comparison Tryp_V_T.py @ 25:c0a6a170163e draft

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24:728b1d375b41

    pass

def blastContigs(test_name,html_resource, database):
    db_path = database
    argString = "blastx -db "+db_path+" -query "+test_name+"_for_blast.fa -outfmt 10 -out "+test_name+"_blast.txt"
    print(argString)
    returncode = subprocess.call(argString, shell=True)
    if returncode != 0:
        return "Error in blastall"
    blast_df = pd.read_csv(""+test_name+"_blast.txt")

    htmlString += tabString + "</table><br><br><br><br><br>"
    htmlString += r"<h3>Weighted Relative Frequencies of Detected Phylotypes.</h3>"
    imgString = r"<img src = '"+ tdict['name']+"_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br>"
    htmlString += imgString

    with open(tdict['html_file'], "w") as htmlfile:
        htmlfile.write(htmlString)



def getPhyloNumber(sac):

    return int(sac[1:i])

def combineFPMK(tdict):
    dir_path = os.path.dirname(os.path.realpath(__file__))+'/'

    fpkm_df = pd.read_csv(dir_path++tdict['name']+'.cuff/genes.fpkm_tracking', sep='\t')

    #fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t')
    #print(fpkm_df.head())
    fpkm_df['locus'] = fpkm_df['locus'].apply(lambda names: names[:names.find(':')])
    #print(fpkm_df.head())

    # plt.text(-0.3, -0.15, title, va="top", wrap="True")
    #plt.tight_layout()
    plt.subplots_adjust(bottom=0.1, top=0.9, left=0.15, right=0.9)
    ax.set_title(title, x=0, wrap='True',ha='left',)

    plt.savefig(tdict['html_resource'] + tdict['name']+"_phylotypes.png")
    if tdict['pdf'] == 'PDF_Yes':
        plt.savefig(tdict['html_resource'] + tdict['name']+"phylotypes.pdf")
    # plt.show()
    pass

# argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}

25:c0a6a170163e

    pass

def blastContigs(test_name,html_resource, database):
    db_path = database
    #argString = "makeblastdb - in " + db_path
    #subprocess.call(argString, shell=True)

    argString = "blastx -db " + db_path + " -query "+test_name+"_for_blast.fa -outfmt 10 -out "+test_name+"_blast.txt"
    print(argString)
    returncode = subprocess.call(argString, shell=True)
    if returncode != 0:
        return "Error in blastall"
    blast_df = pd.read_csv(""+test_name+"_blast.txt")

    htmlString += tabString + "</table><br><br><br><br><br>"
    htmlString += r"<h3>Weighted Relative Frequencies of Detected Phylotypes.</h3>"
    imgString = r"<img src = '"+ tdict['name']+"_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br>"
    htmlString += imgString

    with open(tdict['html_resource']+'/'+tdict['html_file'], "w") as htmlfile:
        htmlfile.write(htmlString)



def getPhyloNumber(sac):

    return int(sac[1:i])

def combineFPMK(tdict):
    dir_path = os.path.dirname(os.path.realpath(__file__))+'/'

    fpkm_df = pd.read_csv(dir_path+tdict['name']+'.cuff/genes.fpkm_tracking', sep='\t')

    #fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t')
    #print(fpkm_df.head())
    fpkm_df['locus'] = fpkm_df['locus'].apply(lambda names: names[:names.find(':')])
    #print(fpkm_df.head())

    # plt.text(-0.3, -0.15, title, va="top", wrap="True")
    #plt.tight_layout()
    plt.subplots_adjust(bottom=0.1, top=0.9, left=0.15, right=0.9)
    ax.set_title(title, x=0, wrap='True',ha='left',)

    plt.savefig(tdict['html_resource'] + '/' + tdict['name']+"_phylotypes.png")
    if tdict['pdf'] == 'PDF_Yes':
        plt.savefig(tdict['html_resource'] + '/' + tdict['name']+"phylotypes.pdf")
    # plt.show()
    pass

# argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}