<p><em>Answer from @fridaymeetssunday, converted from comments:</em></p>
<p>If python-reading is correct, it looks like that is an internally defined module (class) which is in <a href="https://github.com/DovetailGenomics/HiRise_July2015_GR/blob/3cdda0a1a44585b52274c01d7e9e02268e2d337f/scripts/bamtags.py" rel="nofollow noreferrer">here</a>. So basically, it's there.</p>
<p><em>Response from poster:</em></p>
<p>Thank you, guys, so helpful! Yes, that's it. I wasn't aware of the simplicity of import function. I thought it only worked with builtin or pip/conda installed modules. I just had to add the scripts folder to my PATH variable or have the functions in the working directory.</p>

CC BY-SA 4.0
2021-07-08T21:30:45.047Z
2021-07-08T21:30:45.047Z
gringer
<p>Does anyone know this python module, bamtags? I'm using a pipeline (Dovetail Genomics, HiRise) that imports it, but it seems it doesn't exist.</p>
<p>It's  impossible to install it and there is no information on the internet. Does anyone know it?</p>
<p>Additional information:</p>
<p>Hirise is a 3 years old pipeline that uses Chromossome Capture (HiC) data to identify misassembled regions in a genome assembly and then rescaffold them. By integrating 2 different sequencing methods, the confidence of the genome assembly is thus increased.</p>
<p>The workflow is free (we only paid for the data generation). Unfortunately I have no idea what the module does, as I find no information on internet and the scripts are poorly documented. f python-reading is correct, it looks like that is an internally defined module (class) which is in <a href="https://github.com/DovetailGenomics/HiRise_July2015_GR/blob/3cdda0a1a44585b52274c01d7e9e02268e2d337f/scripts/bamtags.py" rel="nofollow noreferrer">here</a>. So basically, it's there. I am not a python expert so maybe others more experience with python development will confirm or deny this.</p>
<p>The only function that is used is the following: <code>BamTags.mate_mapq(aln)</code>, which is inside a loop in aln: <code>for aln in sam.fetch(reference=c1)</code></p>
<p>Thanks,
Ricardo</p>

<python><sam><genomics><hi-c>
Python module bamtags
# Python module bamtags

(Asked by: username_0 on 2018-10-29)

Does anyone know this python module, bamtags? I'm using a pipeline (Dovetail Genomics, HiRise) that imports it, but it seems it doesn't exist.

It's impossible to install it and there is no information on the internet. Does anyone know it?

Additional information:

Hirise is a 3 years old pipeline that uses Chromossome Capture (HiC) data to identify misassembled regions in a genome assembly and then rescaffold them. By integrating 2 different sequencing methods, the confidence of the genome assembly is thus increased.

The workflow is free (we only paid for the data generation). Unfortunately I have no idea what the module does, as I find no information on internet and the scripts are poorly documented. f python-reading is correct, it looks like that is an internally defined module (class) which is in [here](https://github.com/DovetailGenomics/HiRise_July2015_GR/blob/3cdda0a1a44585b52274c01d7e9e02268e2d337f/scripts/bamtags.py). So basically, it's there. I am not a python expert so maybe others more experience with python development will confirm or deny this.

The only function that is used is the following: `BamTags.mate_mapq(aln)`, which is inside a loop in aln: `for aln in sam.fetch(reference=c1)`

Thanks,
Ricardo

**Tags:** python, sam, genomics, hi-c

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## 1 answers

### Answer by username_1 on 2021-07-08. Score: 0 | Accepted answer

*Answer from @fridaymeetssunday, converted from comments:*

If python-reading is correct, it looks like that is an internally defined module (class) which is in [here](https://github.com/DovetailGenomics/HiRise_July2015_GR/blob/3cdda0a1a44585b52274c01d7e9e02268e2d337f/scripts/bamtags.py). So basically, it's there.

*Response from poster:*

Thank you, guys, so helpful! Yes, that's it. I wasn't aware of the simplicity of import function. I thought it only worked with builtin or pip/conda installed modules. I just had to add the scripts folder to my PATH variable or have the functions in the working directory.


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