| Previous 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 b6de14061c479f0418cd89e26d6f5ac26e565a07 |
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modified:
fasta_tabular_converter.py fasta_tabular_converter.xml |
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| diff -r 330dd8a8c31a -r 36388b666bfc fasta_tabular_converter.py --- a/fasta_tabular_converter.py Fri Mar 25 19:29:40 2016 -0400 +++ b/fasta_tabular_converter.py Wed Nov 09 11:24:13 2016 -0500 |
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| @@ -1,10 +1,11 @@ -#!/usr/bin/python +#!/usr/bin/env python # +import argparse +import logging import sys -import string -import argparse from collections import defaultdict + def Parser(): the_parser = argparse.ArgumentParser() the_parser.add_argument( @@ -16,95 +17,90 @@ args = the_parser.parse_args() return args + def readfasta_writetabular(fasta, tabular, mode="oneline"): - F = open(fasta, "r") - for line in F: + for line in fasta: 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=[] + seqdic["".join(stringlist)] += 1 # to dump the sequence of the previous item - try because of first missing stringlist variable + except NameError: + pass + stringlist = [] else: - stringlist.append(line[:-1]) + try: + stringlist.append(line[:-1]) + except UnboundLocalError: # if file went through filter and contains only empty lines + logging.info("first line is empty.") try: - seqdic["".join(stringlist)] += 1 # for the last sequence - except: pass # in case file to convert is empty - F.close() - F = open(tabular, "w") + seqdic["".join(stringlist)] += 1 # for the last sequence + except NameError: + logging.info("input file has not fasta sequences.") for seq in sorted(seqdic, key=seqdic.get, reverse=True): - print >> F, "%s\t%s" % (seq, seqdic[seq]) - F.close() - - + tabular.write("%s\t%s\n" % (seq, seqdic[seq])) + + def readtabular_writefasta(tabular, fasta): - F = open(tabular, "r") - Fw = open(fasta, "w") - counter = 0 - for line in F: - fields = line.split() - for i in range(int(fields[1])): - counter += 1 - print >> Fw, ">%s\n%s" % (counter, fields[0]) - F.close() - Fw.close() + counter = 0 + for line in tabular: + fields = line.split() + for i in range(int(fields[1])): + counter += 1 + fasta.write(">%s\n%s\n" % (counter, fields[0])) + -def readtabular_writefastaweighted (tabular, fasta): - F = open(tabular, "r") - Fw = open(fasta, "w") - counter = 0 - for line in F: - counter += 1 - fields = line[:-1].split() - print >> Fw, ">%s_%s\n%s" % (counter, fields[1], fields[0]) - F.close() - Fw.close() +def readtabular_writefastaweighted(tabular, fasta): + counter = 0 + for line in tabular: + counter += 1 + fields = line[:-1].split() + fasta.write(">%s_%s\n%s\n" % (counter, fields[1], fields[0])) + -def readfastaeighted_writefastaweighted(fastaweigthed_input, fastaweigthed_reparsed): - F = open(fastaweigthed_input, "r") - number_reads = 0 - for line in F: - if line[0] == ">": - weigth = int(line[1:-1].split("_")[-1]) - number_reads += weigth - else: - seqdic[line[:-1]] += weigth - F.close() - F = open(fastaweigthed_reparsed, "w") - n=0 - for seq in sorted(seqdic, key=seqdic.get, reverse=True): - n += 1 - print >> F, ">%s_%s\n%s" % (n, seqdic[seq], seq) - F.close() - print "%s reads collapsed" % number_reads +def readfastaweighted_writefastaweighted(fastaweigthed_input, fastaweigthed_reparsed): + number_reads = 0 + for line in fastaweigthed_input: + if line[0] == ">": + weigth = int(line[1:-1].split("_")[-1]) + number_reads += weigth + else: + seqdic[line[:-1]] += weigth + n = 0 + for seq in sorted(seqdic, key=seqdic.get, reverse=True): + n += 1 + fastaweigthed_reparsed.write(">%s_%s\n%s\n" % (n, seqdic[seq], seq)) + log.info("%s reads collapsed" % number_reads) -def readfastaeighted_writefasta(fastaweigthed, fasta): - F = open(fastaweigthed, "r") - Fw = open(fasta, "w") - counter = 0 - for line in F: - if line[0] == ">": - weigth = int(line[1:-1].split("_")[-1]) - else: - seq = line[:-1] - for i in range (weigth): - counter += 1 - print >> Fw, ">%s\n%s" % (counter, seq) - F.close() - Fw.close() + +def readfastaweighted_writefasta(fastaweigthed, fasta): + counter = 0 + for line in fastaweigthed: + if line[0] == ">": + weigth = int(line[1:-1].split("_")[-1]) + else: + seq = line[:-1] + for i in range(weigth): + counter += 1 + fasta.write(">%s\n%s\n" % (counter, seq)) + 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) + with open(input, "r") as input: + with open(output, "w") as output: + if type == "fasta2tabular": + readfasta_writetabular(input, output) + elif type == "tabular2fasta": + readtabular_writefasta(input, output) + elif type == "tabular2fastaweight": + readtabular_writefastaweighted(input, output) + elif type == "fastaweight2fastaweight": + readfastaweighted_writefastaweighted(input, output) + elif type == "fastaweight2fasta": + readfastaweighted_writefasta(input, output) + if __name__ == "__main__": seqdic = defaultdict(int) args = Parser() - main (args.input, args.output, args.type) + log = logging.getLogger(__name__) + logging.basicConfig(stream=sys.stdout, level=logging.INFO) + main(args.input, args.output, args.type) |
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| diff -r 330dd8a8c31a -r 36388b666bfc fasta_tabular_converter.xml --- a/fasta_tabular_converter.xml Fri Mar 25 19:29:40 2016 -0400 +++ b/fasta_tabular_converter.xml Wed Nov 09 11:24:13 2016 -0500 |
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| @@ -1,10 +1,11 @@ <tool id="fasta_tabular_converter" name="fasta - tabular" version="1.1.0"> <description>conversions</description> - <command interpreter="python">fasta_tabular_converter.py - --input $input - --output $output - --type $switch.conversionType - </command> + <command><![CDATA[ + python '$__tool_directory__'/fasta_tabular_converter.py + --input '$input' + --output '$output' + --type $switch.conversionType + ]]></command> <inputs> <conditional name="switch"> <param name="conversionType" type="select" label="conversion option"> |