <when value="tabular2fasta"> - <param name="input" type="data" format="tabular" label="tabular file to convert to fasta"/> - </when> - <when value="tabular2fastaweight"> - <param name="input" type="data" format="tabular" label="tabular file to convert to fasta weighted"/> - </when> - <when value="fastaweight2fastaweight"> - <param name="input" type="data" format="fasta" label="catenated fasta weighted to recompile" help="Use this option only if you known what you're doing"/> - </when> - <when value="fastaweight2fasta"> - <param name="input" type="data" format="fasta" label="fasta weighted file to convert to fasta"/> - </when> - </conditional> - + <when value="fasta2tabular"> + <param name="input" type="data" format="fasta" label="fasta file to convert to tabular"/> + </when> + <when value="tabular2fasta"> + <param name="input" type="data" format="tabular" label="tabular file to convert to fasta"/> + </when> + <when value="tabular2fastaweight"> + <param name="input" type="data" format="tabular" label="tabular file to convert to fasta weighted"/> + </when> + <when value="fastaweight2fastaweight"> + <param name="input" type="data" format="fasta" label="catenated fasta weighted to recompile" help="Use this option only if you known what you're doing"/> + </when> + <when value="fastaweight2fasta"> + <param name="input" type="data" format="fasta" label="fasta weighted file to convert to fasta"/> + </when> + </conditional> </inputs> <outputs> |