<p>Quick look at your script suggests that you are comparing the XS and AS from different reads. I would recommend removing the continue from the <code>read.has_tag('XS')</code> continue block.</p>

<p>I think that if you filter out <code>is_secondary</code> and <code>is_supplementary</code> you don't need to do the XS to AS comparison assuming whatever generated for BAM did so correctly.</p>

<pre><code>for read in bam.fetch()  
    if read.is_secondary=true  
        continue
    if read.has_tag('XS') &lt;- This block stores XS and then moves on to the next read
        XS = read.get_tag('XS')  
        continue 
    if read.has_tag('AS') 
        AS = read.get_tag('AS')  
    if AS &lt; XS  &lt;- This block compares the AS of the current read to the XS of the previous read that had one.
        read.write(read)  
bam.close()  
</code></pre>

CC BY-SA 4.0
2019-04-13T05:25:43.837Z
I have not tried to executec it as this is my first `python` script i am looking for suggestions. Thank you :).
justaguy
CC BY-SA 4.0
2019-04-13T15:21:54.627Z
I would suggest running the script to determine if it is doing what you want.  What I pointed out above is def a flaw in the logic.
Bioathlete
CC BY-SA 4.0
2019-04-15T13:12:28.430Z
I ran the script (modified it in the post) and there are many syntax errors... being new to `python` I am not sure what is best... what do you suggest? Thanks :).
justaguy
CC BY-SA 4.0
2019-04-15T16:03:27.063Z
I would start will researching how to write to a file.  `read.write(read)` is not correct syntax.  You will need to open a file and write to that.  Go error by error until you have a working script then determine if the out is correct.
Bioathlete
CC BY-SA 4.0
2019-04-13T02:41:48.677Z
2019-04-13T02:41:48.677Z
Bioathlete
<p>I am new to <code>python</code> and trying to learn. The below is an attempt to filter out secondary reads in a <code>bam</code> using <code>pysam</code>. I ran <code>mark duplicates</code> and got an error on several <code>bam</code> files due to secondary alignments. I added comments to each line to illustrate my thought process.  Thank you :).</p>

<p>The specific <code>mark duplicates</code> error:</p>

<pre><code>Value was put into PairInfoMap more than once
</code></pre>

<p>Here is the script:</p>

<pre><code>#! /usr/bin/python  ## call python script
import sys ## import python system functions
import pysam  ## import module

bam = pysam.AlignmentFile(*.bam, "rb")  ## open bam and read
click.echo("Reading BAM file")  ## output message
for read in bam:  ## start loop and iterate over each bam
    if read.is_secondary=true  ## not the primary alignment
    if read.has_tag('XS')  ## look for Secondary Alignment Score tag
        XS = read.get_tag('XS')  ## read and store AS value
    if read.has_tag('AS')  ## look for Alignment Score tag
        AS = read.get_tag('AS')  ## read and store value os XS tag  
    if AS &lt; XS  ## Alignment score less then 
        read.write(read)  ## only print primary alignments
bam.close()  ## end processing
</code></pre>

CC BY-SA 4.0
2019-04-13T02:34:10.017Z
Is there an issue with the script?  If so what is it?  Are you looking for feedback on the script?
Bioathlete
<python><pysam>
filter secondary alignments using pysam
# filter secondary alignments using pysam

(Asked by: username_0 on 2019-04-13)

I am new to python and trying to learn. The below is an attempt to filter out secondary reads in a bam using pysam. I ran mark duplicates and got an error on several bam files due to secondary alignments. I added comments to each line to illustrate my thought process.  Thank you :).
The specific mark duplicates error:
Value was put into PairInfoMap more than once

Here is the script:
#! /usr/bin/python  ## call python script
import sys ## import python system functions
import pysam  ## import module

bam = pysam.AlignmentFile(*.bam, "rb")  ## open bam and read
click.echo("Reading BAM file")  ## output message
for read in bam:  ## start loop and iterate over each bam
    if read.is_secondary=true  ## not the primary alignment
    if read.has_tag('XS')  ## look for Secondary Alignment Score tag
        XS = read.get_tag('XS')  ## read and store AS value
    if read.has_tag('AS')  ## look for Alignment Score tag
        AS = read.get_tag('AS')  ## read and store value os XS tag  
    if AS < XS  ## Alignment score less then 
        read.write(read)  ## only print primary alignments
bam.close()  ## end processing

**Tags:** python, pysam
> **Comments:**
> **username_1**: Is there an issue with the script?  If so what is it?  Are you looking for feedback on the script?  

---

## 1 answers

### Answer by username_1 on 2019-04-13. Score: 3

Quick look at your script suggests that you are comparing the XS and AS from different reads. I would recommend removing the continue from the read.has_tag('XS') continue block.
I think that if you filter out is_secondary and is_supplementary you don't need to do the XS to AS comparison assuming whatever generated for BAM did so correctly.
for read in bam.fetch()  
    if read.is_secondary=true  
        continue
    if read.has_tag('XS') <- This block stores XS and then moves on to the next read
        XS = read.get_tag('XS')  
        continue 
    if read.has_tag('AS') 
        AS = read.get_tag('AS')  
    if AS < XS  <- This block compares the AS of the current read to the XS of the previous read that had one.
        read.write(read)  
bam.close()

> **Comments:**
> **username_0**: I have not tried to executec it as this is my first `python` script i am looking for suggestions. Thank you :).  
> **username_1**: I would suggest running the script to determine if it is doing what you want.  What I pointed out above is def a flaw in the logic.  
> **username_0**: I ran the script (modified it in the post) and there are many syntax errors... being new to `python` I am not sure what is best... what do you suggest? Thanks :).  
> **username_1**: I would start will researching how to write to a file.  `read.write(read)` is not correct syntax.  You will need to open a file and write to that.  Go error by error until you have a working script then determine if the out is correct.  

---

