fix .gitignore

Author: maxibor

.gitignore

@@ -1,101 +1 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# dotenv
-.env
-
-# virtualenv
-.venv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
+*.pyc

lib/__init__.py

@@ -0,0 +1,201 @@
+#!/usr/bin/env python
+
+from numpy import random as npr
+
+def get_basename(file_name):
+    if ("/") in file_name:
+        basename = file_name.split("/")[-1].split(".")[0]
+    else:
+        basename = file_name.split(".")[0]
+    return(basename)
+
+def reverse_complement(dna) :
+    dna = dna.upper()
+    '''
+    Reverse complement a DNA string
+    '''
+    dna = dna[::-1]
+    revcom = []
+    complement = {"A" : "T", "T" : "A" , "G" : "C" , "C" : "G"}
+    for letter in dna :
+        for key in complement.keys() :
+            if letter == key :
+                revcom.append(complement[key])
+
+    return "".join(revcom)
+
+def read_fasta (file_name):
+    """
+    READS FASTA FILE, RETURNS SEQUENCE AS STRING
+    INPUT:
+        file_name(string): path to fasta file
+    OUPUT:
+        result(string): all of the sequences in fasta file, concatenated
+    """
+    result = ""
+    with open(file_name, "r") as f:
+        for line in f:
+            if not line.startswith(">"):
+                line = line.rstrip()
+                result = result+line
+    return([result, len(result)])
+
+def random_insert(read_fasta_out, insert_lengths, read_length, minlen):
+    genome = read_fasta_out[0]
+    genome_length = read_fasta_out[1]
+    result = []
+    for i in insert_lengths:
+        if i >= minlen:
+            insert_start = npr.randint(0, genome_length-read_length)
+            insert_end = insert_start + i + 1
+            insert = genome[insert_start:insert_end]
+            result.append(insert)
+    return(result)
+
+def complement_read(all_inserts, adaptor, read_length):
+    result = []
+    for insert in all_inserts:
+        inlen = len(insert)
+        if inlen < read_length:
+            diff = read_length - inlen
+            to_add = adaptor[0:diff]
+            read = insert+to_add
+        elif inlen == read_length:
+            read = insert
+        elif inlen > read_length:
+            read = insert[0:read_length]
+        result.append(read)
+    return(result)
+
+def add_error(all_reads, error_rate):
+    for i in range(0, len(all_reads)):
+        read = list(all_reads[i])
+        for j in range(0, len(read)):
+            if npr.random() < error_rate:
+                read[j] = npr.choice(["A","T","G","C"])
+                all_reads[i] = "".join(read)
+    return(all_reads)
+
+def prepare_fastq(fastq_dict, fwd_reads, rev_reads, basename, read_length):
+    fastq_dict[basename] = [[] for i in range(2)]
+    cnt = 1
+    for read1, read2 in zip(fwd_reads, rev_reads):
+        towrite_fwd = "@"+basename+"_"+str(cnt)+"/1"+"\n"+read1+"\n+\n"+"d"*read_length+"\n"
+        fastq_dict[basename][0].append(towrite_fwd)
+        towrite_rev = "@"+basename+"_"+str(cnt)+"/2"+"\n"+read2+"\n+\n"+"d"*read_length+"\n"
+        fastq_dict[basename][1].append(towrite_rev)
+        cnt += 1
+    return(fastq_dict)
+
+def write_fastq_multi(fastq_dict, outputfile):
+    with open(outputfile+".1.fastq","w") as f1:
+        with open(outputfile+".2.fastq","w") as f2:
+            for akey in fastq_dict.keys():
+                for reads1 in fastq_dict[akey][0]:
+                    f1.write(reads1)
+                for reads2 in fastq_dict[akey][1]:
+                    f2.write(reads2)
+
+def write_fastq(all_reads, basename, orientation, read_length, outfile):
+    if not outfile:
+        with open(basename+"."+str(orientation)+".fastq", "w") as fw:
+            for read in all_reads:
+                fw.write("@"+basename+"\n")
+                fw.write(read+"\n")
+                fw.write("+\n")
+                fw.write("d"*read_length+"\n")
+    else:
+        with open(outfile+"."+str(orientation)+".fastq", "w") as fw:
+            for read in all_reads:
+                fw.write("@"+basename+"\n")
+                fw.write(read+"\n")
+                fw.write("+\n")
+                fw.write("d"*read_length+"\n")
+
+
+
+def run_read_simulation(INFILE, NREAD, COV, READLEN, INSERLEN, LENDEV, A1, A2, OUTFILE, MINLENGTH, ERR):
+    print("INFILE: ", INFILE)
+    if COV:
+        print("COV: ", COV)
+    else:
+        print("NREAD: ", NREAD)
+    print("READLEN: ", READLEN)
+    print("INSERLEN: ", INSERLEN)
+    print("LENDEV: ", LENDEV)
+    print("A1: ", A1)
+    print("A2: ", A2)
+    print("OUTFILE: ", OUTFILE)
+
+    nread = None
+
+
+    basename = get_basename(INFILE)
+    fasta = read_fasta(INFILE)
+
+    if COV:
+        nread = int(fasta[1]/INSERLEN)
+        print("nread: ", nread)
+
+    insert_lengths = [int(n) for n in npr.normal(INSERLEN, LENDEV, nread)]
+
+
+
+
+    all_inserts = random_insert(fasta, insert_lengths, READLEN, MINLENGTH)
+    fwd_inserts = all_inserts
+    rev_inserts = [reverse_complement(i) for i in all_inserts]
+    fwd_reads = complement_read(fwd_inserts, A1, READLEN)
+    fwd_reads = add_error(fwd_reads, ERR)
+    rev_reads = complement_read(rev_inserts, A2, READLEN)
+    rev_reads = add_error(rev_reads, ERR)
+
+    write_fastq(fwd_reads, basename, 1, READLEN, OUTFILE)
+    write_fastq(rev_reads, basename, 2, READLEN, OUTFILE)
+
+def run_read_simulation_multi(INFILE, NREAD, COV, READLEN, INSERLEN, LENDEV, A1, A2, MINLENGTH, ERR, fastq_dict):
+    print("INFILE: ", INFILE)
+    if COV:
+        print("COV: ", COV)
+    else:
+        print("NREAD: ", NREAD)
+    print("READLEN: ", READLEN)
+    print("INSERLEN: ", INSERLEN)
+    print("LENDEV: ", LENDEV)
+    print("A1: ", A1)
+    print("A2: ", A2)
+    nread = None
+
+
+    basename = get_basename(INFILE)
+    fasta = read_fasta(INFILE)
+
+    if COV:
+        nread = int(fasta[1]/INSERLEN)
+        print("nread: ", nread)
+
+    insert_lengths = [int(n) for n in npr.normal(INSERLEN, LENDEV, nread)]
+
+
+
+
+    all_inserts = random_insert(fasta, insert_lengths, READLEN, MINLENGTH)
+    fwd_inserts = all_inserts
+    rev_inserts = [reverse_complement(i) for i in all_inserts]
+    fwd_reads = complement_read(fwd_inserts, A1, READLEN)
+    fwd_reads = add_error(fwd_reads, ERR)
+    rev_reads = complement_read(rev_inserts, A2, READLEN)
+    rev_reads = add_error(rev_reads, ERR)
+
+    prepare_fastq(fastq_dict = fastq_dict, fwd_reads = fwd_reads, rev_reads = rev_reads, basename = basename, read_length = READLEN)
+    return(nread * INSERLEN)
+
+def write_stat(stat_dict, stat_out):
+    nbases = []
+    for akey in stat_dict:
+        nbases.append(stat_dict[akey])
+    totbases = sum(nbases)
+    with open(stat_out,"w") as fs:
+        fs.write("Organism, percentage of metagenome\n")
+        for akey in stat_dict:
+            fs.write(akey+","+str(stat_dict[akey]/totbases)+"\n")