comparison get_contigs_from_re_archive.py @ 1:814cba36e435 draft

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0:ea6a3059a6af

import argparse
import re
import zipfile
import tempfile
import textwrap

def parse_args():
    '''Argument parsin'''
    description = """
    parsing cap3 assembly aln output

def read_tarean_fasta(fobj):
    ids = []
    s = []
    for i in fobj:
        ii = i.decode('utf-8')
        if ii[0] == ">":
            ids.append(ii)
            s.append("")
        else:
            s[-1] = s[-1] + ii.strip()
    return ids, s

def extract_tarean_contigs_from_re_archive(archive):
    with zipfile.ZipFile(archive, 'r') as zip_object:
        flist = zip_object.infolist()
        seqs_all = []

                    seqs_all += seqs
                    ids_all += ids
    return ids_all, seqs_all


def extract_contigs_from_re_directory(dir, aln_output):
    # TODO
    pass


def filter_contigs(consensus, coverage, min_coverage=5):
    x = "".join([
        s if cov >= min_coverage else " "
        for s, cov in zip(consensus, coverage)

    return consensus_N


def main():
    args = parse_args()
    # extract aln from archive
    ids, seqs = extract_tarean_contigs_from_re_archive(args.re_file)
    aln_file = extract_contigs_from_re_archive(
        args.re_file,
        tempfile.NamedTemporaryFile().name)
    with open(aln_file, 'r') as f1, open(args.fasta, 'w') as ffasta:
        while True:
            contig_name, seq_start = get_header(f1)
            if contig_name:
                consensus, coverage = remove_gaps(*read_contig(f1, seq_start))

1:814cba36e435

import argparse
import re
import zipfile
import tempfile
import textwrap
import os

def parse_args():
    '''Argument parsin'''
    description = """
    parsing cap3 assembly aln output

def read_tarean_fasta(fobj):
    ids = []
    s = []
    for i in fobj:
        if isinstance(i, str):
            ii = i
        else:
            ii = i.decode('utf-8')
        if ii[0] == ">":
            ids.append(ii)
            s.append("")
        else:
            s[-1] = s[-1] + ii.strip()
    return ids, s


def extract_contigs_from_re_directory(re_dir, aln_output):
    with open(aln_output, 'w') as fout:
        for subdir, dirs, files in os.walk(re_dir):
            for fn in files:
                fn_full = subdir + os.sep + fn
                if re.match('^.+seqclust.+[.]aln$', fn_full):
                    print(fn_full)
                    with open(fn_full) as aln:
                        for l in aln:
                            fout.write(l)
    return aln_output



def extract_tarean_contigs_from_re_archive(archive):
    with zipfile.ZipFile(archive, 'r') as zip_object:
        flist = zip_object.infolist()
        seqs_all = []

                    seqs_all += seqs
                    ids_all += ids
    return ids_all, seqs_all


def extract_tarean_contigs_from_re_directory(re_dir):
    seqs_all = []
    ids_all = []
    for subdir, dirs, files in os.walk(re_dir):
        for fn in files:
            fn_full = subdir + os.sep + fn
            if re.match("^.+seqclust.+dir_CL[0-9]+[/]tarean_contigs.fasta", fn_full):
                print (fn_full)
                with open(fn_full) as fobj:
                    ids, seqs = read_tarean_fasta(fobj)
                    # wrap sequences
                    seqs = ["\n".join(textwrap.wrap(s + s, 80)) for s in seqs]
                    seqs_all += seqs
                    ids_all += ids
    return ids_all, seqs_all

def filter_contigs(consensus, coverage, min_coverage=5):
    x = "".join([
        s if cov >= min_coverage else " "
        for s, cov in zip(consensus, coverage)

    return consensus_N


def main():
    args = parse_args()
    if os.path.isdir(args.re_file):
        # extract from directory
        ids, seqs = extract_tarean_contigs_from_re_directory(args.re_file)
        aln_file = extract_contigs_from_re_directory(
            args.re_file,
            tempfile.NamedTemporaryFile().name)
    else:
        # extract aln from archive
        ids, seqs = extract_tarean_contigs_from_re_archive(args.re_file)
        aln_file = extract_contigs_from_re_archive(
            args.re_file,
            tempfile.NamedTemporaryFile().name)

    with open(aln_file, 'r') as f1, open(args.fasta, 'w') as ffasta:
        while True:
            contig_name, seq_start = get_header(f1)
            if contig_name:
                consensus, coverage = remove_gaps(*read_contig(f1, seq_start))