view @ 3:36388b666bfc draft default tip

planemo upload for repository commit b6de14061c479f0418cd89e26d6f5ac26e565a07
author drosofff
date Wed, 09 Nov 2016 11:24:13 -0500
parents 330dd8a8c31a
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#!/usr/bin/env python
import argparse
import logging
import sys
from collections import defaultdict

def Parser():
    the_parser = argparse.ArgumentParser()
        '--input', action="store", type=str, help="input file")
        '--output', action="store", type=str, help="output converted file")
        '--type', action="store", type=str, help="type of convertion")
    args = the_parser.parse_args()
    return args

def readfasta_writetabular(fasta, tabular, mode="oneline"):
    for line in fasta:
        if line[0] == ">":
                seqdic["".join(stringlist)] += 1  # to dump the sequence of the previous item - try because of first missing stringlist variable
            except NameError:
            stringlist = []
            except UnboundLocalError:  # if file went through filter and contains only empty lines
      "first line is empty.")
        seqdic["".join(stringlist)] += 1  # for the last sequence
    except NameError:"input file has not fasta sequences.")
    for seq in sorted(seqdic, key=seqdic.get, reverse=True):
        tabular.write("%s\t%s\n" % (seq, seqdic[seq]))

def readtabular_writefasta(tabular, fasta):
    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):
    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 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
            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))"%s reads collapsed" % number_reads)

def readfastaweighted_writefasta(fastaweigthed, fasta):
    counter = 0
    for line in fastaweigthed:
        if line[0] == ">":
            weigth = int(line[1:-1].split("_")[-1])
            seq = line[:-1]
            for i in range(weigth):
                counter += 1
                fasta.write(">%s\n%s\n" % (counter, seq))

def main(input, output, type):
    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()
    log = logging.getLogger(__name__)
    logging.basicConfig(stream=sys.stdout, level=logging.INFO)
    main(args.input, args.output, args.type)