generate_report.py 文件源码

python
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项目:zika-pipeline 作者: zibraproject 项目源码 文件源码
def dump_cluster(c):
    if os.path.exists("%s_dist_%s_aligned_short.fasta-cluster%d.png" % (prefix, dist, c)):
        print """
## Subcluster %d
        """ % (c)

        if c == 0:
            print "Cluster 0 represents isolates that do not cluster with any other isolates within the distance cut-off, i.e. singleton sequences. The sequences presented are unrelated."

        print """
![Subcluster %d](%s_dist_%s_aligned_short.fasta-cluster%d.pdf.png)
""" % (c, prefix, dist, c)
    else:
        print """
## Subcluster %s

(Tree not shown for clusters with <5 isolates)

Isolates:

        """ % (c)
        for rec in SeqIO.parse(open("%s_dist_%s_aligned_short.fasta-cluster%d" % (prefix, dist, c)), "fasta"):
            print "  - %s" % (rec.id)
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